=>> Building math/R build started at 2025-03-02T17:26:47-06:00 port directory: /usr/ports/math/R package name: R-4.4.3 building for: FreeBSD 142amd64-current-job-04 14.2-RELEASE FreeBSD 14.2-RELEASE amd64 maintained by: jrm@FreeBSD.org port version: 4.4.3 port revision: 0 Makefile datestamp: -rw-r--r-- 1 root wheel 4630 Mar 2 23:13 /usr/ports/math/R/Makefile Ports top last git commit: 0a0e18a32b6a Ports top unclean checkout: no =>> Inspecting /poudriere/data/.m/142amd64-current/04//usr/ports/math/R for modifications to git checkout... no Port dir last git commit: df81348d70a6 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.99.20250209 Host OSVERSION: 1402000 Jail OSVERSION: 1402000 Job Id: 04 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1402000 UNAME_v=FreeBSD 14.2-RELEASE UNAME_r=14.2-RELEASE BLOCKSIZE=K MAIL=/var/mail/root MM_CHARSET=UTF-8 LANG=C.UTF-8 STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin MAKE_OBJDIR_CHECK_WRITABLE=0 LOCALBASE=/usr/local USER=root POUDRIERE_NAME=poudriere-git USE_COLORS=no POUDRIERE_VERSION=3.4.99.20250209 MASTERMNT=/poudriere/data/.m/142amd64-current/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=screen-256color OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/poudriere/data/.m/142amd64-current/04/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=142amd64-current OLDPWD=/poudriere/data/.m/142amd64-current/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.99.20250209 PREFIX=/usr/local POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ===> The following configuration options are available for R-4.4.3: ICU=on: Unicode support via ICU INFO=on: Build and/or install GNU info pages LDOUBLE=on: Long double data type LETTER=on: US letter paper MEMPROF=off: Memory profiling via Rprofmem() and tracemem() NLS=on: Native Language Support OPENMP=on: Parallel processing support via OpenMP RPROF=on: R profiling via Rprof() X11=on: X11 graphics device ====> Require X11 CAIROPANGO=on: Cairo graphics device and Pango multi-language text GHOSTSCRIPT=on: Graphics device for bitmap files via Ghostscript JPEG=on: JPEG graphics device PNG=on: PNG graphics device TCLTK=on: Tcl/Tk GUI toolkit support TEXDOCS=on: Build/Install TeX-dependent documentation files TIFF=on: TIFF image format support ====> Options available for the single BLAS: you have to select exactly one of them ATLAS=off: ATLAS BLAS implementation NETLIB=off: Netlib BLAS implementation OPENBLAS=off: OpenBLAS BLAS implementation RBLAS=on: Use R-bundled BLAS implementation ===> Use 'make config' to modify these settings ---End OPTIONS List--- --MAINTAINER-- jrm@FreeBSD.org --End MAINTAINER-- --PORTVERSION-- 4.4.3 --End PORTVERSION-- --PORTREVISION-- 0 --End PORTREVISION-- --CONFIGURE_ARGS-- --disable-java --enable-R-shlib --with-readline rdocdir=/usr/local/share/doc/R --with-cairo --with-ICU --with-jpeglib --enable-long-double --disable-memory-profiling --enable-openmp --with-libpng --enable-BLAS-shlib --without-blas --without-lapack --enable-R-profiling --with-tcl_config=/usr/local/lib/tcl8.6/tclConfig.sh --with-tcltk --with-tk_config=/usr/local/lib/tk8.6/tkConfig.sh --with-libtiff --with-x --x-libraries=/usr/local/lib --x-includes=/usr/local/include --prefix=/usr/local ${_LATE_CONFIGURE_ARGS} --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- r_cv_header_jpeglib_h=yes R_PAPERSIZE=letter F77="gfortran13" F90="gfortran13" FC="gfortran13" FFLAGS="-O -Wl,-rpath=/usr/local/lib/gcc13" F90FLAGS="-O -Wl,-rpath=/usr/local/lib/gcc13" FCFLAGS="-Wl,-rpath=/usr/local/lib/gcc13" MAKE=/usr/local/bin/gmake ac_cv_path_PERL=/usr/local/bin/perl ac_cv_path_PERL_PATH=/usr/local/bin/perl PERL_USE_UNSAFE_INC=1 PKG_CONFIG=pkgconf XDG_DATA_HOME=/wrkdirs/usr/ports/math/R/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/math/R/work XDG_CACHE_HOME=/wrkdirs/usr/ports/math/R/work/.cache HOME=/wrkdirs/usr/ports/math/R/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/math/R/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/math/R/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh ADDR2LINE="/usr/local/bin/addr2line" AR="/usr/local/bin/ar" AS="/usr/local/bin/as" CPPFILT="/usr/local/bin/c++filt" GPROF="/usr/local/bin/gprof" LD="/usr/local/bin/ld" NM="/usr/local/bin/nm" OBJCOPY="/usr/local/bin/objcopy" OBJDUMP="/usr/local/bin/objdump" RANLIB="/usr/local/bin/ranlib" READELF="/usr/local/bin/readelf" SIZE="/usr/local/bin/size" STRINGS="/usr/local/bin/strings" CMAKE_PREFIX_PATH="/usr/local" CONFIG_SITE=/usr/ports/Templates/config.site lt_cv_sys_max_cmd_len=524288 --End CONFIGURE_ENV-- --MAKE_ENV-- F77="gfortran13" F90="gfortran13" FC="gfortran13" FFLAGS="-O -Wl,-rpath=/usr/local/lib/gcc13" F90FLAGS="-O -Wl,-rpath=/usr/local/lib/gcc13" FCFLAGS="-Wl,-rpath=/usr/local/lib/gcc13" PERL_USE_UNSAFE_INC=1 XDG_DATA_HOME=/wrkdirs/usr/ports/math/R/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/math/R/work XDG_CACHE_HOME=/wrkdirs/usr/ports/math/R/work/.cache HOME=/wrkdirs/usr/ports/math/R/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/math/R/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/math/R/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES ADDR2LINE="/usr/local/bin/addr2line" AR="/usr/local/bin/ar" AS="/usr/local/bin/as" CPPFILT="/usr/local/bin/c++filt" GPROF="/usr/local/bin/gprof" LD="/usr/local/bin/ld" NM="/usr/local/bin/nm" OBJCOPY="/usr/local/bin/objcopy" OBJDUMP="/usr/local/bin/objdump" RANLIB="/usr/local/bin/ranlib" READELF="/usr/local/bin/readelf" SIZE="/usr/local/bin/size" STRINGS="/usr/local/bin/strings" PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing " CPP="cpp" CPPFLAGS="-DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include" LDFLAGS=" -Wl,-rpath=/usr/local/lib/gcc13 -L/usr/local/lib/gcc13 -L/usr/local/lib -fstack-protector-strong " LIBS="-L/usr/local/lib" CXX="c++" CXXFLAGS="-O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -DLIBICONV_PLUG -isystem /usr/local/include " BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- FULLVER=4.4.3 MAJORVER=4 ATLAS="@comment " NO_ATLAS="" CAIROPANGO="" NO_CAIROPANGO="@comment " GHOSTSCRIPT="" NO_GHOSTSCRIPT="@comment " ICU="" NO_ICU="@comment " INFO="" NO_INFO="@comment " JPEG="" NO_JPEG="@comment " LDOUBLE="" NO_LDOUBLE="@comment " LETTER="" NO_LETTER="@comment " MEMPROF="@comment " NO_MEMPROF="" NETLIB="@comment " NO_NETLIB="" NLS="" NO_NLS="@comment " OPENBLAS="@comment " NO_OPENBLAS="" OPENMP="" NO_OPENMP="@comment " PNG="" NO_PNG="@comment " RBLAS="" NO_RBLAS="@comment " RPROF="" NO_RPROF="@comment " TCLTK="" NO_TCLTK="@comment " TEXDOCS="" NO_TEXDOCS="@comment " TIFF="" NO_TIFF="@comment " X11="" NO_X11="@comment " GTK2_VERSION="2.10.0" GTK3_VERSION="3.0.0" GTK4_VERSION="4.0.0" TEXMFDIR="share/texmf" TEXMFDISTDIR="share/texmf-dist" TEXMFLOCALDIR="share/texmf-local" TEXMFVARDIR="share/texmf-var" TEXMFCONFIGDIR="share/texmf-config" FMTUTIL_CNF="share/texmf-config/web2c/fmtutil.cnf" OSREL=14.2 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PERL_VERSION=5.36.3 PERL_VER=5.36 PERL5_MAN1=lib/perl5/site_perl/man/man1 PERL5_MAN3=lib/perl5/site_perl/man/man3 SITE_PERL=lib/perl5/site_perl SITE_ARCH=lib/perl5/site_perl/mach/5.36 DOCSDIR="share/doc/R" EXAMPLESDIR="share/examples/R" DATADIR="share/R" WWWDIR="www/R" ETCDIR="etc/R" --End PLIST_SUB-- --SUB_LIST-- ATLAS="@comment " NO_ATLAS="" CAIROPANGO="" NO_CAIROPANGO="@comment " GHOSTSCRIPT="" NO_GHOSTSCRIPT="@comment " ICU="" NO_ICU="@comment " INFO="" NO_INFO="@comment " JPEG="" NO_JPEG="@comment " LDOUBLE="" NO_LDOUBLE="@comment " LETTER="" NO_LETTER="@comment " MEMPROF="@comment " NO_MEMPROF="" NETLIB="@comment " NO_NETLIB="" NLS="" NO_NLS="@comment " OPENBLAS="@comment " NO_OPENBLAS="" OPENMP="" NO_OPENMP="@comment " PNG="" NO_PNG="@comment " RBLAS="" NO_RBLAS="@comment " RPROF="" NO_RPROF="@comment " TCLTK="" NO_TCLTK="@comment " TEXDOCS="" NO_TEXDOCS="@comment " TIFF="" NO_TIFF="@comment " X11="" NO_X11="@comment " PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/R DOCSDIR=/usr/local/share/doc/R EXAMPLESDIR=/usr/local/share/examples/R WWWDIR=/usr/local/www/R ETCDIR=/usr/local/etc/R --End SUB_LIST-- ---Begin make.conf--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles FORCE_PACKAGE=yes PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes WITH_CCACHE_BUILD=yes CCACHE_DIR=/root/.ccache #### Misc Poudriere #### .include "/etc/make.conf.ports_env" GID=0 UID=0 ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 33554432 stack size (kbytes, -s) 524288 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 63795 open files (-n) 8192 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited pipebuf (-y) unlimited --End resource limits-- =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License GPLv2 accepted by the user =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> R-4.4.3 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.0.6.pkg [142amd64-current-job-04] Installing pkg-2.0.6... [142amd64-current-job-04] Extracting pkg-2.0.6: .......... done ===> R-4.4.3 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of R-4.4.3 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License GPLv2 accepted by the user => R-4.4.3.tar.gz doesn't seem to exist in /portdistfiles/. => Attempting to fetch https://cloud.r-project.org/src/base/R-4/R-4.4.3.tar.gz R-4.4.3.tar.gz 38 MB 36 MBps 01s ===> Fetching all distfiles required by R-4.4.3 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by R-4.4.3 for building => SHA256 Checksum OK for R-4.4.3.tar.gz. =========================================================================== =>> Debug: gather_distfiles: missing '/poudriere/distfiles//R-4.4.3.tar.gz'=================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by R-4.4.3 for building ===> Extracting for R-4.4.3 => SHA256 Checksum OK for R-4.4.3.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Patching for R-4.4.3 ===> Applying extra patch /usr/ports/math/R/files/extra-patch-src_extra_blas_Makefile.in ===> Applying extra patch /usr/ports/math/R/files/extra-patch-src_modules_lapack_Makefile.in ===> Applying FreeBSD patches for R-4.4.3 from /usr/ports/math/R/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> R-4.4.3 depends on executable: texi2any - not found ===> Installing existing package /packages/All/texinfo-7.1_8,1.pkg [142amd64-current-job-04] Installing texinfo-7.1_8,1... [142amd64-current-job-04] `-- Installing gettext-runtime-0.23.1... [142amd64-current-job-04] | `-- Installing indexinfo-0.3.1_1... [142amd64-current-job-04] | `-- Extracting indexinfo-0.3.1_1: .... done [142amd64-current-job-04] `-- Extracting gettext-runtime-0.23.1: .......... done [142amd64-current-job-04] `-- Installing libiconv-1.17_1... [142amd64-current-job-04] `-- Extracting libiconv-1.17_1: .......... done [142amd64-current-job-04] `-- Installing p5-Locale-libintl-1.35... [142amd64-current-job-04] | `-- Installing perl5-5.36.3_2... [142amd64-current-job-04] | `-- Extracting perl5-5.36.3_2: .......... done [142amd64-current-job-04] `-- Extracting p5-Locale-libintl-1.35: .......... done [142amd64-current-job-04] `-- Installing p5-Text-Unidecode-1.30... [142amd64-current-job-04] `-- Extracting p5-Text-Unidecode-1.30: .......... done [142amd64-current-job-04] `-- Installing p5-Unicode-EastAsianWidth-12.0... [142amd64-current-job-04] `-- Extracting p5-Unicode-EastAsianWidth-12.0: ...... done [142amd64-current-job-04] Extracting texinfo-7.1_8,1: .......... done ===> R-4.4.3 depends on executable: texi2any - found ===> Returning to build of R-4.4.3 ===> R-4.4.3 depends on executable: gfortran13 - not found ===> Installing existing package /packages/All/gcc13-13.3.0.pkg [142amd64-current-job-04] Installing gcc13-13.3.0... [142amd64-current-job-04] `-- Installing binutils-2.44,1... [142amd64-current-job-04] | `-- Installing elfutils-0.187_2... [142amd64-current-job-04] | | `-- Installing argp-standalone-1.5.0_1... [142amd64-current-job-04] | | `-- Extracting argp-standalone-1.5.0_1: ......... done [142amd64-current-job-04] | | `-- Installing curl-8.12.1... [142amd64-current-job-04] | | `-- Installing brotli-1.1.0,1... [142amd64-current-job-04] | | `-- Extracting brotli-1.1.0,1: .......... done [142amd64-current-job-04] | | `-- Installing c-ares-1.34.4... [142amd64-current-job-04] | | `-- Extracting c-ares-1.34.4: .......... done [142amd64-current-job-04] | | `-- Installing krb5-1.21.3... [142amd64-current-job-04] | | | `-- Installing libedit-3.1.20240808,1... [142amd64-current-job-04] | | | `-- Extracting libedit-3.1.20240808,1: .......... done [142amd64-current-job-04] | | | `-- Installing openldap26-client-2.6.9_1... [142amd64-current-job-04] | | | `-- Installing cyrus-sasl-2.1.28_5... [142amd64-current-job-04] | | | | `-- Installing lmdb-0.9.33,1... [142amd64-current-job-04] | | | | `-- Extracting lmdb-0.9.33,1: .......... done *** Added group `cyrus' (id 60) *** Added user `cyrus' (id 60) [142amd64-current-job-04] | | | `-- Extracting cyrus-sasl-2.1.28_5: .......... done [142amd64-current-job-04] | | | `-- Extracting openldap26-client-2.6.9_1: .......... done [142amd64-current-job-04] | | `-- Extracting krb5-1.21.3: .......... done [142amd64-current-job-04] | | `-- Installing libidn2-2.3.7... [142amd64-current-job-04] | | | `-- Installing libunistring-1.3... [142amd64-current-job-04] | | | `-- Extracting libunistring-1.3: .......... done [142amd64-current-job-04] | | `-- Extracting libidn2-2.3.7: .......... done [142amd64-current-job-04] | | `-- Installing libnghttp2-1.64.0... [142amd64-current-job-04] | | `-- Extracting libnghttp2-1.64.0: .......... done [142amd64-current-job-04] | | `-- Installing libssh2-1.11.1,3... [142amd64-current-job-04] | | `-- Extracting libssh2-1.11.1,3: .......... done [142amd64-current-job-04] | | `-- Installing zstd-1.5.7... [142amd64-current-job-04] | | | `-- Installing liblz4-1.10.0,1... [142amd64-current-job-04] | | | `-- Extracting liblz4-1.10.0,1: .......... done [142amd64-current-job-04] | | `-- Extracting zstd-1.5.7: .......... done [142amd64-current-job-04] | | `-- Extracting curl-8.12.1: .......... done [142amd64-current-job-04] | `-- Extracting elfutils-0.187_2: .......... done [142amd64-current-job-04] `-- Extracting binutils-2.44,1: .......... done [142amd64-current-job-04] `-- Installing gmp-6.3.0... [142amd64-current-job-04] `-- Extracting gmp-6.3.0: .......... done [142amd64-current-job-04] `-- Installing isl-0.27... [142amd64-current-job-04] `-- Extracting isl-0.27: .......... done [142amd64-current-job-04] `-- Installing mpc-1.3.1_1... [142amd64-current-job-04] | `-- Installing mpfr-4.2.1,1... [142amd64-current-job-04] | `-- Extracting mpfr-4.2.1,1: .......... done [142amd64-current-job-04] `-- Extracting mpc-1.3.1_1: ......... done [142amd64-current-job-04] Extracting gcc13-13.3.0: .......... done ===== Message from cyrus-sasl-2.1.28_5: -- You can use sasldb2 for authentication, to add users use: saslpasswd2 -c username If you want to enable SMTP AUTH with the system Sendmail, read Sendmail.README NOTE: This port has been compiled with a default pwcheck_method of auxprop. If you want to authenticate your user by /etc/passwd, PAM or LDAP, install ports/security/cyrus-sasl2-saslauthd and set sasl_pwcheck_method to saslauthd after installing the Cyrus-IMAPd 2.X port. You should also check the /usr/local/lib/sasl2/*.conf files for the correct pwcheck_method. If you want to use GSSAPI mechanism, install ports/security/cyrus-sasl2-gssapi. If you want to use SRP mechanism, install ports/security/cyrus-sasl2-srp. If you want to use LDAP auxprop plugin, install ports/security/cyrus-sasl2-ldapdb. ===== Message from openldap26-client-2.6.9_1: -- The OpenLDAP client package has been successfully installed. Edit /usr/local/etc/openldap/ldap.conf to change the system-wide client defaults. Try `man ldap.conf' and visit the OpenLDAP FAQ-O-Matic at http://www.OpenLDAP.org/faq/index.cgi?file=3 for more information. ===== Message from gcc13-13.3.0: -- To ensure binaries built with this toolchain find appropriate versions of the necessary run-time libraries, you may want to link using -Wl,-rpath=/usr/local/lib/gcc13 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. ===> R-4.4.3 depends on executable: gfortran13 - found ===> Returning to build of R-4.4.3 ===> R-4.4.3 depends on package: gmake>=4.4.1 - not found ===> Installing existing package /packages/All/gmake-4.4.1.pkg [142amd64-current-job-04] Installing gmake-4.4.1... [142amd64-current-job-04] Extracting gmake-4.4.1: .......... done ===> R-4.4.3 depends on package: gmake>=4.4.1 - found ===> Returning to build of R-4.4.3 ===> R-4.4.3 depends on package: gettext-runtime>=0.22_1 - found ===> R-4.4.3 depends on executable: msgfmt - not found ===> Installing existing package /packages/All/gettext-tools-0.23.1.pkg [142amd64-current-job-04] Installing gettext-tools-0.23.1... [142amd64-current-job-04] `-- Installing libtextstyle-0.23.1... [142amd64-current-job-04] `-- Extracting libtextstyle-0.23.1: .......... done [142amd64-current-job-04] Extracting gettext-tools-0.23.1: .......... done ===> R-4.4.3 depends on executable: msgfmt - found ===> Returning to build of R-4.4.3 ===> R-4.4.3 depends on package: pkgconf>=1.3.0_1 - not found ===> Installing existing package /packages/All/pkgconf-2.3.0,1.pkg [142amd64-current-job-04] Installing pkgconf-2.3.0,1... [142amd64-current-job-04] Extracting pkgconf-2.3.0,1: .......... done ===> R-4.4.3 depends on package: pkgconf>=1.3.0_1 - found ===> Returning to build of R-4.4.3 ===> R-4.4.3 depends on package: ghostscript10>=10.02.0 - not found ===> Installing existing package /packages/All/ghostscript10-10.04.0.pkg [142amd64-current-job-04] Installing ghostscript10-10.04.0... [142amd64-current-job-04] `-- Installing cups-2.4.11... [142amd64-current-job-04] | `-- Installing dbus-1.14.10_5,1... [142amd64-current-job-04] | | `-- Installing expat-2.6.4... [142amd64-current-job-04] | | `-- Extracting expat-2.6.4: .......... done [142amd64-current-job-04] | | `-- Installing libICE-1.1.1,1... [142amd64-current-job-04] | | `-- Extracting libICE-1.1.1,1: .......... done [142amd64-current-job-04] | | `-- Installing libSM-1.2.4,1... [142amd64-current-job-04] | | `-- Extracting libSM-1.2.4,1: .......... done [142amd64-current-job-04] | | `-- Installing libX11-1.8.9,1... [142amd64-current-job-04] | | `-- Installing libxcb-1.17.0... [142amd64-current-job-04] | | | `-- Installing libXau-1.0.11... [142amd64-current-job-04] | | | `-- Extracting libXau-1.0.11: .......... done [142amd64-current-job-04] | | | `-- Installing libXdmcp-1.1.5... [142amd64-current-job-04] | | | `-- Installing xorgproto-2024.1... [142amd64-current-job-04] | | | `-- Extracting xorgproto-2024.1: .......... done [142amd64-current-job-04] | | | `-- Extracting libXdmcp-1.1.5: ......... done [142amd64-current-job-04] | | `-- Extracting libxcb-1.17.0: .......... done [142amd64-current-job-04] | | `-- Extracting libX11-1.8.9,1: .......... done ===> Creating groups Creating group 'messagebus' with gid '556' ===> Creating users Creating user 'messagebus' with uid '556' [142amd64-current-job-04] | `-- Extracting dbus-1.14.10_5,1: ......... done [142amd64-current-job-04] | `-- Installing gnutls-3.8.9... [142amd64-current-job-04] | | `-- Installing libtasn1-4.20.0_1... [142amd64-current-job-04] | | `-- Extracting libtasn1-4.20.0_1: .......... done [142amd64-current-job-04] | | `-- Installing nettle-3.10.1... [142amd64-current-job-04] | | `-- Extracting nettle-3.10.1: .......... done [142amd64-current-job-04] | | `-- Installing p11-kit-0.25.5... [142amd64-current-job-04] | | `-- Installing libffi-3.4.6... [142amd64-current-job-04] | | `-- Extracting libffi-3.4.6: .......... done [142amd64-current-job-04] | | `-- Extracting p11-kit-0.25.5: .......... done [142amd64-current-job-04] | | `-- Installing unbound-1.22.0_1... [142amd64-current-job-04] | | `-- Installing libevent-2.1.12... [142amd64-current-job-04] | | `-- Extracting libevent-2.1.12: .......... done [142amd64-current-job-04] | | `-- Installing libsodium-1.0.19... [142amd64-current-job-04] | | `-- Extracting libsodium-1.0.19: .......... done ===> Creating groups Using existing group 'unbound' ===> Creating users Using existing user 'unbound' [142amd64-current-job-04] | | `-- Extracting unbound-1.22.0_1: .......... done [142amd64-current-job-04] | `-- Extracting gnutls-3.8.9: .......... done [142amd64-current-job-04] | `-- Installing libpaper-1.1.28_1... [142amd64-current-job-04] | `-- Extracting libpaper-1.1.28_1: .......... done ===> Creating groups Creating group 'cups' with gid '193' ===> Creating users Creating user 'cups' with uid '193' [142amd64-current-job-04] `-- Extracting cups-2.4.11: .......... done [142amd64-current-job-04] `-- Installing fontconfig-2.15.0_3,1... [142amd64-current-job-04] | `-- Installing freetype2-2.13.3... [142amd64-current-job-04] | | `-- Installing png-1.6.45... [142amd64-current-job-04] | | `-- Extracting png-1.6.45: .......... done [142amd64-current-job-04] | `-- Extracting freetype2-2.13.3: .......... done [142amd64-current-job-04] `-- Extracting fontconfig-2.15.0_3,1: .......... done [142amd64-current-job-04] `-- Installing jbig2dec-0.20_1... [142amd64-current-job-04] `-- Extracting jbig2dec-0.20_1: .......... done [142amd64-current-job-04] `-- Installing jpeg-turbo-3.1.0... [142amd64-current-job-04] `-- Extracting jpeg-turbo-3.1.0: .......... done [142amd64-current-job-04] `-- Installing lcms2-2.17... [142amd64-current-job-04] | `-- Installing tiff-4.7.0... [142amd64-current-job-04] | | `-- Installing jbigkit-2.1_3... [142amd64-current-job-04] | | `-- Extracting jbigkit-2.1_3: .......... done [142amd64-current-job-04] | | `-- Installing lerc-4.0.0... [142amd64-current-job-04] | | `-- Extracting lerc-4.0.0: ........ done [142amd64-current-job-04] | | `-- Installing libdeflate-1.22... [142amd64-current-job-04] | | `-- Extracting libdeflate-1.22: .......... done [142amd64-current-job-04] | `-- Extracting tiff-4.7.0: .......... done [142amd64-current-job-04] `-- Extracting lcms2-2.17: .......... done [142amd64-current-job-04] `-- Installing leptonica-1.82.0_2... [142amd64-current-job-04] | `-- Installing giflib-5.2.2... [142amd64-current-job-04] | `-- Extracting giflib-5.2.2: .......... done [142amd64-current-job-04] | `-- Installing webp-1.5.0... [142amd64-current-job-04] | `-- Extracting webp-1.5.0: .......... done [142amd64-current-job-04] `-- Extracting leptonica-1.82.0_2: .......... done [142amd64-current-job-04] `-- Installing libXext-1.3.6,1... [142amd64-current-job-04] `-- Extracting libXext-1.3.6,1: .......... done [142amd64-current-job-04] `-- Installing libXt-1.3.0,1... [142amd64-current-job-04] `-- Extracting libXt-1.3.0,1: .......... done [142amd64-current-job-04] `-- Installing libarchive-3.7.7_2,1... [142amd64-current-job-04] | `-- Installing lzo2-2.10_1... [142amd64-current-job-04] | `-- Extracting lzo2-2.10_1: .......... done [142amd64-current-job-04] `-- Extracting libarchive-3.7.7_2,1: .......... done [142amd64-current-job-04] `-- Installing libidn-1.42... [142amd64-current-job-04] `-- Extracting libidn-1.42: .......... done [142amd64-current-job-04] `-- Installing openjpeg-2.5.3... [142amd64-current-job-04] `-- Extracting openjpeg-2.5.3: .......... done [142amd64-current-job-04] `-- Installing poppler-data-0.4.12... [142amd64-current-job-04] `-- Extracting poppler-data-0.4.12: .......... done [142amd64-current-job-04] `-- Installing tesseract-5.5.0_1... [142amd64-current-job-04] | `-- Installing cairo-1.18.2,3... [142amd64-current-job-04] | | `-- Installing glib-2.80.5_1,2... [142amd64-current-job-04] | | `-- Installing pcre2-10.45... [142amd64-current-job-04] | | | `-- Installing readline-8.2.13_2... [142amd64-current-job-04] | | | `-- Extracting readline-8.2.13_2: .......... done [142amd64-current-job-04] | | `-- Extracting pcre2-10.45: .......... done [142amd64-current-job-04] | | `-- Installing py311-packaging-24.2... [142amd64-current-job-04] | | | `-- Installing python311-3.11.11... [142amd64-current-job-04] | | | `-- Installing mpdecimal-4.0.0... [142amd64-current-job-04] | | | `-- Extracting mpdecimal-4.0.0: .......... done [142amd64-current-job-04] | | | `-- Extracting python311-3.11.11: .......... done [142amd64-current-job-04] | | `-- Extracting py311-packaging-24.2: .......... done [142amd64-current-job-04] | | `-- Extracting glib-2.80.5_1,2: .......... done [142amd64-current-job-04] | | `-- Installing libXrender-0.9.11... [142amd64-current-job-04] | | `-- Extracting libXrender-0.9.11: .......... done [142amd64-current-job-04] | | `-- Installing pixman-0.44.2... [142amd64-current-job-04] | | `-- Extracting pixman-0.44.2: ......... done [142amd64-current-job-04] | `-- Extracting cairo-1.18.2,3: .......... done [142amd64-current-job-04] | `-- Installing harfbuzz-10.3.0... [142amd64-current-job-04] | | `-- Installing graphite2-1.3.14... [142amd64-current-job-04] | | `-- Extracting graphite2-1.3.14: .......... done [142amd64-current-job-04] | `-- Extracting harfbuzz-10.3.0: .......... done [142amd64-current-job-04] | `-- Installing icu-76.1,1... [142amd64-current-job-04] | `-- Extracting icu-76.1,1: .......... done [142amd64-current-job-04] | `-- Installing pango-1.56.1... [142amd64-current-job-04] | | `-- Installing fribidi-1.0.16... [142amd64-current-job-04] | | `-- Extracting fribidi-1.0.16: .......... done [142amd64-current-job-04] | | `-- Installing libXft-2.3.8... [142amd64-current-job-04] | | `-- Extracting libXft-2.3.8: .......... done [142amd64-current-job-04] | | `-- Installing libthai-0.1.29_1... [142amd64-current-job-04] | | `-- Installing libdatrie-0.2.13_2... [142amd64-current-job-04] | | `-- Extracting libdatrie-0.2.13_2: .......... done [142amd64-current-job-04] | | `-- Extracting libthai-0.1.29_1: .......... done [142amd64-current-job-04] | `-- Extracting pango-1.56.1: .......... done [142amd64-current-job-04] | `-- Installing tesseract-data-4.1.0... [142amd64-current-job-04] | `-- Extracting tesseract-data-4.1.0: .......... done [142amd64-current-job-04] `-- Extracting tesseract-5.5.0_1: .......... done [142amd64-current-job-04] `-- Installing urw-base35-fonts-20200910... [142amd64-current-job-04] | `-- Installing mkfontscale-1.2.3... [142amd64-current-job-04] | | `-- Installing libfontenc-1.1.8... [142amd64-current-job-04] | | `-- Extracting libfontenc-1.1.8: ......... done [142amd64-current-job-04] | `-- Extracting mkfontscale-1.2.3: ....... done [142amd64-current-job-04] `-- Extracting urw-base35-fonts-20200910: .......... done [142amd64-current-job-04] Extracting ghostscript10-10.04.0: .......... done ==> Running trigger: fontconfig.ucl Running fc-cache to build fontconfig cache... ==> Running trigger: gio-modules.ucl Generating GIO modules cache ==> Running trigger: glib-schemas.ucl Compiling glib schemas No schema files found: doing nothing. ===== Message from freetype2-2.13.3: -- The 2.7.x series now uses the new subpixel hinting mode (V40 port's option) as the default, emulating a modern version of ClearType. This change inevitably leads to different rendering results, and you might change port's options to adapt it to your taste (or use the new "FREETYPE_PROPERTIES" environment variable). The environment variable "FREETYPE_PROPERTIES" can be used to control the driver properties. Example: FREETYPE_PROPERTIES=truetype:interpreter-version=35 \ cff:no-stem-darkening=1 \ autofitter:warping=1 This allows to select, say, the subpixel hinting mode at runtime for a given application. If LONG_PCF_NAMES port's option was enabled, the PCF family names may include the foundry and information whether they contain wide characters. For example, "Sony Fixed" or "Misc Fixed Wide", instead of "Fixed". This can be disabled at run time with using pcf:no-long-family-names property, if needed. Example: FREETYPE_PROPERTIES=pcf:no-long-family-names=1 How to recreate fontconfig cache with using such environment variable, if needed: # env FREETYPE_PROPERTIES=pcf:no-long-family-names=1 fc-cache -fsv The controllable properties are listed in the section "Controlling FreeType Modules" in the reference's table of contents (/usr/local/share/doc/freetype2/reference/index.html, if documentation was installed). ===== Message from leptonica-1.82.0_2: -- To use gplot (the optional programmatic interface to gnuplot), the math/gnuplot port must be installed. ===== Message from python311-3.11.11: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py311-gdbm databases/py-gdbm@py311 py311-sqlite3 databases/py-sqlite3@py311 py311-tkinter x11-toolkits/py-tkinter@py311 ===== Message from ghostscript10-10.04.0: -- This package installs a script named dvipdf that depends on dvips. If you want to use this script you need to install print/tex-dvipsk. ===> R-4.4.3 depends on package: ghostscript10>=10.02.0 - found ===> Returning to build of R-4.4.3 ===> R-4.4.3 depends on file: /usr/local/share/texmf-var/web2c/tex/tex.fmt - not found ===> Installing existing package /packages/All/tex-formats-20240312.pkg [142amd64-current-job-04] Installing tex-formats-20240312... [142amd64-current-job-04] `-- Installing tex-basic-engines-20240312... [142amd64-current-job-04] | `-- Installing tex-kpathsea-6.4.0... [142amd64-current-job-04] | `-- Extracting tex-kpathsea-6.4.0: .......... done [142amd64-current-job-04] | `-- Installing tex-web2c-20240312... [142amd64-current-job-04] | | `-- Installing mpfi-1.5.4... [142amd64-current-job-04] | | `-- Extracting mpfi-1.5.4: .......... done [142amd64-current-job-04] | | `-- Installing tex-ptexenc-1.4.6... 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[142amd64-current-job-04] | `-- Extracting texlive-tlmgr-20240312: ......... done [142amd64-current-job-04] | `-- Installing xpdfopen-20240312... [142amd64-current-job-04] | `-- Extracting xpdfopen-20240312: .... done [142amd64-current-job-04] `-- Extracting texlive-base-20240312_1: .......... done [142amd64-current-job-04] `-- Installing texlive-texmf-20240312_1... [142amd64-current-job-04] `-- Extracting texlive-texmf-20240312_1: .......... done [142amd64-current-job-04] Extracting tex-formats-20240312: .......... done ===== Message from libimagequant-4.3.4_1: -- ===> NOTICE: The libimagequant port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://docs.freebsd.org/en/articles/contributing/#ports-contributing ===> R-4.4.3 depends on file: /usr/local/share/texmf-var/web2c/tex/tex.fmt - found ===> Returning to build of R-4.4.3 ===> R-4.4.3 depends on executable: dvips - not found ===> Installing existing package /packages/All/tex-dvipsk-20240312.pkg [142amd64-current-job-04] Installing tex-dvipsk-20240312... [142amd64-current-job-04] Extracting tex-dvipsk-20240312: .......... done ===> R-4.4.3 depends on executable: dvips - found ===> Returning to build of R-4.4.3 ===> R-4.4.3 depends on file: /usr/local/bin/as - found ===> R-4.4.3 depends on package: perl5>=5.36<5.37 - found ===> R-4.4.3 depends on file: /usr/local/libdata/pkgconfig/ice.pc - found ===> R-4.4.3 depends on file: /usr/local/libdata/pkgconfig/sm.pc - found ===> R-4.4.3 depends on file: /usr/local/libdata/pkgconfig/x11.pc - found ===> R-4.4.3 depends on file: /usr/local/libdata/pkgconfig/xext.pc - found ===> R-4.4.3 depends on file: /usr/local/libdata/pkgconfig/xmu.pc - found ===> R-4.4.3 depends on file: /usr/local/libdata/pkgconfig/xscrnsaver.pc - not found ===> Installing existing package /packages/All/libXScrnSaver-1.2.4_1.pkg [142amd64-current-job-04] Installing libXScrnSaver-1.2.4_1... [142amd64-current-job-04] Extracting libXScrnSaver-1.2.4_1: .......... done ===> R-4.4.3 depends on file: /usr/local/libdata/pkgconfig/xscrnsaver.pc - found ===> Returning to build of R-4.4.3 ===> R-4.4.3 depends on file: /usr/local/libdata/pkgconfig/xt.pc - found ===> R-4.4.3 depends on file: /usr/local/bin/ccache - not found ===> Installing existing package /packages/All/ccache-3.7.12_8.pkg [142amd64-current-job-04] Installing ccache-3.7.12_8... [142amd64-current-job-04] Extracting ccache-3.7.12_8: .......... done Create compiler links... create symlink for cc create symlink for cc (world) create symlink for c++ create symlink for c++ (world) create symlink for CC create symlink for CC (world) create symlink for gcc13 create symlink for gcc13 (world) create symlink for g++13 create symlink for g++13 (world) create symlink for cpp13 create symlink for cpp13 (world) create symlink for clang create symlink for clang (world) create symlink for clang++ create symlink for clang++ (world) ===== Message from ccache-3.7.12_8: -- NOTE: Please read /usr/local/share/doc/ccache/ccache-howto-freebsd.txt for information on using ccache with FreeBSD ports and src. ===> R-4.4.3 depends on file: /usr/local/bin/ccache - found ===> Returning to build of R-4.4.3 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> R-4.4.3 depends on shared library: libcurl.so - found (/usr/local/lib/libcurl.so) ===> R-4.4.3 depends on shared library: libdeflate.so - found (/usr/local/lib/libdeflate.so) ===> R-4.4.3 depends on shared library: libpcre2-8.so - found (/usr/local/lib/libpcre2-8.so) ===> R-4.4.3 depends on shared library: libharfbuzz.so - found (/usr/local/lib/libharfbuzz.so) ===> R-4.4.3 depends on shared library: libicui18n.so - found (/usr/local/lib/libicui18n.so) ===> R-4.4.3 depends on shared library: libpng.so - found (/usr/local/lib/libpng.so) ===> R-4.4.3 depends on shared library: libtiff.so - found (/usr/local/lib/libtiff.so) ===> R-4.4.3 depends on shared library: libreadline.so.8 - found (/usr/local/lib/libreadline.so.8) ===> R-4.4.3 depends on shared library: libintl.so - found (/usr/local/lib/libintl.so) ===> R-4.4.3 depends on shared library: libcairo.so - found (/usr/local/lib/libcairo.so) ===> R-4.4.3 depends on shared library: libglib-2.0.so - found (/usr/local/lib/libglib-2.0.so) ===> R-4.4.3 depends on shared library: libintl.so - found (/usr/local/lib/libintl.so) ===> R-4.4.3 depends on shared library: libharfbuzz.so - found (/usr/local/lib/libharfbuzz.so) ===> R-4.4.3 depends on shared library: libpango-1.0.so - found (/usr/local/lib/libpango-1.0.so) ===> R-4.4.3 depends on shared library: libjpeg.so - found (/usr/local/lib/libjpeg.so) ===> R-4.4.3 depends on shared library: libtk86.so - not found ===> Installing existing package /packages/All/tk86-8.6.16.pkg [142amd64-current-job-04] Installing tk86-8.6.16... [142amd64-current-job-04] `-- Installing tcl86-8.6.16_2... [142amd64-current-job-04] `-- Extracting tcl86-8.6.16_2: .......... done [142amd64-current-job-04] Extracting tk86-8.6.16: .......... done ===> R-4.4.3 depends on shared library: libtk86.so - found (/usr/local/lib/libtk86.so) ===> Returning to build of R-4.4.3 ===> R-4.4.3 depends on shared library: libtcl86.so - found (/usr/local/lib/libtcl86.so) ===> R-4.4.3 depends on shared library: libkpathsea.so - found (/usr/local/lib/libkpathsea.so) =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for R-4.4.3 configure: loading site script /usr/ports/Templates/config.site checking build system type... amd64-portbld-freebsd14.2 checking host system type... amd64-portbld-freebsd14.2 loading site script './config.site' loading build-specific script './config.site' checking for pwd... /bin/pwd checking whether builddir is srcdir... yes checking whether ln -s works... yes checking for /usr/local/bin/ar... /usr/local/bin/ar checking for a BSD-compatible install... /usr/bin/install -c checking for sed... 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(cached) no checking whether included gettext is requested... no checking for GNU gettext in libc... no checking for GNU gettext in libintl... yes checking whether to use NLS... yes checking where the gettext function comes from... external libintl checking how to link with libintl... /usr/local/lib/libintl.so -Wl,-rpath -Wl,/usr/local/lib Finished configuring src/extra/intl directory checking whether OpenMP SIMD reduction is supported... yes using as R_SHELL for scripts ... /bin/sh configure: creating ./config.status config.status: creating Makeconf config.status: creating Makefile config.status: creating doc/Makefile config.status: creating doc/html/Makefile config.status: creating doc/manual/Makefile config.status: creating etc/Makefile config.status: creating etc/Makeconf config.status: creating etc/Renviron config.status: creating etc/javaconf config.status: creating etc/ldpaths config.status: creating m4/Makefile config.status: creating po/Makefile config.status: creating share/Makefile config.status: creating src/Makefile config.status: creating src/appl/Makefile config.status: creating src/extra/Makefile config.status: creating src/extra/blas/Makefile config.status: creating src/extra/intl/Makefile config.status: creating src/extra/tre/Makefile config.status: creating src/extra/tzone/Makefile config.status: creating src/extra/xdr/Makefile config.status: creating src/include/Makefile config.status: creating src/include/Rmath.h0 config.status: creating src/include/R_ext/Makefile config.status: creating src/library/Recommended/Makefile config.status: creating src/library/Makefile config.status: creating src/library/base/DESCRIPTION config.status: creating src/library/base/Makefile config.status: creating src/library/compiler/DESCRIPTION config.status: creating src/library/compiler/Makefile config.status: creating src/library/datasets/DESCRIPTION config.status: creating src/library/datasets/Makefile config.status: creating src/library/graphics/DESCRIPTION config.status: creating src/library/graphics/Makefile config.status: creating src/library/graphics/src/Makefile config.status: creating src/library/grDevices/DESCRIPTION config.status: creating src/library/grDevices/Makefile config.status: creating src/library/grDevices/src/Makefile config.status: creating src/library/grDevices/src/cairo/Makefile config.status: creating src/library/grid/DESCRIPTION config.status: creating src/library/grid/Makefile config.status: creating src/library/grid/src/Makefile config.status: creating src/library/methods/DESCRIPTION config.status: creating src/library/methods/Makefile config.status: creating src/library/methods/src/Makefile config.status: creating src/library/parallel/DESCRIPTION config.status: creating src/library/parallel/Makefile config.status: creating src/library/parallel/src/Makefile config.status: creating src/library/profile/Makefile config.status: creating src/library/stats/DESCRIPTION config.status: creating src/library/stats/Makefile config.status: creating src/library/stats/src/Makefile config.status: creating src/library/stats4/DESCRIPTION config.status: creating src/library/stats4/Makefile config.status: creating src/library/splines/DESCRIPTION config.status: creating src/library/splines/Makefile config.status: creating src/library/splines/src/Makefile config.status: creating src/library/tcltk/DESCRIPTION config.status: creating src/library/tcltk/Makefile config.status: creating src/library/tcltk/src/Makefile config.status: creating src/library/tools/DESCRIPTION config.status: creating src/library/tools/Makefile config.status: creating src/library/tools/src/Makefile config.status: creating src/library/translations/DESCRIPTION config.status: creating src/library/translations/Makefile config.status: creating src/library/utils/DESCRIPTION config.status: creating src/library/utils/Makefile config.status: creating src/library/utils/src/Makefile config.status: creating src/main/Makefile config.status: creating src/modules/Makefile config.status: creating src/modules/X11/Makefile config.status: creating src/modules/internet/Makefile config.status: creating src/modules/lapack/Makefile config.status: creating src/nmath/Makefile config.status: creating src/nmath/standalone/Makefile config.status: creating src/scripts/Makefile config.status: creating src/scripts/R.sh config.status: creating src/scripts/Rcmd config.status: creating src/scripts/javareconf config.status: creating src/scripts/mkinstalldirs config.status: creating src/scripts/pager config.status: creating src/scripts/rtags config.status: creating src/unix/Makefile config.status: creating tests/Makefile config.status: creating tests/Embedding/Makefile config.status: creating tests/Examples/Makefile config.status: creating tools/Makefile config.status: creating src/include/config.h config.status: executing libtool commands config.status: executing stamp-h commands R is now configured for amd64-portbld-freebsd14.2 Source directory: . Installation directory: /usr/local C compiler: cc -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing Fortran fixed-form compiler: gfortran13 -O -Wl,-rpath=/usr/local/lib/gcc13 Default C++ compiler: c++ -std=gnu++17 -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -DLIBICONV_PLUG -isystem /usr/local/include C++11 compiler: c++ -std=gnu++11 -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -DLIBICONV_PLUG -isystem /usr/local/include C++14 compiler: c++ -std=gnu++14 -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -DLIBICONV_PLUG -isystem /usr/local/include C++17 compiler: c++ -std=gnu++17 -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -DLIBICONV_PLUG -isystem /usr/local/include C++20 compiler: c++ -std=gnu++20 -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -DLIBICONV_PLUG -isystem /usr/local/include C++23 compiler: c++ -std=gnu++23 -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -DLIBICONV_PLUG -isystem /usr/local/include Fortran free-form compiler: gfortran13 -Wl,-rpath=/usr/local/lib/gcc13 Obj-C compiler: cc -g -O2 -fobjc-exceptions Interfaces supported: X11, tcltk External libraries: pcre2, readline, curl, libdeflate Additional capabilities: PNG, JPEG, TIFF, NLS, cairo, ICU Options enabled: shared R library, shared BLAS, R profiling, libdeflate for lazyload Capabilities skipped: Options not enabled: memory profiling Recommended packages: yes configure: WARNING: I could not determine a browser configure: WARNING: I could not determine a PDF viewer =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for R-4.4.3 gmake[1]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/m4' gmake[1]: Nothing to be done for 'R'. gmake[1]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/m4' gmake[1]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/tools' gmake[1]: Nothing to be done for 'R'. gmake[1]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/tools' gmake[1]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc' gmake[2]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/html' gmake[2]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/html' gmake[2]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual' gmake[2]: Nothing to be done for 'R'. gmake[2]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual' gmake[1]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc' gmake[1]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/etc' gmake[1]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/etc' gmake[1]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/share' gmake[1]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/share' gmake[1]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src' gmake[2]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/scripts' creating src/scripts/R.fe gmake[3]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/scripts' mkdir ../../bin gmake[3]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/scripts' gmake[2]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/scripts' gmake[2]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/include' mkdir ../../include gmake[3]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/include/R_ext' mkdir ../../../include/R_ext gmake[3]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/include/R_ext' gmake[2]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/include' gmake[2]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/extra' gmake[3]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/extra/blas' gmake[3]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/extra/xdr' gmake[3]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/extra/tre' making xdr.d from xdr.c making xdr_float.d from xdr_float.c gmake[4]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/extra/blas' gfortran13 -fpic -O -Wl,-rpath=/usr/local/lib/gcc13 -c blas.f -o blas.o gfortran13 -fpic -O -Wl,-rpath=/usr/local/lib/gcc13 -c blas2.f90 -o blas2.o making xdr_mem.d from xdr_mem.c gmake[4]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/extra/tre' making regcomp.d from regcomp.c gfortran13 -fpic -O -Wl,-rpath=/usr/local/lib/gcc13 -c cmplxblas.f -o cmplxblas.o gfortran13 -fpic -O -Wl,-rpath=/usr/local/lib/gcc13 -c cmplxblas2.f90 -o cmplxblas2.o making regerror.d from regerror.c making regexec.d from regexec.c making xdr_stdio.d from xdr_stdio.c making tre-ast.d from tre-ast.c making tre-compile.d from tre-compile.c making tre-match-approx.d from tre-match-approx.c gmake[4]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/extra/xdr' cc -I. -I. -I../../../src/include -I../../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -c xdr.c -o xdr.o cc -I. -I. -I../../../src/include -I../../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -c xdr_float.c -o xdr_float.o making tre-match-backtrack.d from tre-match-backtrack.c cc -I. -I. -I../../../src/include -I../../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -c xdr_mem.c -o xdr_mem.o cc -I. -I. -I../../../src/include -I../../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -c xdr_stdio.c -o xdr_stdio.o making tre-match-parallel.d from tre-match-parallel.c making tre-mem.d from tre-mem.c making tre-parse.d from tre-parse.c /usr/local/bin/ar -cr libxdr.a xdr.o xdr_float.o xdr_mem.o xdr_stdio.o making tre-stack.d from tre-stack.c /usr/local/bin/ranlib libxdr.a gmake[4]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/extra/xdr' gmake[3]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/extra/xdr' gmake[4]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/extra/tre' gmake[4]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/extra/tre' cc -I. -I. -I../../../src/include -I../../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -c regcomp.c -o regcomp.o cc -I. -I. -I../../../src/include -I../../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -c regerror.c -o regerror.o cc -I. -I. -I../../../src/include -I../../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -c regexec.c -o regexec.o cc -I. -I. -I../../../src/include -I../../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -c tre-ast.c -o tre-ast.o cc -I. -I. -I../../../src/include -I../../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -c tre-compile.c -o tre-compile.o cc -I. -I. -I../../../src/include -I../../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -c tre-match-approx.c -o tre-match-approx.o cc -I. -I. -I../../../src/include -I../../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -c tre-match-backtrack.c -o tre-match-backtrack.o cc -I. -I. -I../../../src/include -I../../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -c tre-match-parallel.c -o tre-match-parallel.o cc -I. -I. -I../../../src/include -I../../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -c tre-mem.c -o tre-mem.o cc -I. -I. -I../../../src/include -I../../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -c tre-parse.c -o tre-parse.o cc -I. -I. -I../../../src/include -I../../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -c tre-stack.c -o tre-stack.o /usr/local/bin/ar -cr libtre.a regcomp.o regerror.o regexec.o tre-ast.o tre-compile.o tre-match-approx.o tre-match-backtrack.o tre-match-parallel.o tre-mem.o tre-parse.o tre-stack.o /usr/local/bin/ranlib libtre.a gmake[4]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/extra/tre' gmake[3]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/extra/tre' cc -shared -fopenmp -Wl,-rpath=/usr/local/lib/gcc13 -L/usr/local/lib/gcc13 -L/usr/local/lib -fstack-protector-strong -o libRblas.so blas.o blas2.o cmplxblas.o cmplxblas2.o -Wl,-soname,libRblas.so.4 -L/usr/local/lib/gcc13/gcc/x86_64-portbld-freebsd14.2/13.3.0 -L/usr/local/x86_64-portbld-freebsd14.2/lib -lgfortran -lm -lssp_nonshared -lquadmath gmake[4]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/extra/blas' gmake[4]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/extra/blas' mkdir /wrkdirs/usr/ports/math/R/work/R-4.4.3/lib gmake[4]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/extra/blas' gmake[3]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/extra/blas' gmake[2]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/extra' gmake[2]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/appl' making integrate.d from integrate.c making interv.d from interv.c making maxcol.d from maxcol.c making optim.d from optim.c making pretty.d from pretty.c making uncmin.d from uncmin.c gmake[3]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/appl' cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c integrate.c -o integrate.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c interv.c -o interv.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c maxcol.c -o maxcol.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c optim.c -o optim.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c pretty.c -o pretty.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c uncmin.c -o uncmin.o gfortran13 -fpic -O -Wl,-rpath=/usr/local/lib/gcc13 -c dchdc.f -o dchdc.o gfortran13 -fpic -O -Wl,-rpath=/usr/local/lib/gcc13 -c dpbfa.f -o dpbfa.o gfortran13 -fpic -O -Wl,-rpath=/usr/local/lib/gcc13 -c dpbsl.f -o dpbsl.o gfortran13 -fpic -O -Wl,-rpath=/usr/local/lib/gcc13 -c dpoco.f -o dpoco.o gfortran13 -fpic -O -Wl,-rpath=/usr/local/lib/gcc13 -c dpodi.f -o dpodi.o gfortran13 -fpic -O -Wl,-rpath=/usr/local/lib/gcc13 -c dpofa.f -o dpofa.o gfortran13 -fpic -O -Wl,-rpath=/usr/local/lib/gcc13 -c dposl.f -o dposl.o gfortran13 -fpic -O -Wl,-rpath=/usr/local/lib/gcc13 -c dqrdc.f -o dqrdc.o gfortran13 -fpic -O -Wl,-rpath=/usr/local/lib/gcc13 -c dqrdc2.f -o dqrdc2.o gfortran13 -fpic -O -Wl,-rpath=/usr/local/lib/gcc13 -c dqrls.f -o dqrls.o gfortran13 -fpic -O -Wl,-rpath=/usr/local/lib/gcc13 -c dqrsl.f -o dqrsl.o gfortran13 -fpic -O -Wl,-rpath=/usr/local/lib/gcc13 -c dqrutl.f -o dqrutl.o gfortran13 -fpic -O -Wl,-rpath=/usr/local/lib/gcc13 -c dsvdc.f -o dsvdc.o gfortran13 -fpic -O -Wl,-rpath=/usr/local/lib/gcc13 -c dtrco.f -o dtrco.o gfortran13 -fpic -O -Wl,-rpath=/usr/local/lib/gcc13 -c dtrsl.f -o dtrsl.o /usr/local/bin/ar -cr libappl.a integrate.o interv.o maxcol.o optim.o pretty.o uncmin.o dchdc.o dpbfa.o dpbsl.o dpoco.o dpodi.o dpofa.o dposl.o dqrdc.o dqrdc2.o dqrls.o dqrsl.o dqrutl.o dsvdc.o dtrco.o dtrsl.o /usr/local/bin/ranlib libappl.a gmake[3]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/appl' gmake[2]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/appl' gmake[2]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/nmath' making mlutils.d from mlutils.c making d1mach.d from d1mach.c making i1mach.d from i1mach.c making fmax2.d from fmax2.c making fmin2.d from fmin2.c making fprec.d from fprec.c making fround.d from fround.c making ftrunc.d from ftrunc.c making sign.d from sign.c making imin2.d from imin2.c making imax2.d from imax2.c making fsign.d from fsign.c making chebyshev.d from chebyshev.c making log1p.d from log1p.c making lgammacor.d from lgammacor.c making gammalims.d from gammalims.c making stirlerr.d from stirlerr.c making bd0.d from bd0.c making gamma.d from gamma.c making lgamma.d from lgamma.c making beta.d from beta.c making polygamma.d from polygamma.c making gamma_cody.d from gamma_cody.c making lbeta.d from lbeta.c making bessel_i.d from bessel_i.c making cospi.d from cospi.c making bessel_k.d from bessel_k.c making bessel_y.d from bessel_y.c making bessel_j.d from bessel_j.c making choose.d from choose.c making snorm.d from snorm.c making sexp.d from sexp.c making dgamma.d from dgamma.c making pgamma.d from pgamma.c making qgamma.d from qgamma.c making rgamma.d from rgamma.c making qbeta.d from qbeta.c making pbeta.d from pbeta.c making rbeta.d from rbeta.c making dbeta.d from dbeta.c making dunif.d from dunif.c making qunif.d from qunif.c making runif.d from runif.c making punif.d from punif.c making dnorm.d from dnorm.c making pnorm.d from pnorm.c making qnorm.d from qnorm.c making rnorm.d from rnorm.c making dlnorm.d from dlnorm.c making plnorm.d from plnorm.c making rlnorm.d from rlnorm.c making qlnorm.d from qlnorm.c making df.d from df.c making pf.d from pf.c making qf.d from qf.c making rf.d from rf.c making dnf.d from dnf.c making dt.d from dt.c making pt.d from pt.c making qt.d from qt.c making rt.d from rt.c making dnt.d from dnt.c making dchisq.d from dchisq.c making pchisq.d from pchisq.c making rchisq.d from rchisq.c making qchisq.d from qchisq.c making rnchisq.d from rnchisq.c making dbinom.d from dbinom.c making pbinom.d from pbinom.c making qbinom.d from qbinom.c making rbinom.d from rbinom.c making rmultinom.d from rmultinom.c making pcauchy.d from pcauchy.c making dcauchy.d from dcauchy.c making qcauchy.d from qcauchy.c making rcauchy.d from rcauchy.c making dexp.d from dexp.c making pexp.d from pexp.c making qexp.d from qexp.c making rexp.d from rexp.c making dgeom.d from dgeom.c making rgeom.d from rgeom.c making pgeom.d from pgeom.c making dhyper.d from dhyper.c making phyper.d from phyper.c making qgeom.d from qgeom.c making rhyper.d from rhyper.c making pnbinom.d from pnbinom.c making dnbinom.d from dnbinom.c making qhyper.d from qhyper.c making qnbinom.d from qnbinom.c making qnbinom_mu.d from qnbinom_mu.c making rnbinom.d from rnbinom.c making dpois.d from dpois.c making ppois.d from ppois.c making qpois.d from qpois.c making rpois.d from rpois.c making dweibull.d from dweibull.c making pweibull.d from pweibull.c making qweibull.d from qweibull.c making rweibull.d from rweibull.c making dlogis.d from dlogis.c making plogis.d from plogis.c making rlogis.d from rlogis.c making qlogis.d from qlogis.c making dnchisq.d from dnchisq.c making pnchisq.d from pnchisq.c making qnchisq.d from qnchisq.c making dnbeta.d from dnbeta.c making pnbeta.d from pnbeta.c making qnbeta.d from qnbeta.c making pnf.d from pnf.c making pnt.d from pnt.c making qnf.d from qnf.c making qnt.d from qnt.c making ptukey.d from ptukey.c making qtukey.d from qtukey.c making toms708.d from toms708.c making wilcox.d from wilcox.c making signrank.d from signrank.c gmake[3]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/nmath' cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c mlutils.c -o mlutils.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c d1mach.c -o d1mach.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c i1mach.c -o i1mach.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c fmax2.c -o fmax2.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c fmin2.c -o fmin2.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c fprec.c -o fprec.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c fround.c -o fround.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c ftrunc.c -o ftrunc.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c sign.c -o sign.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c fsign.c -o fsign.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c imax2.c -o imax2.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c imin2.c -o imin2.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c chebyshev.c -o chebyshev.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c log1p.c -o log1p.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c lgammacor.c -o lgammacor.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c gammalims.c -o gammalims.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c stirlerr.c -o stirlerr.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c bd0.c -o bd0.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c gamma.c -o gamma.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c lgamma.c -o lgamma.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c gamma_cody.c -o gamma_cody.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c beta.c -o beta.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c lbeta.c -o lbeta.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c polygamma.c -o polygamma.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c cospi.c -o cospi.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c bessel_i.c -o bessel_i.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c bessel_j.c -o bessel_j.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c bessel_k.c -o bessel_k.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c bessel_y.c -o bessel_y.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c choose.c -o choose.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c snorm.c -o snorm.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c sexp.c -o sexp.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c dgamma.c -o dgamma.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c pgamma.c -o pgamma.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c qgamma.c -o qgamma.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c rgamma.c -o rgamma.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c dbeta.c -o dbeta.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c pbeta.c -o pbeta.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c qbeta.c -o qbeta.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c rbeta.c -o rbeta.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c dunif.c -o dunif.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c punif.c -o punif.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c qunif.c -o qunif.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c runif.c -o runif.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c dnorm.c -o dnorm.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c pnorm.c -o pnorm.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c qnorm.c -o qnorm.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c rnorm.c -o rnorm.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c dlnorm.c -o dlnorm.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c plnorm.c -o plnorm.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c qlnorm.c -o qlnorm.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c rlnorm.c -o rlnorm.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c df.c -o df.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c pf.c -o pf.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c qf.c -o qf.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c rf.c -o rf.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c dnf.c -o dnf.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c dt.c -o dt.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c pt.c -o pt.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c qt.c -o qt.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c rt.c -o rt.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c dnt.c -o dnt.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c dchisq.c -o dchisq.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c pchisq.c -o pchisq.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c qchisq.c -o qchisq.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c rchisq.c -o rchisq.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c rnchisq.c -o rnchisq.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c dbinom.c -o dbinom.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c pbinom.c -o pbinom.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c qbinom.c -o qbinom.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c rbinom.c -o rbinom.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c rmultinom.c -o rmultinom.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c dcauchy.c -o dcauchy.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c pcauchy.c -o pcauchy.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c qcauchy.c -o qcauchy.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c rcauchy.c -o rcauchy.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c dexp.c -o dexp.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c pexp.c -o pexp.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c qexp.c -o qexp.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c rexp.c -o rexp.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c dgeom.c -o dgeom.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c pgeom.c -o pgeom.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c qgeom.c -o qgeom.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c rgeom.c -o rgeom.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c dhyper.c -o dhyper.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c phyper.c -o phyper.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c qhyper.c -o qhyper.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c rhyper.c -o rhyper.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c dnbinom.c -o dnbinom.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c pnbinom.c -o pnbinom.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c qnbinom.c -o qnbinom.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c qnbinom_mu.c -o qnbinom_mu.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c rnbinom.c -o rnbinom.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c dpois.c -o dpois.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c ppois.c -o ppois.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c qpois.c -o qpois.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c rpois.c -o rpois.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c dweibull.c -o dweibull.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c pweibull.c -o pweibull.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c qweibull.c -o qweibull.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c rweibull.c -o rweibull.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c dlogis.c -o dlogis.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c plogis.c -o plogis.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c qlogis.c -o qlogis.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c rlogis.c -o rlogis.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c dnchisq.c -o dnchisq.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c pnchisq.c -o pnchisq.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c qnchisq.c -o qnchisq.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c dnbeta.c -o dnbeta.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c pnbeta.c -o pnbeta.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c qnbeta.c -o qnbeta.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c pnf.c -o pnf.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c pnt.c -o pnt.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c qnf.c -o qnf.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c qnt.c -o qnt.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c ptukey.c -o ptukey.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c qtukey.c -o qtukey.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c toms708.c -o toms708.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c wilcox.c -o wilcox.o cc -I. -I../../src/include -I../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c signrank.c -o signrank.o /usr/local/bin/ar -cr libnmath.a mlutils.o d1mach.o i1mach.o fmax2.o fmin2.o fprec.o fround.o ftrunc.o sign.o fsign.o imax2.o imin2.o chebyshev.o log1p.o lgammacor.o gammalims.o stirlerr.o bd0.o gamma.o lgamma.o gamma_cody.o beta.o lbeta.o polygamma.o cospi.o bessel_i.o bessel_j.o bessel_k.o bessel_y.o choose.o snorm.o sexp.o dgamma.o pgamma.o qgamma.o rgamma.o dbeta.o pbeta.o qbeta.o rbeta.o dunif.o punif.o qunif.o runif.o dnorm.o pnorm.o qnorm.o rnorm.o dlnorm.o plnorm.o qlnorm.o rlnorm.o df.o pf.o qf.o rf.o dnf.o dt.o pt.o qt.o rt.o dnt.o dchisq.o pchisq.o qchisq.o rchisq.o rnchisq.o dbinom.o pbinom.o qbinom.o rbinom.o rmultinom.o dcauchy.o pcauchy.o qcauchy.o rcauchy.o dexp.o pexp.o qexp.o rexp.o dgeom.o pgeom.o qgeom.o rgeom.o dhyper.o phyper.o qhyper.o rhyper.o dnbinom.o pnbinom.o qnbinom.o qnbinom_mu.o rnbinom.o dpois.o ppois.o qpois.o rpois.o dweibull.o pweibull.o qweibull.o rweibull.o dlogis.o plogis.o qlogis.o rlogis.o dnchisq.o pnchisq.o qnchisq.o dnbeta.o pnbeta.o qnbeta.o pnf.o pnt.o qnf.o qnt.o ptukey.o qtukey.o toms708.o wilcox.o signrank.o /usr/local/bin/ranlib libnmath.a gmake[3]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/nmath' gmake[2]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/nmath' gmake[2]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/unix' config.status: creating src/unix/Makefile making Rembedded.d from Rembedded.c making dynload.d from dynload.c making system.d from system.c making sys-unix.d from sys-unix.c making sys-std.d from sys-std.c making X11.d from X11.c gmake[3]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/unix' cc -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c Rembedded.c -o Rembedded.o cc -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c dynload.c -o dynload.o cc -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c system.c -o system.o cc -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c sys-unix.c -o sys-unix.o cc -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c sys-std.c -o sys-std.o cc -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c X11.c -o X11.o /usr/local/bin/ar -cr libunix.a Rembedded.o dynload.o system.o sys-unix.o sys-std.o X11.o /usr/local/bin/ranlib libunix.a gmake[3]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/unix' gmake[3]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/unix' cc -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc13 -L/usr/local/lib/gcc13 -L/usr/local/lib -fstack-protector-strong -DR_HOME='"/wrkdirs/usr/ports/math/R/work/R-4.4.3"' \ -o Rscript ./Rscript.c gmake[3]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/unix' gmake[2]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/unix' gmake[2]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/main' config.status: creating src/main/Makefile making CommandLineArgs.d from CommandLineArgs.c making Renviron.d from Renviron.c making Rdynload.d from Rdynload.c making RNG.d from RNG.c making agrep.d from agrep.c making altclasses.d from altclasses.c making altrep.d from altrep.c making arithmetic.d from arithmetic.c making array.d from array.c making apply.d from apply.c making bind.d from bind.c making attrib.d from attrib.c making builtin.d from builtin.c making character.d from character.c making clippath.d from clippath.c making coerce.d from coerce.c making colors.d from colors.c making complex.d from complex.c making connections.d from connections.c making context.d from context.c making datetime.d from datetime.c making cum.d from cum.c making debug.d from debug.c making dcf.d from dcf.c making deparse.d from deparse.c making devices.d from devices.c making dotcode.d from dotcode.c making dounzip.d from dounzip.c making dstruct.d from dstruct.c making duplicate.d from duplicate.c making edit.d from edit.c making engine.d from engine.c making envir.d from envir.c making errors.d from errors.c making eval.d from eval.c making flexiblas.d from flexiblas.c making format.d from format.c making gevents.d from gevents.c making gram.d from gram.c making gram-ex.d from gram-ex.c making graphics.d from graphics.c making grep.d from grep.c making identical.d from identical.c making inspect.d from inspect.c making internet.d from internet.c making inlined.d from inlined.c making lapack.d from lapack.c making iosupport.d from iosupport.c making localecharset.d from localecharset.c making machine.d from machine.c making main.d from main.c making list.d from list.c making logic.d from logic.c making mask.d from mask.c making mapply.d from mapply.c making match.d from match.c making memory.d from memory.c making names.d from names.c making objects.d from objects.c making options.d from options.c making paste.d from paste.c making patterns.d from patterns.c making platform.d from platform.c making plot.d from plot.c making plotmath.d from plotmath.c making print.d from print.c making plot3d.d from plot3d.c making printarray.d from printarray.c making printutils.d from printutils.c making qsort.d from qsort.c making printvector.d from printvector.c making radixsort.d from radixsort.c making random.d from random.c making raw.d from raw.c making registration.d from registration.c making relop.d from relop.c making rlocale.d from rlocale.c making saveload.d from saveload.c making scan.d from scan.c making seq.d from seq.c making serialize.d from serialize.c making sort.d from sort.c making source.d from source.c making split.d from split.c making sprintf.d from sprintf.c making startup.d from startup.c making subassign.d from subassign.c making subset.d from subset.c making summary.d from summary.c making sysutils.d from sysutils.c making unique.d from unique.c making times.d from times.c making util.d from util.c making version.d from version.c making g_alab_her.d from g_alab_her.c making subscript.d from subscript.c making g_cntrlify.d from g_cntrlify.c making g_her_glyph.d from g_her_glyph.c making g_fontdb.d from g_fontdb.c making Rmain.d from Rmain.c making alloca.d from alloca.c making strdup.d from strdup.c making mkdtemp.d from mkdtemp.c making strncasecmp.d from strncasecmp.c gmake[3]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/main' cc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c CommandLineArgs.c -o CommandLineArgs.o cc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c Rdynload.c -o Rdynload.o cc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c Renviron.c -o Renviron.o cc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c RNG.c -o RNG.o cc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c agrep.c -o agrep.o cc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c altclasses.c -o altclasses.o cc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c altrep.c -o altrep.o cc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c apply.c -o apply.o cc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c arithmetic.c -o arithmetic.o cc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c array.c -o array.o cc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c attrib.c -o attrib.o cc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c bind.c -o bind.o cc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c builtin.c -o builtin.o cc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c character.c -o character.o cc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c clippath.c -o clippath.o cc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c coerce.c -o coerce.o cc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c colors.c -o colors.o cc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c complex.c -o complex.o cc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c connections.c -o connections.o cc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c context.c -o context.o cc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c cum.c -o cum.o cc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c dcf.c -o dcf.o cc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c datetime.c -o datetime.o cc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c debug.c -o debug.o cc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c deparse.c -o deparse.o cc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c devices.c -o devices.o cc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c dotcode.c -o dotcode.o cc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c dounzip.c -o dounzip.o cc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c dstruct.c -o dstruct.o cc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c duplicate.c -o duplicate.o cc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c edit.c -o edit.o cc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c engine.c -o engine.o cc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c envir.c -o envir.o cc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c errors.c -o errors.o cc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c eval.c -o eval.o cc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c flexiblas.c -o flexiblas.o cc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c format.c -o format.o cc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c gevents.c -o gevents.o cc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c gram.c -o gram.o cc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c gram-ex.c -o gram-ex.o cc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c graphics.c -o graphics.o cc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c grep.c -o grep.o cc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c identical.c -o identical.o cc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c inlined.c -o inlined.o cc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c inspect.c -o inspect.o cc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c internet.c -o internet.o cc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c iosupport.c -o iosupport.o cc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c lapack.c -o lapack.o cc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c list.c -o list.o cc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c localecharset.c -o localecharset.o cc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c logic.c -o logic.o cc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c machine.c -o machine.o cc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c main.c -o main.o cc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c mapply.c -o mapply.o cc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c mask.c -o mask.o cc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c match.c -o match.o cc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c memory.c -o memory.o cc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c names.c -o names.o cc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c objects.c -o objects.o cc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c options.c -o options.o cc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c paste.c -o paste.o cc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c patterns.c -o patterns.o cc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c platform.c -o platform.o cc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c plot.c -o plot.o cc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c plot3d.c -o plot3d.o cc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c plotmath.c -o plotmath.o cc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c print.c -o print.o cc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c printarray.c -o printarray.o cc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c printvector.c -o printvector.o cc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c printutils.c -o printutils.o cc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c qsort.c -o qsort.o cc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c radixsort.c -o radixsort.o cc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c random.c -o random.o cc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c raw.c -o raw.o cc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c registration.c -o registration.o cc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c relop.c -o relop.o cc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c rlocale.c -o rlocale.o cc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c saveload.c -o saveload.o cc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c scan.c -o scan.o cc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c seq.c -o seq.o cc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c serialize.c -o serialize.o cc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c sort.c -o sort.o cc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c source.c -o source.o cc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c split.c -o split.o cc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c sprintf.c -o sprintf.o cc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c startup.c -o startup.o cc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c subassign.c -o subassign.o cc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c subscript.c -o subscript.o cc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c subset.c -o subset.o cc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c summary.c -o summary.o cc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c sysutils.c -o sysutils.o cc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c times.c -o times.o cc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c unique.c -o unique.o cc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c util.c -o util.o cc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c version.c -o version.o cc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c g_alab_her.c -o g_alab_her.o cc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c g_cntrlify.c -o g_cntrlify.o cc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c g_fontdb.c -o g_fontdb.o cc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c g_her_glyph.c -o g_her_glyph.o gfortran13 -fpic -O -Wl,-rpath=/usr/local/lib/gcc13 -c xxxpr.f -o xxxpr.o cc -shared -fopenmp -Wl,-rpath=/usr/local/lib/gcc13 -L/usr/local/lib/gcc13 -L/usr/local/lib -fstack-protector-strong -Wl,-soname,libR.so.4 -o libR.so CommandLineArgs.o Rdynload.o Renviron.o RNG.o agrep.o altclasses.o altrep.o apply.o arithmetic.o array.o attrib.o bind.o builtin.o character.o clippath.o coerce.o colors.o complex.o connections.o context.o cum.o dcf.o datetime.o debug.o deparse.o devices.o dotcode.o dounzip.o dstruct.o duplicate.o edit.o engine.o envir.o errors.o eval.o flexiblas.o format.o gevents.o gram.o gram-ex.o graphics.o grep.o identical.o inlined.o inspect.o internet.o iosupport.o lapack.o list.o localecharset.o logic.o machine.o main.o mapply.o mask.o match.o memory.o names.o objects.o options.o paste.o patterns.o platform.o plot.o plot3d.o plotmath.o print.o printarray.o printvector.o printutils.o qsort.o radixsort.o random.o raw.o registration.o relop.o rlocale.o saveload.o scan.o seq.o serialize.o sort.o source.o split.o sprintf.o startup.o subassign.o subscript.o subset.o summary.o sysutils.o times.o unique.o util.o version.o g_alab_her.o g_cntrlify.o g_fontdb.o g_her_glyph.o xxxpr.o `ls ../unix/*.o ../appl/*.o ../nmath/*.o` ../extra/tre/libtre.a ../extra/xdr/libxdr.a -L"../../lib" -lRblas -L/usr/local/lib/gcc13/gcc/x86_64-portbld-freebsd14.2/13.3.0 -L/usr/local/x86_64-portbld-freebsd14.2/lib -lgfortran -lm -lssp_nonshared -lquadmath /usr/local/lib/libintl.so -Wl,-rpath -Wl,/usr/local/lib -lreadline -L/usr/local/lib -L/usr/local/lib -lpcre2-8 -ldeflate -llzma -lbz2 -lz -lrt -ldl -lm -licuuc -licui18n gmake[4]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/main' mkdir /wrkdirs/usr/ports/math/R/work/R-4.4.3/bin/exec gmake[4]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/main' gmake[3]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/main' gmake[3]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/main' cc -I../../src/extra -I../../src/extra/xdr -I. -I../../src/include -I../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I../../src/nmath -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c Rmain.c -o Rmain.o cc -Wl,--export-dynamic -fopenmp -L"../../lib" -Wl,-rpath=/usr/local/lib/gcc13 -L/usr/local/lib/gcc13 -L/usr/local/lib -fstack-protector-strong -o R.bin Rmain.o -lR -lRblas gmake[4]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/main' gmake[4]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/main' gmake[3]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/main' gmake[2]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/main' gmake[2]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/modules' gmake[3]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/modules/internet' gmake[3]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/modules/X11' gmake[3]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/modules/lapack' making devX11.d from devX11.c making Rhttpd.d from Rhttpd.c making Lapack.d from Lapack.c making Rsock.d from Rsock.c making rotated.d from rotated.c making libcurl.d from libcurl.c making internet.d from internet.c making sock.d from sock.c making sockconn.d from sockconn.c making rbitmap.d from rbitmap.c gmake[4]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/modules/lapack' gfortran13 -fpic -O -Wl,-rpath=/usr/local/lib/gcc13 -c dlamch.f -o dlamch.o gfortran13 -fpic -O -Wl,-rpath=/usr/local/lib/gcc13 -c dlapack.f -o dlapack.o gfortran13 -fpic -O -Wl,-rpath=/usr/local/lib/gcc13 -c cmplx.f -o cmplx.o gfortran13 -fpic -O -Wl,-rpath=/usr/local/lib/gcc13 -c la_constants.f90 -o la_constants.o gmake[4]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/modules/X11' cc -I/usr/local/include/libpng16 -I/usr/local/include -I. -I../../../src/include -I../../../src/include -I/usr/local/include -I/usr/local/include/pango-1.0 -I/usr/local/include -pthread -I/usr/local/include/fribidi -I/usr/local/include/harfbuzz -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include/cairo -I/usr/local/include/freetype2 -I/usr/local/include/libpng16 -I/usr/local/include/pixman-1 -D_THREAD_SAFE -I../../../src/library/grDevices/src/cairo -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c devX11.c -o devX11.o gmake[4]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/modules/internet' cc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -c Rhttpd.c -o Rhttpd.o cc -I/usr/local/include/libpng16 -I/usr/local/include -I. -I../../../src/include -I../../../src/include -I/usr/local/include -I/usr/local/include/pango-1.0 -I/usr/local/include -pthread -I/usr/local/include/fribidi -I/usr/local/include/harfbuzz -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include/cairo -I/usr/local/include/freetype2 -I/usr/local/include/libpng16 -I/usr/local/include/pixman-1 -D_THREAD_SAFE -I../../../src/library/grDevices/src/cairo -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c rotated.c -o rotated.o cc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -c Rsock.c -o Rsock.o gfortran13 -fpic -O -Wl,-rpath=/usr/local/lib/gcc13 -c dlartg.f90 -o dlartg.o cc -I/usr/local/include/libpng16 -I/usr/local/include -I. -I../../../src/include -I../../../src/include -I/usr/local/include -I/usr/local/include/pango-1.0 -I/usr/local/include -pthread -I/usr/local/include/fribidi -I/usr/local/include/harfbuzz -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include/cairo -I/usr/local/include/freetype2 -I/usr/local/include/libpng16 -I/usr/local/include/pixman-1 -D_THREAD_SAFE -I../../../src/library/grDevices/src/cairo -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c rbitmap.c -o rbitmap.o cc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -c internet.c -o internet.o cc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -c libcurl.c -o libcurl.o gfortran13 -fpic -O -Wl,-rpath=/usr/local/lib/gcc13 -c la_xisnan.f90 -o la_xisnan.o cc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -c sock.c -o sock.o cc -I/usr/local/include/libpng16 -I/usr/local/include -I. -I../../../src/include -I../../../src/include -I/usr/local/include -I/usr/local/include/pango-1.0 -I/usr/local/include -pthread -I/usr/local/include/fribidi -I/usr/local/include/harfbuzz -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include/cairo -I/usr/local/include/freetype2 -I/usr/local/include/libpng16 -I/usr/local/include/pixman-1 -D_THREAD_SAFE -I../../../src/library/grDevices/src/cairo -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c dataentry.c -o dataentry.o gfortran13 -fpic -O -Wl,-rpath=/usr/local/lib/gcc13 -c zlartg.f90 -o zlartg.o cc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fvisibility=hidden -c sockconn.c -o sockconn.o gfortran13 -fpic -O -Wl,-rpath=/usr/local/lib/gcc13 -c zlassq.f90 -o zlassq.o cc -shared -L"../../../lib" -Wl,-rpath=/usr/local/lib/gcc13 -L/usr/local/lib/gcc13 -L/usr/local/lib -fstack-protector-strong -o internet.so Rhttpd.o Rsock.o internet.o libcurl.o sock.o sockconn.o -L/usr/local/lib -lcurl -lR gfortran13 -fpic -O -Wl,-rpath=/usr/local/lib/gcc13 -c dlassq.f90 -o dlassq.o gmake[5]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/modules/internet' mkdir /wrkdirs/usr/ports/math/R/work/R-4.4.3/modules gmake[5]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/modules/internet' gmake[4]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/modules/internet' gmake[3]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/modules/internet' cc -shared -L"../../../lib" -Wl,-rpath=/usr/local/lib/gcc13 -L/usr/local/lib/gcc13 -L/usr/local/lib -fstack-protector-strong -o R_X11.so devX11.o rotated.o rbitmap.o -L/usr/local/lib -ltiff -L/usr/local/lib -ljpeg -L/usr/local/lib -lpng16 -lSM -lICE -L/usr/local/lib -lpangocairo-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lintl -lharfbuzz -L/lib -lz -lpng16 -lcairo -lX11 -lXext -L/usr/local/lib -lX11 -lXt -lXmu -lR -lm cc -shared -L"../../../lib" -Wl,-rpath=/usr/local/lib/gcc13 -L/usr/local/lib/gcc13 -L/usr/local/lib -fstack-protector-strong -o R_de.so dataentry.o -lSM -lICE -L/usr/local/lib -lpangocairo-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lintl -lharfbuzz -L/lib -lz -lpng16 -lcairo -lX11 -lXext -L/usr/local/lib -lX11 -lXt -lXmu -lR -lm gmake[4]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/modules/X11' gmake[4]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/modules/X11' gmake[4]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/modules/X11' gmake[3]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/modules/X11' cc -shared -fopenmp -Wl,-rpath=/usr/local/lib/gcc13 -L/usr/local/lib/gcc13 -L/usr/local/lib -fstack-protector-strong -o libRlapack.so dlamch.o dlapack.o cmplx.o dlartg.o dlassq.o la_constants.o la_xisnan.o zlartg.o zlassq.o -Wl,-soname,libRlapack.so.4 -L"../../../lib" -lRblas -L/usr/local/lib/gcc13/gcc/x86_64-portbld-freebsd14.2/13.3.0 -L/usr/local/x86_64-portbld-freebsd14.2/lib -lgfortran -lm -lssp_nonshared -lquadmath gmake[4]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/modules/lapack' gmake[4]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/modules/lapack' cc -I. -I../../../src/include -I../../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c Lapack.c -o Lapack.o cc -I. -I../../../src/include -I../../../src/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c ../../main/flexiblas.c -o flexiblas.o cc -shared -L"../../../lib" -Wl,-rpath=/usr/local/lib/gcc13 -L/usr/local/lib/gcc13 -L/usr/local/lib -fstack-protector-strong -o lapack.so Lapack.o flexiblas.o -lR -L"../../../lib" -lRlapack -L"../../../lib" -lRblas -L/usr/local/lib/gcc13/gcc/x86_64-portbld-freebsd14.2/13.3.0 -L/usr/local/x86_64-portbld-freebsd14.2/lib -lgfortran -lm -lssp_nonshared -lquadmath gmake[5]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/modules/lapack' /wrkdirs/usr/ports/math/R/work/R-4.4.3/lib/libRlapack.so is unchanged gmake[5]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/modules/lapack' gmake[4]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/modules/lapack' gmake[3]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/modules/lapack' gmake[2]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/modules' gmake[2]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library' mkdir ../../library gmake[3]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/profile' building system startup profile mkdir ../../../library/base mkdir ../../../library/base/R gmake[3]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/profile' gmake[3]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/translations' building package 'translations' mkdir ../../../library/translations gmake[4]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/translations' gmake[4]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/translations' gmake[3]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/translations' gmake[3]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/base' building package 'base' gmake[4]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/base' mkdir ../../../library/base/demo gmake[4]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/base' gmake[3]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/base' gmake[3]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/tools' building package 'tools' mkdir ../../../library/tools gmake[4]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/tools' mkdir ../../../library/tools/R gmake[4]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/tools' gmake[4]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/tools' gmake[5]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/tools/src' making text.d from text.c making init.d from init.c making Rmd5.d from Rmd5.c making md5.d from md5.c making signals.d from signals.c making install.d from install.c making getfmts.d from getfmts.c making http.d from http.c making gramLatex.d from gramLatex.c making gramRd.d from gramRd.c making pdscan.d from pdscan.c cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c text.c -o text.o cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c init.c -o init.o cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c Rmd5.c -o Rmd5.o cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c md5.c -o md5.o cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c signals.c -o signals.o cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c install.c -o install.o cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c getfmts.c -o getfmts.o cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c http.c -o http.o cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c gramLatex.c -o gramLatex.o cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c gramRd.c -o gramRd.o cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c pdscan.c -o pdscan.o cc -shared -L../../../../lib -Wl,-rpath=/usr/local/lib/gcc13 -L/usr/local/lib/gcc13 -L/usr/local/lib -fstack-protector-strong -o tools.so text.o init.o Rmd5.o md5.o signals.o install.o getfmts.o http.o gramLatex.o gramRd.o pdscan.o -L../../../../lib -lR gmake[6]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/tools/src' mkdir ../../../../library/tools/libs gmake[6]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/tools/src' gmake[5]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/tools/src' gmake[4]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/tools' gmake[4]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/tools' installing 'sysdata.rda' gmake[4]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/tools' gmake[3]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/tools' gmake[3]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/compiler' building package 'compiler' mkdir ../../../library/compiler gmake[4]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/compiler' mkdir ../../../library/compiler/R gmake[4]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/compiler' gmake[4]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/compiler' byte-compiling package 'compiler' gmake[4]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/compiler' gmake[3]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/compiler' gmake[3]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/base' byte-compiling package 'base' gmake[3]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/base' gmake[3]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/tools' byte-compiling package 'tools' gmake[3]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/tools' gmake[3]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/utils' building package 'utils' mkdir ../../../library/utils mkdir ../../../library/utils/doc gmake[4]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/utils' mkdir ../../../library/utils/R mkdir ../../../library/utils/Sweave mkdir ../../../library/utils/misc gmake[4]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/utils' gmake[4]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/utils' gmake[5]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/utils/src' making init.d from init.c making io.d from io.c making size.d from size.c making sock.d from sock.c making stubs.d from stubs.c making utils.d from utils.c making hashtab.d from hashtab.c cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c init.c -o init.o cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c io.c -o io.o cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c size.c -o size.o cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c sock.c -o sock.o cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c stubs.c -o stubs.o cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c utils.c -o utils.o cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c hashtab.c -o hashtab.o cc -shared -L../../../../lib -Wl,-rpath=/usr/local/lib/gcc13 -L/usr/local/lib/gcc13 -L/usr/local/lib -fstack-protector-strong -o utils.so init.o io.o size.o sock.o stubs.o utils.o hashtab.o -L../../../../lib -lR gmake[6]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/utils/src' mkdir ../../../../library/utils/libs gmake[6]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/utils/src' gmake[5]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/utils/src' gmake[4]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/utils' gmake[4]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/utils' installing 'sysdata.rda' gmake[4]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/utils' gmake[4]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/utils' byte-compiling package 'utils' gmake[4]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/utils' gmake[3]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/utils' gmake[3]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/grDevices' building package 'grDevices' mkdir ../../../library/grDevices gmake[4]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/grDevices' mkdir ../../../library/grDevices/R mkdir ../../../library/grDevices/afm mkdir ../../../library/grDevices/enc mkdir ../../../library/grDevices/fonts mkdir ../../../library/grDevices/fonts/Roboto mkdir ../../../library/grDevices/fonts/Montserrat mkdir ../../../library/grDevices/fonts/Montserrat/static mkdir ../../../library/grDevices/icc gmake[4]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/grDevices' gmake[4]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/grDevices' gmake[5]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/grDevices/src' making axis_scales.d from axis_scales.c making chull.d from chull.c making devices.d from devices.c making init.d from init.c making stubs.d from stubs.c making colors.d from colors.c making clippath.d from clippath.c making patterns.d from patterns.c making mask.d from mask.c making group.d from group.c making devCairo.d from devCairo.c making devPicTeX.d from devPicTeX.c making devPS.d from devPS.c making devQuartz.d from devQuartz.c cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c axis_scales.c -o axis_scales.o cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c chull.c -o chull.o cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c devices.c -o devices.o cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c init.c -o init.o cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c stubs.c -o stubs.o cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c colors.c -o colors.o cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c clippath.c -o clippath.o cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c patterns.c -o patterns.o cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c mask.c -o mask.o cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c group.c -o group.o cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c devCairo.c -o devCairo.o cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c devPicTeX.c -o devPicTeX.o cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c devPS.c -o devPS.o cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c devQuartz.c -o devQuartz.o cc -shared -L../../../../lib -Wl,-rpath=/usr/local/lib/gcc13 -L/usr/local/lib/gcc13 -L/usr/local/lib -fstack-protector-strong -o grDevices.so axis_scales.o chull.o devices.o init.o stubs.o colors.o clippath.o patterns.o mask.o group.o devCairo.o devPicTeX.o devPS.o devQuartz.o -lz -L../../../../lib -lR gmake[6]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/grDevices/src' gmake[7]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/grDevices/src/cairo' making cairoBM.d from cairoBM.c mkdir ../../../../library/grDevices/libs gmake[8]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/grDevices/src/cairo' gmake[9]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/grDevices/src/cairo' cc -I. -I../../../../../src/include -I../../../../../src/include -I/usr/local/include/pango-1.0 -I/usr/local/include -pthread -I/usr/local/include/fribidi -I/usr/local/include/harfbuzz -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include/cairo -I/usr/local/include/freetype2 -D_THREAD_SAFE -I/usr/local/include/pixman-1 -I/usr/local/include/libpng16 -I../../../../../src/modules/X11 -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DHAVE_CONFIG_H -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c cairoBM.c -o cairoBM.o cc -shared -L"../../../../../lib" -Wl,-rpath=/usr/local/lib/gcc13 -L/usr/local/lib/gcc13 -L/usr/local/lib -fstack-protector-strong -o cairo.so cairoBM.o ../../../../../src/modules/X11/rbitmap.o -L/usr/local/lib -ltiff -L/usr/local/lib -ljpeg -L/usr/local/lib -lpng16 -L/usr/local/lib -lpangocairo-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lintl -lharfbuzz -L/lib -lz -lcairo -lpng16 -L"../../../../../lib" -lR -lm gmake[9]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/grDevices/src/cairo' gmake[8]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/grDevices/src/cairo' gmake[7]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/grDevices/src/cairo' gmake[6]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/grDevices/src' gmake[5]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/grDevices/src' gmake[4]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/grDevices' gmake[4]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/grDevices' byte-compiling package 'grDevices' gmake[4]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/grDevices' gmake[3]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/grDevices' gmake[3]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/graphics' building package 'graphics' mkdir ../../../library/graphics gmake[4]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/graphics' mkdir ../../../library/graphics/R gmake[4]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/graphics' gmake[4]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/graphics' gmake[5]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/graphics/src' making init.d from init.c making base.d from base.c making graphics.d from graphics.c making par.d from par.c making plot.d from plot.c making plot3d.d from plot3d.c cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c init.c -o init.o making stem.d from stem.c cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c base.c -o base.o cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c graphics.c -o graphics.o cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c par.c -o par.o cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c plot.c -o plot.o cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c plot3d.c -o plot3d.o cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c stem.c -o stem.o cc -shared -L../../../../lib -Wl,-rpath=/usr/local/lib/gcc13 -L/usr/local/lib/gcc13 -L/usr/local/lib -fstack-protector-strong -o graphics.so init.o base.o graphics.o par.o plot.o plot3d.o stem.o -L../../../../lib -lR gmake[6]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/graphics/src' mkdir ../../../../library/graphics/libs gmake[6]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/graphics/src' gmake[5]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/graphics/src' gmake[4]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/graphics' gmake[4]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/graphics' byte-compiling package 'graphics' gmake[4]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/graphics' gmake[3]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/graphics' gmake[3]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/stats' building package 'stats' mkdir ../../../library/stats gmake[4]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/stats' mkdir ../../../library/stats/R gmake[4]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/stats' gmake[4]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/stats' gmake[5]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/stats/src' making init.d from init.c making kmeans.d from kmeans.c making ansari.d from ansari.c making chisqsim.d from chisqsim.c making d2x2xk.d from d2x2xk.c making fexact.d from fexact.c making kendall.d from kendall.c making bandwidths.d from bandwidths.c making line.d from line.c making ks.d from ks.c making smooth.d from smooth.c making prho.d from prho.c making swilk.d from swilk.c making loessc.d from loessc.c making monoSpl.d from monoSpl.c making ksmooth.d from ksmooth.c making isoreg.d from isoreg.c making Srunmed.d from Srunmed.c making dblcen.d from dblcen.c making distance.d from distance.c making hclust-utils.d from hclust-utils.c making nls.d from nls.c making rWishart.d from rWishart.c making HoltWinters.d from HoltWinters.c making PPsum.d from PPsum.c making arima.d from arima.c making burg.d from burg.c making filter.d from filter.c making mAR.d from mAR.c making starma.d from starma.c making pacf.d from pacf.c making port.d from port.c making family.d from family.c making sbart.d from sbart.c making approx.d from approx.c making lowess.d from lowess.c making massdist.d from massdist.c making loglin.d from loglin.c making splines.d from splines.c making lm.d from lm.c making complete_cases.d from complete_cases.c making cov.d from cov.c making deriv.d from deriv.c making fft.d from fft.c making model.d from model.c making fourier.d from fourier.c making optim.d from optim.c making optimize.d from optimize.c making integrate.d from integrate.c making random.d from random.c making distn.d from distn.c making zeroin.d from zeroin.c making rcont.d from rcont.c making influence.d from influence.c cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c init.c -o init.o cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c kmeans.c -o kmeans.o cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c ansari.c -o ansari.o cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c bandwidths.c -o bandwidths.o cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c chisqsim.c -o chisqsim.o cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c d2x2xk.c -o d2x2xk.o cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c fexact.c -o fexact.o cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c kendall.c -o kendall.o cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c ks.c -o ks.o cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c line.c -o line.o cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c smooth.c -o smooth.o cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c prho.c -o prho.o cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c swilk.c -o swilk.o cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c ksmooth.c -o ksmooth.o cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c loessc.c -o loessc.o cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c monoSpl.c -o monoSpl.o cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c isoreg.c -o isoreg.o cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c Srunmed.c -o Srunmed.o cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c dblcen.c -o dblcen.o cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c distance.c -o distance.o cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c hclust-utils.c -o hclust-utils.o cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c nls.c -o nls.o cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c rWishart.c -o rWishart.o cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c HoltWinters.c -o HoltWinters.o cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c PPsum.c -o PPsum.o cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c arima.c -o arima.o cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c burg.c -o burg.o cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c filter.c -o filter.o cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c mAR.c -o mAR.o cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c pacf.c -o pacf.o cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c starma.c -o starma.o cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c port.c -o port.o cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c family.c -o family.o cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c sbart.c -o sbart.o cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c approx.c -o approx.o cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c loglin.c -o loglin.o cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c lowess.c -o lowess.o cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c massdist.c -o massdist.o cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c splines.c -o splines.o cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c lm.c -o lm.o cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c complete_cases.c -o complete_cases.o cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c cov.c -o cov.o cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c deriv.c -o deriv.o cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c fft.c -o fft.o cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c fourier.c -o fourier.o cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c model.c -o model.o cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c optim.c -o optim.o cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c optimize.c -o optimize.o cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c integrate.c -o integrate.o cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c random.c -o random.o cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c distn.c -o distn.o cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c zeroin.c -o zeroin.o cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c rcont.c -o rcont.o cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c influence.c -o influence.o gfortran13 -fvisibility=hidden -fpic -O -Wl,-rpath=/usr/local/lib/gcc13 -c bsplvd.f -o bsplvd.o gfortran13 -fvisibility=hidden -fpic -O -Wl,-rpath=/usr/local/lib/gcc13 -c bvalue.f -o bvalue.o gfortran13 -fvisibility=hidden -fpic -O -Wl,-rpath=/usr/local/lib/gcc13 -c bvalus.f -o bvalus.o gfortran13 -fvisibility=hidden -fpic -O -Wl,-rpath=/usr/local/lib/gcc13 -c loessf.f -o loessf.o gfortran13 -fvisibility=hidden -fpic -O -Wl,-rpath=/usr/local/lib/gcc13 -c ppr.f -o ppr.o gfortran13 -fvisibility=hidden -fpic -O -Wl,-rpath=/usr/local/lib/gcc13 -c qsbart.f -o qsbart.o gfortran13 -fvisibility=hidden -fpic -O -Wl,-rpath=/usr/local/lib/gcc13 -c sgram.f -o sgram.o gfortran13 -fvisibility=hidden -fpic -O -Wl,-rpath=/usr/local/lib/gcc13 -c sinerp.f -o sinerp.o gfortran13 -fvisibility=hidden -fpic -O -Wl,-rpath=/usr/local/lib/gcc13 -c sslvrg.f -o sslvrg.o gfortran13 -fvisibility=hidden -fpic -O -Wl,-rpath=/usr/local/lib/gcc13 -c stxwx.f -o stxwx.o gfortran13 -fvisibility=hidden -fpic -O -Wl,-rpath=/usr/local/lib/gcc13 -c hclust.f -o hclust.o gfortran13 -fvisibility=hidden -fpic -O -Wl,-rpath=/usr/local/lib/gcc13 -c kmns.f -o kmns.o gfortran13 -fvisibility=hidden -fpic -O -Wl,-rpath=/usr/local/lib/gcc13 -c eureka.f -o eureka.o gfortran13 -fvisibility=hidden -fpic -O -Wl,-rpath=/usr/local/lib/gcc13 -c stl.f -o stl.o gfortran13 -fpic -O -Wl,-rpath=/usr/local/lib/gcc13 -c portsrc.f -o portsrc.o gfortran13 -fvisibility=hidden -fpic -O -Wl,-rpath=/usr/local/lib/gcc13 -c lminfl.f -o lminfl.o cc -shared -L../../../../lib -Wl,-rpath=/usr/local/lib/gcc13 -L/usr/local/lib/gcc13 -L/usr/local/lib -fstack-protector-strong -o stats.so init.o kmeans.o ansari.o bandwidths.o chisqsim.o d2x2xk.o fexact.o kendall.o ks.o line.o smooth.o prho.o swilk.o ksmooth.o loessc.o monoSpl.o isoreg.o Srunmed.o dblcen.o distance.o hclust-utils.o nls.o rWishart.o HoltWinters.o PPsum.o arima.o burg.o filter.o mAR.o pacf.o starma.o port.o family.o sbart.o approx.o loglin.o lowess.o massdist.o splines.o lm.o complete_cases.o cov.o deriv.o fft.o fourier.o model.o optim.o optimize.o integrate.o random.o distn.o zeroin.o rcont.o influence.o bsplvd.o bvalue.o bvalus.o loessf.o ppr.o qsbart.o sgram.o sinerp.o sslvrg.o stxwx.o hclust.o kmns.o eureka.o stl.o portsrc.o lminfl.o -fopenmp -L../../../../lib -lRlapack -L../../../../lib -lRblas -L/usr/local/lib/gcc13/gcc/x86_64-portbld-freebsd14.2/13.3.0 -L/usr/local/x86_64-portbld-freebsd14.2/lib -lgfortran -lm -lssp_nonshared -lquadmath -L../../../../lib -lR gmake[6]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/stats/src' mkdir ../../../../library/stats/libs gmake[6]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/stats/src' gmake[5]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/stats/src' gmake[4]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/stats' gmake[4]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/stats' byte-compiling package 'stats' gmake[4]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/stats' gmake[3]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/stats' gmake[3]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/datasets' building package 'datasets' mkdir ../../../library/datasets gmake[4]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/datasets' gmake[4]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/datasets' mkdir ../../../library/datasets/data gmake[3]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/datasets' gmake[3]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/methods' building package 'methods' mkdir ../../../library/methods gmake[4]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/methods' mkdir ../../../library/methods/R gmake[4]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/methods' gmake[4]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/methods' gmake[5]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/methods/src' making do_substitute_direct.d from do_substitute_direct.c making init.d from init.c making slot.d from slot.c making methods_list_dispatch.d from methods_list_dispatch.c making class_support.d from class_support.c cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c do_substitute_direct.c -o do_substitute_direct.o cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c init.c -o init.o making utils.d from utils.c making tests.d from tests.c cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c methods_list_dispatch.c -o methods_list_dispatch.o cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c slot.c -o slot.o cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c class_support.c -o class_support.o cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c tests.c -o tests.o cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c utils.c -o utils.o cc -shared -L../../../../lib -Wl,-rpath=/usr/local/lib/gcc13 -L/usr/local/lib/gcc13 -L/usr/local/lib -fstack-protector-strong -o methods.so do_substitute_direct.o init.o methods_list_dispatch.o slot.o class_support.o tests.o utils.o -L../../../../lib -lR gmake[6]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/methods/src' mkdir ../../../../library/methods/libs gmake[6]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/methods/src' gmake[5]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/methods/src' gmake[4]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/methods' gmake[4]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/methods' byte-compiling package 'methods' initializing class and method definitions ... done gmake[4]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/methods' gmake[3]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/methods' gmake[3]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/grid' building package 'grid' mkdir ../../../library/grid mkdir ../../../library/grid/doc gmake[4]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/grid' mkdir ../../../library/grid/R gmake[4]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/grid' gmake[4]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/grid' gmake[5]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/grid/src' making clippath.d from clippath.c making gpar.d from gpar.c making grid.d from grid.c making just.d from just.c making layout.d from layout.c making mask.d from mask.c making matrix.d from matrix.c making path.d from path.c making register.d from register.c making state.d from state.c making typeset.d from typeset.c making unit.d from unit.c making util.d from util.c making viewport.d from viewport.c cc -I"../../../../include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c clippath.c -o clippath.o cc -I"../../../../include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c gpar.c -o gpar.o cc -I"../../../../include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c grid.c -o grid.o cc -I"../../../../include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c just.c -o just.o cc -I"../../../../include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c layout.c -o layout.o cc -I"../../../../include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c mask.c -o mask.o cc -I"../../../../include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c matrix.c -o matrix.o cc -I"../../../../include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c path.c -o path.o cc -I"../../../../include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c register.c -o register.o cc -I"../../../../include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c state.c -o state.o cc -I"../../../../include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c typeset.c -o typeset.o cc -I"../../../../include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c unit.c -o unit.o cc -I"../../../../include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c util.c -o util.o cc -I"../../../../include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c viewport.c -o viewport.o cc -shared -L../../../../lib -Wl,-rpath=/usr/local/lib/gcc13 -L/usr/local/lib/gcc13 -L/usr/local/lib -fstack-protector-strong -o grid.so clippath.o gpar.o grid.o just.o layout.o mask.o matrix.o path.o register.o state.o typeset.o unit.o util.o viewport.o -L../../../../lib -lR gmake[6]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/grid/src' mkdir ../../../../library/grid/libs gmake[6]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/grid/src' gmake[5]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/grid/src' gmake[4]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/grid' gmake[4]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/grid' byte-compiling package 'grid' gmake[4]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/grid' gmake[3]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/grid' gmake[3]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/splines' building package 'splines' mkdir ../../../library/splines gmake[4]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/splines' mkdir ../../../library/splines/R gmake[4]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/splines' gmake[4]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/splines' gmake[5]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/splines/src' cc -I"../../../../include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c splines.c -o splines.o making splines.d from splines.c cc -shared -L../../../../lib -Wl,-rpath=/usr/local/lib/gcc13 -L/usr/local/lib/gcc13 -L/usr/local/lib -fstack-protector-strong -o splines.so splines.o -L../../../../lib -lR gmake[6]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/splines/src' mkdir ../../../../library/splines/libs gmake[6]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/splines/src' gmake[5]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/splines/src' gmake[4]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/splines' gmake[4]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/splines' byte-compiling package 'splines' gmake[4]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/splines' gmake[3]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/splines' gmake[3]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/stats4' building package 'stats4' mkdir ../../../library/stats4 gmake[4]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/stats4' mkdir ../../../library/stats4/R gmake[4]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/stats4' gmake[4]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/stats4' byte-compiling package 'stats4' gmake[4]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/stats4' gmake[3]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/stats4' gmake[3]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/tcltk' building package 'tcltk' mkdir ../../../library/tcltk mkdir ../../../library/tcltk/R gmake[4]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/tcltk' mkdir ../../../library/tcltk/exec gmake[4]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/tcltk' gmake[4]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/tcltk/src' making init.d from init.c making tcltk.d from tcltk.c cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include/tcl8.6 -I/usr/local/include/tk8.6 -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c init.c -o init.o making tcltk_unix.d from tcltk_unix.c cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include/tcl8.6 -I/usr/local/include/tk8.6 -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c tcltk.c -o tcltk.o cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include/tcl8.6 -I/usr/local/include/tk8.6 -I/usr/local/include -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c tcltk_unix.c -o tcltk_unix.o cc -shared -L../../../../lib -Wl,-rpath=/usr/local/lib/gcc13 -L/usr/local/lib/gcc13 -L/usr/local/lib -fstack-protector-strong -o tcltk.so init.o tcltk.o tcltk_unix.o -L/usr/local/lib -ltcl86 -L/usr/local/lib -ltk86 -L/usr/local/lib -lX11 -lXss -lXext -lm -L../../../../lib -lR gmake[5]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/tcltk/src' mkdir ../../../../library/tcltk/libs gmake[5]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/tcltk/src' gmake[4]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/tcltk/src' gmake[4]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/tcltk' byte-compiling package 'tcltk' gmake[4]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/tcltk' gmake[3]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/tcltk' gmake[3]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/parallel' building package 'parallel' mkdir ../../../library/parallel mkdir ../../../library/parallel/doc gmake[4]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/parallel' mkdir ../../../library/parallel/R gmake[4]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/parallel' gmake[4]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/parallel' gmake[5]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/parallel/src' making init.d from init.c making rngstream.d from rngstream.c cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c init.c -o init.o making fork.d from fork.c cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c rngstream.c -o rngstream.o cc -I"../../../../include" -DNDEBUG -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c fork.c -o fork.o cc -shared -L../../../../lib -Wl,-rpath=/usr/local/lib/gcc13 -L/usr/local/lib/gcc13 -L/usr/local/lib -fstack-protector-strong -o parallel.so init.o rngstream.o fork.o -L../../../../lib -lR gmake[6]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/parallel/src' mkdir ../../../../library/parallel/libs gmake[6]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/parallel/src' gmake[5]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/parallel/src' gmake[4]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/parallel' gmake[4]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/parallel' byte-compiling package 'parallel' gmake[4]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/parallel' gmake[3]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/parallel' gmake[3]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/base' gmake[3]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/base' installing parsed NAMESPACE files gmake[2]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library' gmake[1]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src' gmake[1]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/tests' gmake[1]: Nothing to be done for 'R'. gmake[1]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/tests' you should 'make docs' now ... gmake[1]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3' gmake[1]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc' gmake[1]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3' gmake[1]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library' building/updating vignettes for package 'grid' ... creating doc/NEWS creating doc/NEWS.pdf building/updating vignettes for package 'parallel' ... building/updating vignettes for package 'utils' ... building/updating vignettes for package 'stats' ... processing 'reshape.Rnw' gmake[2]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual' creating doc/manual/R-FAQ.html creating doc/manual/version.texi creating doc/manual/R-admin.html creating doc/manual/R-data.html creating doc/manual/R-exts.html creating doc/manual/R-intro.html creating doc/manual/R-ints.html creating doc/manual/R-lang.html gmake[1]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library' gmake[3]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/html' gmake[3]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/html' gmake[2]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual' gmake[1]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc' gmake[1]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library' gmake[2]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library' installing parsed Rd gmake[3]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library' graphics grDevices methods datasets utils splines tools tcltk grid stats4 parallel compiler base stats gmake[3]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library' gmake[2]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library' gmake[2]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library' building/updating package metadata ... gmake[2]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library' gmake[2]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library' writing package indices gmake[3]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library' gmake[3]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library' gmake[2]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library' gmake[1]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library' gmake[1]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/Recommended' gmake[2]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/Recommended' begin installing recommended package lattice begin installing recommended package MASS begin installing recommended package codetools begin installing recommended package foreign begin installing recommended package KernSmooth begin installing recommended package rpart * installing *source* package ‘codetools’ ... ** package ‘codetools’ successfully unpacked and MD5 sums checked ** using non-staged installation ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (codetools) begin installing recommended package nnet * installing *source* package ‘KernSmooth’ ... ** package ‘KernSmooth’ successfully unpacked and MD5 sums checked ** using non-staged installation ** libs using C compiler: ‘FreeBSD clang version 18.1.6 (https://github.com/llvm/llvm-project.git llvmorg-18.1.6-0-g1118c2e05e67)’ using Fortran compiler: ‘GNU Fortran (FreeBSD Ports Collection) 13.3.0’ gmake[3]: Entering directory '/tmp/RtmpP2HZWO/R.INSTALL16f435aa2ac3/KernSmooth/src' gfortran13 -fpic -O -Wl,-rpath=/usr/local/lib/gcc13 -c blkest.f -o blkest.o gfortran13 -fpic -O -Wl,-rpath=/usr/local/lib/gcc13 -c cp.f -o cp.o gfortran13 -fpic -O -Wl,-rpath=/usr/local/lib/gcc13 -c dgedi.f -o dgedi.o gfortran13 -fpic -O -Wl,-rpath=/usr/local/lib/gcc13 -c dgefa.f -o dgefa.o gfortran13 -fpic -O -Wl,-rpath=/usr/local/lib/gcc13 -c dgesl.f -o dgesl.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c init.c -o init.o gfortran13 -fpic -O -Wl,-rpath=/usr/local/lib/gcc13 -c linbin.f -o linbin.o gfortran13 -fpic -O -Wl,-rpath=/usr/local/lib/gcc13 -c linbin2D.f -o linbin2D.o gfortran13 -fpic -O -Wl,-rpath=/usr/local/lib/gcc13 -c locpoly.f -o locpoly.o gfortran13 -fpic -O -Wl,-rpath=/usr/local/lib/gcc13 -c rlbin.f -o rlbin.o gfortran13 -fpic -O -Wl,-rpath=/usr/local/lib/gcc13 -c sdiag.f -o sdiag.o gfortran13 -fpic -O -Wl,-rpath=/usr/local/lib/gcc13 -c sstdiag.f -o sstdiag.o cc -shared -L/wrkdirs/usr/ports/math/R/work/R-4.4.3/lib -Wl,-rpath=/usr/local/lib/gcc13 -L/usr/local/lib/gcc13 -L/usr/local/lib -fstack-protector-strong -o KernSmooth.so blkest.o cp.o dgedi.o dgefa.o dgesl.o init.o linbin.o linbin2D.o locpoly.o rlbin.o sdiag.o sstdiag.o -L/wrkdirs/usr/ports/math/R/work/R-4.4.3/lib -lRblas -L/usr/local/lib/gcc13/gcc/x86_64-portbld-freebsd14.2/13.3.0 -L/usr/local/x86_64-portbld-freebsd14.2/lib -lgfortran -lm -lssp_nonshared -lquadmath -L/wrkdirs/usr/ports/math/R/work/R-4.4.3/lib -lR gmake[3]: Leaving directory '/tmp/RtmpP2HZWO/R.INSTALL16f435aa2ac3/KernSmooth/src' installing to /wrkdirs/usr/ports/math/R/work/R-4.4.3/library/KernSmooth/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (KernSmooth) begin installing recommended package spatial * installing *source* package ‘nnet’ ... ** package ‘nnet’ successfully unpacked and MD5 sums checked ** using non-staged installation ** libs using C compiler: ‘FreeBSD clang version 18.1.6 (https://github.com/llvm/llvm-project.git llvmorg-18.1.6-0-g1118c2e05e67)’ gmake[3]: Entering directory '/tmp/RtmpANqZ5Z/R.INSTALL1705566845836/nnet/src' cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c nnet.c -o nnet.o cc -shared -L/wrkdirs/usr/ports/math/R/work/R-4.4.3/lib -Wl,-rpath=/usr/local/lib/gcc13 -L/usr/local/lib/gcc13 -L/usr/local/lib -fstack-protector-strong -o nnet.so nnet.o -L/wrkdirs/usr/ports/math/R/work/R-4.4.3/lib -lR gmake[3]: Leaving directory '/tmp/RtmpANqZ5Z/R.INSTALL1705566845836/nnet/src' installing to /wrkdirs/usr/ports/math/R/work/R-4.4.3/library/nnet/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (nnet) * installing *source* package ‘foreign’ ... ** package ‘foreign’ successfully unpacked and MD5 sums checked ** using non-staged installation ** libs using C compiler: ‘FreeBSD clang version 18.1.6 (https://github.com/llvm/llvm-project.git llvmorg-18.1.6-0-g1118c2e05e67)’ gmake[3]: Entering directory '/tmp/RtmptAU9q7/R.INSTALL16f367238e/foreign/src' cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c R_systat.c -o R_systat.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c Rdbfread.c -o Rdbfread.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c Rdbfwrite.c -o Rdbfwrite.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c SASxport.c -o SASxport.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c avl.c -o avl.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c dbfopen.c -o dbfopen.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c file-handle.c -o file-handle.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c format.c -o format.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c init.c -o init.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c minitab.c -o minitab.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c pfm-read.c -o pfm-read.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c sfm-read.c -o sfm-read.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c spss.c -o spss.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c stataread.c -o stataread.o cc -shared -L/wrkdirs/usr/ports/math/R/work/R-4.4.3/lib -Wl,-rpath=/usr/local/lib/gcc13 -L/usr/local/lib/gcc13 -L/usr/local/lib -fstack-protector-strong -o foreign.so R_systat.o Rdbfread.o Rdbfwrite.o SASxport.o avl.o dbfopen.o file-handle.o format.o init.o minitab.o pfm-read.o sfm-read.o spss.o stataread.o -L/wrkdirs/usr/ports/math/R/work/R-4.4.3/lib -lR gmake[3]: Leaving directory '/tmp/RtmptAU9q7/R.INSTALL16f367238e/foreign/src' installing to /wrkdirs/usr/ports/math/R/work/R-4.4.3/library/foreign/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (foreign) * installing *source* package ‘spatial’ ... ** package ‘spatial’ successfully unpacked and MD5 sums checked ** using non-staged installation ** libs using C compiler: ‘FreeBSD clang version 18.1.6 (https://github.com/llvm/llvm-project.git llvmorg-18.1.6-0-g1118c2e05e67)’ gmake[3]: Entering directory '/tmp/RtmpzkF04y/R.INSTALL1712845a97d87/spatial/src' cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c init.c -o init.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c krc.c -o krc.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c pps.c -o pps.o cc -shared -L/wrkdirs/usr/ports/math/R/work/R-4.4.3/lib -Wl,-rpath=/usr/local/lib/gcc13 -L/usr/local/lib/gcc13 -L/usr/local/lib -fstack-protector-strong -o spatial.so init.o krc.o pps.o -L/wrkdirs/usr/ports/math/R/work/R-4.4.3/lib -lR gmake[3]: Leaving directory '/tmp/RtmpzkF04y/R.INSTALL1712845a97d87/spatial/src' installing to /wrkdirs/usr/ports/math/R/work/R-4.4.3/library/spatial/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (spatial) * installing *source* package ‘rpart’ ... ** package ‘rpart’ successfully unpacked and MD5 sums checked ** using non-staged installation ** libs using C compiler: ‘FreeBSD clang version 18.1.6 (https://github.com/llvm/llvm-project.git llvmorg-18.1.6-0-g1118c2e05e67)’ gmake[3]: Entering directory '/tmp/RtmpSI5tdR/R.INSTALL16f55af79849/rpart/src' cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c anova.c -o anova.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c anovapred.c -o anovapred.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c branch.c -o branch.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c bsplit.c -o bsplit.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c choose_surg.c -o choose_surg.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c fix_cp.c -o fix_cp.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c free_tree.c -o free_tree.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c gini.c -o gini.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c graycode.c -o graycode.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c init.c -o init.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c insert_split.c -o insert_split.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c make_cp_list.c -o make_cp_list.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c make_cp_table.c -o make_cp_table.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c mysort.c -o mysort.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c nodesplit.c -o nodesplit.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c partition.c -o partition.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c poisson.c -o poisson.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c pred_rpart.c -o pred_rpart.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c print_tree.c -o print_tree.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c rpart.c -o rpart.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c rpart_callback.c -o rpart_callback.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c rpartexp.c -o rpartexp.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c rpartexp2.c -o rpartexp2.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c rpcountup.c -o rpcountup.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c rpmatrix.c -o rpmatrix.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c rundown.c -o rundown.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c rundown2.c -o rundown2.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c surrogate.c -o surrogate.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c usersplit.c -o usersplit.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c xpred.c -o xpred.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c xval.c -o xval.o cc -shared -L/wrkdirs/usr/ports/math/R/work/R-4.4.3/lib -Wl,-rpath=/usr/local/lib/gcc13 -L/usr/local/lib/gcc13 -L/usr/local/lib -fstack-protector-strong -o rpart.so anova.o anovapred.o branch.o bsplit.o choose_surg.o fix_cp.o free_tree.o gini.o graycode.o init.o insert_split.o make_cp_list.o make_cp_table.o mysort.o nodesplit.o partition.o poisson.o pred_rpart.o print_tree.o rpart.o rpart_callback.o rpartexp.o rpartexp2.o rpcountup.o rpmatrix.o rundown.o rundown2.o surrogate.o usersplit.o xpred.o xval.o -L/wrkdirs/usr/ports/math/R/work/R-4.4.3/lib -lR gmake[3]: Leaving directory '/tmp/RtmpSI5tdR/R.INSTALL16f55af79849/rpart/src' installing to /wrkdirs/usr/ports/math/R/work/R-4.4.3/library/rpart/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (rpart) * installing *source* package ‘MASS’ ... ** package ‘MASS’ successfully unpacked and MD5 sums checked ** using non-staged installation ** libs using C compiler: ‘FreeBSD clang version 18.1.6 (https://github.com/llvm/llvm-project.git llvmorg-18.1.6-0-g1118c2e05e67)’ gmake[3]: Entering directory '/tmp/Rtmp0M5nSn/R.INSTALL16f224ba47ae3/MASS/src' cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c MASS.c -o MASS.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c lqs.c -o lqs.o cc -shared -L/wrkdirs/usr/ports/math/R/work/R-4.4.3/lib -Wl,-rpath=/usr/local/lib/gcc13 -L/usr/local/lib/gcc13 -L/usr/local/lib -fstack-protector-strong -o MASS.so MASS.o lqs.o -L/wrkdirs/usr/ports/math/R/work/R-4.4.3/lib -lR gmake[3]: Leaving directory '/tmp/Rtmp0M5nSn/R.INSTALL16f224ba47ae3/MASS/src' installing to /wrkdirs/usr/ports/math/R/work/R-4.4.3/library/MASS/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (MASS) begin installing recommended package cluster begin installing recommended package class * installing *source* package ‘class’ ... ** package ‘class’ successfully unpacked and MD5 sums checked ** using non-staged installation ** libs using C compiler: ‘FreeBSD clang version 18.1.6 (https://github.com/llvm/llvm-project.git llvmorg-18.1.6-0-g1118c2e05e67)’ gmake[3]: Entering directory '/tmp/RtmptlfiCg/R.INSTALL1728e317cfc01/class/src' cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c class.c -o class.o cc -shared -L/wrkdirs/usr/ports/math/R/work/R-4.4.3/lib -Wl,-rpath=/usr/local/lib/gcc13 -L/usr/local/lib/gcc13 -L/usr/local/lib -fstack-protector-strong -o class.so class.o -L/wrkdirs/usr/ports/math/R/work/R-4.4.3/lib -lR gmake[3]: Leaving directory '/tmp/RtmptlfiCg/R.INSTALL1728e317cfc01/class/src' installing to /wrkdirs/usr/ports/math/R/work/R-4.4.3/library/class/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (class) * installing *source* package ‘lattice’ ... ** package ‘lattice’ successfully unpacked and MD5 sums checked ** using non-staged installation ** libs using C compiler: ‘FreeBSD clang version 18.1.6 (https://github.com/llvm/llvm-project.git llvmorg-18.1.6-0-g1118c2e05e67)’ gmake[3]: Entering directory '/tmp/RtmpaXr9wX/R.INSTALL16f1f5d1845fb/lattice/src' cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c init.c -o init.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c threeDplot.c -o threeDplot.o cc -shared -L/wrkdirs/usr/ports/math/R/work/R-4.4.3/lib -Wl,-rpath=/usr/local/lib/gcc13 -L/usr/local/lib/gcc13 -L/usr/local/lib -fstack-protector-strong -o lattice.so init.o threeDplot.o -L/wrkdirs/usr/ports/math/R/work/R-4.4.3/lib -lR gmake[3]: Leaving directory '/tmp/RtmpaXr9wX/R.INSTALL16f1f5d1845fb/lattice/src' installing to /wrkdirs/usr/ports/math/R/work/R-4.4.3/library/lattice/libs ** R ** data *** moving datasets to lazyload DB ** demo ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (lattice) begin installing recommended package nlme begin installing recommended package Matrix * installing *source* package ‘cluster’ ... ** package ‘cluster’ successfully unpacked and MD5 sums checked ** using non-staged installation ** libs using C compiler: ‘FreeBSD clang version 18.1.6 (https://github.com/llvm/llvm-project.git llvmorg-18.1.6-0-g1118c2e05e67)’ gmake[3]: Entering directory '/tmp/RtmpYqUBoF/R.INSTALL1728c57fb903e/cluster/src' cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c clara.c -o clara.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c daisy.c -o daisy.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c dysta.c -o dysta.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c fanny.c -o fanny.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c init.c -o init.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c mona.c -o mona.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c pam.c -o pam.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c sildist.c -o sildist.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c spannel.c -o spannel.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c twins.c -o twins.o cc -shared -L/wrkdirs/usr/ports/math/R/work/R-4.4.3/lib -Wl,-rpath=/usr/local/lib/gcc13 -L/usr/local/lib/gcc13 -L/usr/local/lib -fstack-protector-strong -o cluster.so clara.o daisy.o dysta.o fanny.o init.o mona.o pam.o sildist.o spannel.o twins.o -L/wrkdirs/usr/ports/math/R/work/R-4.4.3/lib -lR gmake[3]: Leaving directory '/tmp/RtmpYqUBoF/R.INSTALL1728c57fb903e/cluster/src' installing to /wrkdirs/usr/ports/math/R/work/R-4.4.3/library/cluster/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (cluster) * installing *source* package ‘nlme’ ... ** package ‘nlme’ successfully unpacked and MD5 sums checked ** using non-staged installation ** libs using C compiler: ‘FreeBSD clang version 18.1.6 (https://github.com/llvm/llvm-project.git llvmorg-18.1.6-0-g1118c2e05e67)’ using Fortran compiler: ‘GNU Fortran (FreeBSD Ports Collection) 13.3.0’ gmake[3]: Entering directory '/tmp/RtmplHVdBU/R.INSTALL173754260869a/nlme/src' gfortran13 -fpic -O -Wl,-rpath=/usr/local/lib/gcc13 -c chol.f -o chol.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c corStruct.c -o corStruct.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c gnls.c -o gnls.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c init.c -o init.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c matrix.c -o matrix.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c nlOptimizer.c -o nlOptimizer.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c nlme.c -o nlme.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c nlmefit.c -o nlmefit.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c pdMat.c -o pdMat.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c pythag.c -o pythag.o gfortran13 -fpic -O -Wl,-rpath=/usr/local/lib/gcc13 -c rs.f -o rs.o cc -shared -L/wrkdirs/usr/ports/math/R/work/R-4.4.3/lib -Wl,-rpath=/usr/local/lib/gcc13 -L/usr/local/lib/gcc13 -L/usr/local/lib -fstack-protector-strong -o nlme.so chol.o corStruct.o gnls.o init.o matrix.o nlOptimizer.o nlme.o nlmefit.o pdMat.o pythag.o rs.o -L/usr/local/lib/gcc13/gcc/x86_64-portbld-freebsd14.2/13.3.0 -L/usr/local/x86_64-portbld-freebsd14.2/lib -lgfortran -lm -lssp_nonshared -lquadmath -L/wrkdirs/usr/ports/math/R/work/R-4.4.3/lib -lR gmake[3]: Leaving directory '/tmp/RtmplHVdBU/R.INSTALL173754260869a/nlme/src' installing to /wrkdirs/usr/ports/math/R/work/R-4.4.3/library/nlme/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (nlme) * installing *source* package ‘Matrix’ ... ** package ‘Matrix’ successfully unpacked and MD5 sums checked ** using non-staged installation ** libs using C compiler: ‘FreeBSD clang version 18.1.6 (https://github.com/llvm/llvm-project.git llvmorg-18.1.6-0-g1118c2e05e67)’ gmake[3]: Entering directory '/tmp/RtmpET1FvR/R.INSTALL1737b42b56282/Matrix/src' cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -I"SuiteSparse/SuiteSparse_config" -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c Csparse.c -o Csparse.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -I"SuiteSparse/SuiteSparse_config" -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c attrib.c -o attrib.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -I"SuiteSparse/SuiteSparse_config" -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c bind.c -o bind.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -I"SuiteSparse/SuiteSparse_config" -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c cholmod-common.c -o cholmod-common.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -I"SuiteSparse/SuiteSparse_config" -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c cholmod-etc.c -o cholmod-etc.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -I"SuiteSparse/SuiteSparse_config" -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c coerce.c -o coerce.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -I"SuiteSparse/SuiteSparse_config" -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c cs-etc.c -o cs-etc.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -I"SuiteSparse/SuiteSparse_config" -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c dense.c -o dense.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -I"SuiteSparse/SuiteSparse_config" -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c determinant.c -o determinant.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -I"SuiteSparse/SuiteSparse_config" -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c expm.c -o expm.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -I"SuiteSparse/SuiteSparse_config" -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c factor.c -o factor.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -I"SuiteSparse/SuiteSparse_config" -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c idz.c -o idz.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -I"SuiteSparse/SuiteSparse_config" -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c init.c -o init.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -I"SuiteSparse/SuiteSparse_config" -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c kappa.c -o kappa.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -I"SuiteSparse/SuiteSparse_config" -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c matmult.c -o matmult.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -I"SuiteSparse/SuiteSparse_config" -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c objects.c -o objects.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -I"SuiteSparse/SuiteSparse_config" -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c perm.c -o perm.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -I"SuiteSparse/SuiteSparse_config" -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c solve.c -o solve.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -I"SuiteSparse/SuiteSparse_config" -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c sparse.c -o sparse.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -I"SuiteSparse/SuiteSparse_config" -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c subassign.c -o subassign.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -I"SuiteSparse/SuiteSparse_config" -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c subscript.c -o subscript.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -I"SuiteSparse/SuiteSparse_config" -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c utils-R.c -o utils-R.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -I"SuiteSparse/SuiteSparse_config" -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c utils.c -o utils.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -I"SuiteSparse/SuiteSparse_config" -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c validity.c -o validity.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -I"SuiteSparse/SuiteSparse_config" -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fvisibility=hidden -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c vector.c -o vector.o cd SuiteSparse/CHOLMOD && /usr/local/bin/gmake clean all CC="cc" CPPFLAGS="-DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I\"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include\" -I\"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include\" -DNDEBUG -DNPRINT -DNTIMER" CFLAGS="-O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden" AR="/usr/local/bin/ar" RANLIB="/usr/local/bin/ranlib" gmake[4]: Entering directory '/tmp/RtmpET1FvR/R.INSTALL1737b42b56282/Matrix/src/SuiteSparse/CHOLMOD' cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Check/cholmod_check.c -o Check/cholmod_check.o cd SuiteSparse/CCOLAMD && /usr/local/bin/gmake clean all CC="cc" CPPFLAGS="-DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I\"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include\" -I\"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include\" -DNDEBUG -DNPRINT -DNTIMER" CFLAGS="-O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden" AR="/usr/local/bin/ar" RANLIB="/usr/local/bin/ranlib" gmake[4]: Entering directory '/tmp/RtmpET1FvR/R.INSTALL1737b42b56282/Matrix/src/SuiteSparse/CCOLAMD' cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/ccolamd.c -o Source/ccolamd.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Check/cholmod_l_check.c -o Check/cholmod_l_check.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/ccolamd_l.c -o Source/ccolamd_l.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/ccolamd_version.c -o Source/ccolamd_version.o rm -f CCOLAMD.a /usr/local/bin/ar -cr CCOLAMD.a Source/ccolamd.o Source/ccolamd_l.o Source/ccolamd_version.o /usr/local/bin/ranlib CCOLAMD.a gmake[4]: Leaving directory '/tmp/RtmpET1FvR/R.INSTALL1737b42b56282/Matrix/src/SuiteSparse/CCOLAMD' cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Check/cholmod_read.c -o Check/cholmod_read.o cd SuiteSparse/CAMD && /usr/local/bin/gmake clean all CC="cc" CPPFLAGS="-DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I\"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include\" -I\"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include\" -DNDEBUG -DNPRINT -DNTIMER" CFLAGS="-O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden" AR="/usr/local/bin/ar" RANLIB="/usr/local/bin/ranlib" gmake[4]: Entering directory '/tmp/RtmpET1FvR/R.INSTALL1737b42b56282/Matrix/src/SuiteSparse/CAMD' cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/camd_1.c -o Source/camd_1.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Check/cholmod_l_read.c -o Check/cholmod_l_read.o cd SuiteSparse/COLAMD && /usr/local/bin/gmake clean all CC="cc" CPPFLAGS="-DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I\"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include\" -I\"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include\" -DNDEBUG -DNPRINT -DNTIMER" CFLAGS="-O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden" AR="/usr/local/bin/ar" RANLIB="/usr/local/bin/ranlib" gmake[4]: Entering directory '/tmp/RtmpET1FvR/R.INSTALL1737b42b56282/Matrix/src/SuiteSparse/COLAMD' cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/colamd.c -o Source/colamd.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/camd_l1.c -o Source/camd_l1.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/colamd_l.c -o Source/colamd_l.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/camd_2.c -o Source/camd_2.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Check/cholmod_write.c -o Check/cholmod_write.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/camd_l2.c -o Source/camd_l2.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/colamd_version.c -o Source/colamd_version.o rm -f COLAMD.a cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/camd_aat.c -o Source/camd_aat.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Check/cholmod_l_write.c -o Check/cholmod_l_write.o /usr/local/bin/ar -cr COLAMD.a Source/colamd.o Source/colamd_l.o Source/colamd_version.o /usr/local/bin/ranlib COLAMD.a gmake[4]: Leaving directory '/tmp/RtmpET1FvR/R.INSTALL1737b42b56282/Matrix/src/SuiteSparse/COLAMD' cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/camd_l_aat.c -o Source/camd_l_aat.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Cholesky/cholmod_amd.c -o Cholesky/cholmod_amd.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/camd_control.c -o Source/camd_control.o cd SuiteSparse/AMD && /usr/local/bin/gmake clean all CC="cc" CPPFLAGS="-DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I\"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include\" -I\"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include\" -DNDEBUG -DNPRINT -DNTIMER" CFLAGS="-O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden" AR="/usr/local/bin/ar" RANLIB="/usr/local/bin/ranlib" gmake[4]: Entering directory '/tmp/RtmpET1FvR/R.INSTALL1737b42b56282/Matrix/src/SuiteSparse/AMD' cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/amd_1.c -o Source/amd_1.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Cholesky/cholmod_l_amd.c -o Cholesky/cholmod_l_amd.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/camd_l_control.c -o Source/camd_l_control.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/amd_l1.c -o Source/amd_l1.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/amd_2.c -o Source/amd_2.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/camd_defaults.c -o Source/camd_defaults.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/camd_l_defaults.c -o Source/camd_l_defaults.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/amd_l2.c -o Source/amd_l2.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Cholesky/cholmod_analyze.c -o Cholesky/cholmod_analyze.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/amd_aat.c -o Source/amd_aat.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/camd_dump.c -o Source/camd_dump.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/camd_l_dump.c -o Source/camd_l_dump.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/amd_l_aat.c -o Source/amd_l_aat.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/camd_info.c -o Source/camd_info.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Cholesky/cholmod_l_analyze.c -o Cholesky/cholmod_l_analyze.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/amd_control.c -o Source/amd_control.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/camd_l_info.c -o Source/camd_l_info.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/amd_l_control.c -o Source/amd_l_control.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/camd_order.c -o Source/camd_order.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/amd_defaults.c -o Source/amd_defaults.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/camd_l_order.c -o Source/camd_l_order.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Cholesky/cholmod_colamd.c -o Cholesky/cholmod_colamd.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/camd_postorder.c -o Source/camd_postorder.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Cholesky/cholmod_l_colamd.c -o Cholesky/cholmod_l_colamd.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/amd_l_defaults.c -o Source/amd_l_defaults.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/camd_l_postorder.c -o Source/camd_l_postorder.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Cholesky/cholmod_etree.c -o Cholesky/cholmod_etree.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/amd_dump.c -o Source/amd_dump.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/camd_preprocess.c -o Source/camd_preprocess.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/camd_l_preprocess.c -o Source/camd_l_preprocess.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/amd_l_dump.c -o Source/amd_l_dump.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/camd_valid.c -o Source/camd_valid.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Cholesky/cholmod_l_etree.c -o Cholesky/cholmod_l_etree.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/amd_info.c -o Source/amd_info.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/camd_l_valid.c -o Source/camd_l_valid.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/amd_l_info.c -o Source/amd_l_info.o cd SuiteSparse/CXSparse && /usr/local/bin/gmake clean all CC="cc" CPPFLAGS="-DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I\"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include\" -I\"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include\" -DNDEBUG -DNPRINT -DNTIMER" CFLAGS="-O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden" AR="/usr/local/bin/ar" RANLIB="/usr/local/bin/ranlib" gmake[4]: Entering directory '/tmp/RtmpET1FvR/R.INSTALL1737b42b56282/Matrix/src/SuiteSparse/CXSparse' cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_add.c -o Source/cs_add.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/camd_version.c -o Source/camd_version.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/amd_order.c -o Source/amd_order.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Cholesky/cholmod_factorize.c -o Cholesky/cholmod_factorize.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_dl_add.c -o Source/cs_dl_add.o rm -f CAMD.a /usr/local/bin/ar -cr CAMD.a Source/camd_1.o Source/camd_l1.o Source/camd_2.o Source/camd_l2.o Source/camd_aat.o Source/camd_l_aat.o Source/camd_control.o Source/camd_l_control.o Source/camd_defaults.o Source/camd_l_defaults.o Source/camd_dump.o Source/camd_l_dump.o Source/camd_info.o Source/camd_l_info.o Source/camd_order.o Source/camd_l_order.o Source/camd_postorder.o Source/camd_l_postorder.o Source/camd_preprocess.o Source/camd_l_preprocess.o Source/camd_valid.o Source/camd_l_valid.o Source/camd_version.o /usr/local/bin/ranlib CAMD.a gmake[4]: Leaving directory '/tmp/RtmpET1FvR/R.INSTALL1737b42b56282/Matrix/src/SuiteSparse/CAMD' cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Cholesky/cholmod_l_factorize.c -o Cholesky/cholmod_l_factorize.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_ci_add.c -o Source/cs_ci_add.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/amd_l_order.c -o Source/amd_l_order.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/amd_post_tree.c -o Source/amd_post_tree.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_cl_add.c -o Source/cs_cl_add.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/amd_l_post_tree.c -o Source/amd_l_post_tree.o cd SuiteSparse/SuiteSparse_config && /usr/local/bin/gmake clean all CC="cc" CPPFLAGS="-DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I\"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include\" -I\"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include\" -DNDEBUG -DNPRINT -DNTIMER" CFLAGS="-O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden" AR="/usr/local/bin/ar" RANLIB="/usr/local/bin/ranlib" cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_amd.c -o Source/cs_amd.o gmake[4]: Entering directory '/tmp/RtmpET1FvR/R.INSTALL1737b42b56282/Matrix/src/SuiteSparse/SuiteSparse_config' cc -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c SuiteSparse_config.c -o SuiteSparse_config.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Cholesky/cholmod_postorder.c -o Cholesky/cholmod_postorder.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_dl_amd.c -o Source/cs_dl_amd.o rm -f SuiteSparse_config.a cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/amd_postorder.c -o Source/amd_postorder.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_ci_amd.c -o Source/cs_ci_amd.o /usr/local/bin/ar -cr SuiteSparse_config.a SuiteSparse_config.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Cholesky/cholmod_l_postorder.c -o Cholesky/cholmod_l_postorder.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_cl_amd.c -o Source/cs_cl_amd.o /usr/local/bin/ranlib SuiteSparse_config.a cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_chol.c -o Source/cs_chol.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/amd_l_postorder.c -o Source/amd_l_postorder.o gmake[4]: Leaving directory '/tmp/RtmpET1FvR/R.INSTALL1737b42b56282/Matrix/src/SuiteSparse/SuiteSparse_config' cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Cholesky/cholmod_rcond.c -o Cholesky/cholmod_rcond.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/amd_preprocess.c -o Source/amd_preprocess.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_dl_chol.c -o Source/cs_dl_chol.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/amd_l_preprocess.c -o Source/amd_l_preprocess.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Cholesky/cholmod_l_rcond.c -o Cholesky/cholmod_l_rcond.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/amd_valid.c -o Source/amd_valid.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_ci_chol.c -o Source/cs_ci_chol.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/amd_l_valid.c -o Source/amd_l_valid.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_cl_chol.c -o Source/cs_cl_chol.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_cholsol.c -o Source/cs_cholsol.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/amd_version.c -o Source/amd_version.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Cholesky/cholmod_resymbol.c -o Cholesky/cholmod_resymbol.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_dl_cholsol.c -o Source/cs_dl_cholsol.o rm -f AMD.a /usr/local/bin/ar -cr AMD.a Source/amd_1.o Source/amd_l1.o Source/amd_2.o Source/amd_l2.o Source/amd_aat.o Source/amd_l_aat.o Source/amd_control.o Source/amd_l_control.o Source/amd_defaults.o Source/amd_l_defaults.o Source/amd_dump.o Source/amd_l_dump.o Source/amd_info.o Source/amd_l_info.o Source/amd_order.o Source/amd_l_order.o Source/amd_post_tree.o Source/amd_l_post_tree.o Source/amd_postorder.o Source/amd_l_postorder.o Source/amd_preprocess.o Source/amd_l_preprocess.o Source/amd_valid.o Source/amd_l_valid.o Source/amd_version.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_ci_cholsol.c -o Source/cs_ci_cholsol.o /usr/local/bin/ranlib AMD.a gmake[4]: Leaving directory '/tmp/RtmpET1FvR/R.INSTALL1737b42b56282/Matrix/src/SuiteSparse/AMD' cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_cl_cholsol.c -o Source/cs_cl_cholsol.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Cholesky/cholmod_l_resymbol.c -o Cholesky/cholmod_l_resymbol.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_compress.c -o Source/cs_compress.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_dl_compress.c -o Source/cs_dl_compress.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_ci_compress.c -o Source/cs_ci_compress.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Cholesky/cholmod_rowcolcounts.c -o Cholesky/cholmod_rowcolcounts.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_cl_compress.c -o Source/cs_cl_compress.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_convert.c -o Source/cs_convert.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Cholesky/cholmod_l_rowcolcounts.c -o Cholesky/cholmod_l_rowcolcounts.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_counts.c -o Source/cs_counts.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Cholesky/cholmod_rowfac.c -o Cholesky/cholmod_rowfac.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_dl_counts.c -o Source/cs_dl_counts.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Cholesky/cholmod_l_rowfac.c -o Cholesky/cholmod_l_rowfac.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_ci_counts.c -o Source/cs_ci_counts.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_cl_counts.c -o Source/cs_cl_counts.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Cholesky/cholmod_solve.c -o Cholesky/cholmod_solve.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_cumsum.c -o Source/cs_cumsum.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_dl_cumsum.c -o Source/cs_dl_cumsum.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_ci_cumsum.c -o Source/cs_ci_cumsum.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_cl_cumsum.c -o Source/cs_cl_cumsum.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_dfs.c -o Source/cs_dfs.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_dl_dfs.c -o Source/cs_dl_dfs.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_ci_dfs.c -o Source/cs_ci_dfs.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_cl_dfs.c -o Source/cs_cl_dfs.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_dmperm.c -o Source/cs_dmperm.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Cholesky/cholmod_l_solve.c -o Cholesky/cholmod_l_solve.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_dl_dmperm.c -o Source/cs_dl_dmperm.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_ci_dmperm.c -o Source/cs_ci_dmperm.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_cl_dmperm.c -o Source/cs_cl_dmperm.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Cholesky/cholmod_spsolve.c -o Cholesky/cholmod_spsolve.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_droptol.c -o Source/cs_droptol.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_dl_droptol.c -o Source/cs_dl_droptol.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_ci_droptol.c -o Source/cs_ci_droptol.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Cholesky/cholmod_l_spsolve.c -o Cholesky/cholmod_l_spsolve.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_cl_droptol.c -o Source/cs_cl_droptol.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_dropzeros.c -o Source/cs_dropzeros.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_dl_dropzeros.c -o Source/cs_dl_dropzeros.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_ci_dropzeros.c -o Source/cs_ci_dropzeros.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_aat.c -o Utility/cholmod_aat.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_cl_dropzeros.c -o Source/cs_cl_dropzeros.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_l_aat.c -o Utility/cholmod_l_aat.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_dupl.c -o Source/cs_dupl.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_dl_dupl.c -o Source/cs_dl_dupl.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_ci_dupl.c -o Source/cs_ci_dupl.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_add.c -o Utility/cholmod_add.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_cl_dupl.c -o Source/cs_cl_dupl.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_entry.c -o Source/cs_entry.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_dl_entry.c -o Source/cs_dl_entry.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_l_add.c -o Utility/cholmod_l_add.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_ci_entry.c -o Source/cs_ci_entry.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_cl_entry.c -o Source/cs_cl_entry.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_add_size_t.c -o Utility/cholmod_add_size_t.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_ereach.c -o Source/cs_ereach.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_l_add_size_t.c -o Utility/cholmod_l_add_size_t.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_alloc_factor.c -o Utility/cholmod_alloc_factor.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_l_alloc_factor.c -o Utility/cholmod_l_alloc_factor.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_alloc_work.c -o Utility/cholmod_alloc_work.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_dl_ereach.c -o Source/cs_dl_ereach.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_ci_ereach.c -o Source/cs_ci_ereach.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_cl_ereach.c -o Source/cs_cl_ereach.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_etree.c -o Source/cs_etree.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_l_alloc_work.c -o Utility/cholmod_l_alloc_work.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_allocate_dense.c -o Utility/cholmod_allocate_dense.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_dl_etree.c -o Source/cs_dl_etree.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_l_allocate_dense.c -o Utility/cholmod_l_allocate_dense.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_allocate_factor.c -o Utility/cholmod_allocate_factor.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_ci_etree.c -o Source/cs_ci_etree.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_l_allocate_factor.c -o Utility/cholmod_l_allocate_factor.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_cl_etree.c -o Source/cs_cl_etree.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_allocate_sparse.c -o Utility/cholmod_allocate_sparse.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_fkeep.c -o Source/cs_fkeep.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_dl_fkeep.c -o Source/cs_dl_fkeep.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_l_allocate_sparse.c -o Utility/cholmod_l_allocate_sparse.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_allocate_triplet.c -o Utility/cholmod_allocate_triplet.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_ci_fkeep.c -o Source/cs_ci_fkeep.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_cl_fkeep.c -o Source/cs_cl_fkeep.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_l_allocate_triplet.c -o Utility/cholmod_l_allocate_triplet.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_gaxpy.c -o Source/cs_gaxpy.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_dl_gaxpy.c -o Source/cs_dl_gaxpy.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_ci_gaxpy.c -o Source/cs_ci_gaxpy.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_cl_gaxpy.c -o Source/cs_cl_gaxpy.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_happly.c -o Source/cs_happly.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_dl_happly.c -o Source/cs_dl_happly.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_allocate_work.c -o Utility/cholmod_allocate_work.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_l_allocate_work.c -o Utility/cholmod_l_allocate_work.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_ci_happly.c -o Source/cs_ci_happly.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_cl_happly.c -o Source/cs_cl_happly.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_band.c -o Utility/cholmod_band.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_l_band.c -o Utility/cholmod_l_band.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_house.c -o Source/cs_house.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_band_nnz.c -o Utility/cholmod_band_nnz.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_dl_house.c -o Source/cs_dl_house.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_l_band_nnz.c -o Utility/cholmod_l_band_nnz.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_ci_house.c -o Source/cs_ci_house.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_calloc.c -o Utility/cholmod_calloc.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_l_calloc.c -o Utility/cholmod_l_calloc.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_cl_house.c -o Source/cs_cl_house.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_change_factor.c -o Utility/cholmod_change_factor.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_ipvec.c -o Source/cs_ipvec.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_l_change_factor.c -o Utility/cholmod_l_change_factor.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_dl_ipvec.c -o Source/cs_dl_ipvec.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_ci_ipvec.c -o Source/cs_ci_ipvec.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_clear_flag.c -o Utility/cholmod_clear_flag.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_cl_ipvec.c -o Source/cs_cl_ipvec.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_l_clear_flag.c -o Utility/cholmod_l_clear_flag.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_leaf.c -o Source/cs_leaf.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_dl_leaf.c -o Source/cs_dl_leaf.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_copy.c -o Utility/cholmod_copy.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_ci_leaf.c -o Source/cs_ci_leaf.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_l_copy.c -o Utility/cholmod_l_copy.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_cl_leaf.c -o Source/cs_cl_leaf.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_load.c -o Source/cs_load.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_dl_load.c -o Source/cs_dl_load.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_copy_dense.c -o Utility/cholmod_copy_dense.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_ci_load.c -o Source/cs_ci_load.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_cl_load.c -o Source/cs_cl_load.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_l_copy_dense.c -o Utility/cholmod_l_copy_dense.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_lsolve.c -o Source/cs_lsolve.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_copy_dense2.c -o Utility/cholmod_copy_dense2.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_dl_lsolve.c -o Source/cs_dl_lsolve.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_ci_lsolve.c -o Source/cs_ci_lsolve.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_cl_lsolve.c -o Source/cs_cl_lsolve.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_ltsolve.c -o Source/cs_ltsolve.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_l_copy_dense2.c -o Utility/cholmod_l_copy_dense2.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_dl_ltsolve.c -o Source/cs_dl_ltsolve.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_copy_factor.c -o Utility/cholmod_copy_factor.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_ci_ltsolve.c -o Source/cs_ci_ltsolve.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_l_copy_factor.c -o Utility/cholmod_l_copy_factor.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_cl_ltsolve.c -o Source/cs_cl_ltsolve.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_lu.c -o Source/cs_lu.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_dl_lu.c -o Source/cs_dl_lu.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_ci_lu.c -o Source/cs_ci_lu.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_copy_sparse.c -o Utility/cholmod_copy_sparse.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_cl_lu.c -o Source/cs_cl_lu.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_l_copy_sparse.c -o Utility/cholmod_l_copy_sparse.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_lusol.c -o Source/cs_lusol.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_dl_lusol.c -o Source/cs_dl_lusol.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_copy_triplet.c -o Utility/cholmod_copy_triplet.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_ci_lusol.c -o Source/cs_ci_lusol.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_l_copy_triplet.c -o Utility/cholmod_l_copy_triplet.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_cl_lusol.c -o Source/cs_cl_lusol.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_malloc.c -o Source/cs_malloc.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_dl_malloc.c -o Source/cs_dl_malloc.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_cumsum.c -o Utility/cholmod_cumsum.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_ci_malloc.c -o Source/cs_ci_malloc.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_l_cumsum.c -o Utility/cholmod_l_cumsum.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_cl_malloc.c -o Source/cs_cl_malloc.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_dbound.c -o Utility/cholmod_dbound.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_maxtrans.c -o Source/cs_maxtrans.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_dl_maxtrans.c -o Source/cs_dl_maxtrans.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_l_dbound.c -o Utility/cholmod_l_dbound.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_defaults.c -o Utility/cholmod_defaults.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_l_defaults.c -o Utility/cholmod_l_defaults.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_ci_maxtrans.c -o Source/cs_ci_maxtrans.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_dense_nnz.c -o Utility/cholmod_dense_nnz.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_l_dense_nnz.c -o Utility/cholmod_l_dense_nnz.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_cl_maxtrans.c -o Source/cs_cl_maxtrans.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_dense_to_sparse.c -o Utility/cholmod_dense_to_sparse.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_l_dense_to_sparse.c -o Utility/cholmod_l_dense_to_sparse.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_multiply.c -o Source/cs_multiply.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_dl_multiply.c -o Source/cs_dl_multiply.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_divcomplex.c -o Utility/cholmod_divcomplex.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_l_divcomplex.c -o Utility/cholmod_l_divcomplex.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_ci_multiply.c -o Source/cs_ci_multiply.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_ensure_dense.c -o Utility/cholmod_ensure_dense.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_cl_multiply.c -o Source/cs_cl_multiply.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_l_ensure_dense.c -o Utility/cholmod_l_ensure_dense.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_error.c -o Utility/cholmod_error.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_norm.c -o Source/cs_norm.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_dl_norm.c -o Source/cs_dl_norm.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_ci_norm.c -o Source/cs_ci_norm.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_l_error.c -o Utility/cholmod_l_error.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_eye.c -o Utility/cholmod_eye.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_cl_norm.c -o Source/cs_cl_norm.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_permute.c -o Source/cs_permute.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_l_eye.c -o Utility/cholmod_l_eye.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_factor_to_sparse.c -o Utility/cholmod_factor_to_sparse.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_dl_permute.c -o Source/cs_dl_permute.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_ci_permute.c -o Source/cs_ci_permute.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_l_factor_to_sparse.c -o Utility/cholmod_l_factor_to_sparse.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_cl_permute.c -o Source/cs_cl_permute.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_pinv.c -o Source/cs_pinv.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_finish.c -o Utility/cholmod_finish.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_dl_pinv.c -o Source/cs_dl_pinv.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_ci_pinv.c -o Source/cs_ci_pinv.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_cl_pinv.c -o Source/cs_cl_pinv.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_post.c -o Source/cs_post.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_l_finish.c -o Utility/cholmod_l_finish.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_dl_post.c -o Source/cs_dl_post.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_ci_post.c -o Source/cs_ci_post.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_free.c -o Utility/cholmod_free.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_cl_post.c -o Source/cs_cl_post.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_l_free.c -o Utility/cholmod_l_free.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_print.c -o Source/cs_print.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_dl_print.c -o Source/cs_dl_print.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_free_dense.c -o Utility/cholmod_free_dense.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_ci_print.c -o Source/cs_ci_print.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_cl_print.c -o Source/cs_cl_print.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_l_free_dense.c -o Utility/cholmod_l_free_dense.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_free_factor.c -o Utility/cholmod_free_factor.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_pvec.c -o Source/cs_pvec.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_l_free_factor.c -o Utility/cholmod_l_free_factor.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_free_sparse.c -o Utility/cholmod_free_sparse.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_dl_pvec.c -o Source/cs_dl_pvec.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_l_free_sparse.c -o Utility/cholmod_l_free_sparse.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_ci_pvec.c -o Source/cs_ci_pvec.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_free_triplet.c -o Utility/cholmod_free_triplet.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_cl_pvec.c -o Source/cs_cl_pvec.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_l_free_triplet.c -o Utility/cholmod_l_free_triplet.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_free_work.c -o Utility/cholmod_free_work.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_qr.c -o Source/cs_qr.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_dl_qr.c -o Source/cs_dl_qr.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_ci_qr.c -o Source/cs_ci_qr.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_l_free_work.c -o Utility/cholmod_l_free_work.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_cl_qr.c -o Source/cs_cl_qr.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_qrsol.c -o Source/cs_qrsol.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_hypot.c -o Utility/cholmod_hypot.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_dl_qrsol.c -o Source/cs_dl_qrsol.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_l_hypot.c -o Utility/cholmod_l_hypot.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_ci_qrsol.c -o Source/cs_ci_qrsol.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_malloc.c -o Utility/cholmod_malloc.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_l_malloc.c -o Utility/cholmod_l_malloc.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_cl_qrsol.c -o Source/cs_cl_qrsol.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_maxrank.c -o Utility/cholmod_maxrank.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_randperm.c -o Source/cs_randperm.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_dl_randperm.c -o Source/cs_dl_randperm.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_l_maxrank.c -o Utility/cholmod_l_maxrank.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_memdebug.c -o Utility/cholmod_memdebug.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_ci_randperm.c -o Source/cs_ci_randperm.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_mult_size_t.c -o Utility/cholmod_mult_size_t.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_cl_randperm.c -o Source/cs_cl_randperm.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_l_mult_size_t.c -o Utility/cholmod_l_mult_size_t.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_reach.c -o Source/cs_reach.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_mult_uint64_t.c -o Utility/cholmod_mult_uint64_t.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_dl_reach.c -o Source/cs_dl_reach.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_nnz.c -o Utility/cholmod_nnz.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_l_nnz.c -o Utility/cholmod_l_nnz.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_ones.c -o Utility/cholmod_ones.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_ci_reach.c -o Source/cs_ci_reach.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_l_ones.c -o Utility/cholmod_l_ones.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_cl_reach.c -o Source/cs_cl_reach.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_pack_factor.c -o Utility/cholmod_pack_factor.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_scatter.c -o Source/cs_scatter.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_l_pack_factor.c -o Utility/cholmod_l_pack_factor.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_dl_scatter.c -o Source/cs_dl_scatter.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_ptranspose.c -o Utility/cholmod_ptranspose.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_l_ptranspose.c -o Utility/cholmod_l_ptranspose.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_realloc.c -o Utility/cholmod_realloc.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_ci_scatter.c -o Source/cs_ci_scatter.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_cl_scatter.c -o Source/cs_cl_scatter.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_l_realloc.c -o Utility/cholmod_l_realloc.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_scc.c -o Source/cs_scc.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_realloc_multiple.c -o Utility/cholmod_realloc_multiple.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_l_realloc_multiple.c -o Utility/cholmod_l_realloc_multiple.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_dl_scc.c -o Source/cs_dl_scc.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_reallocate_column.c -o Utility/cholmod_reallocate_column.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_ci_scc.c -o Source/cs_ci_scc.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_l_reallocate_column.c -o Utility/cholmod_l_reallocate_column.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_cl_scc.c -o Source/cs_cl_scc.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_reallocate_factor.c -o Utility/cholmod_reallocate_factor.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_schol.c -o Source/cs_schol.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_l_reallocate_factor.c -o Utility/cholmod_l_reallocate_factor.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_reallocate_sparse.c -o Utility/cholmod_reallocate_sparse.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_dl_schol.c -o Source/cs_dl_schol.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_ci_schol.c -o Source/cs_ci_schol.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_l_reallocate_sparse.c -o Utility/cholmod_l_reallocate_sparse.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_cl_schol.c -o Source/cs_cl_schol.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_spsolve.c -o Source/cs_spsolve.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_reallocate_triplet.c -o Utility/cholmod_reallocate_triplet.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_dl_spsolve.c -o Source/cs_dl_spsolve.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_l_reallocate_triplet.c -o Utility/cholmod_l_reallocate_triplet.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_sbound.c -o Utility/cholmod_sbound.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_ci_spsolve.c -o Source/cs_ci_spsolve.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_l_sbound.c -o Utility/cholmod_l_sbound.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_cl_spsolve.c -o Source/cs_cl_spsolve.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_score_comp.c -o Utility/cholmod_score_comp.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_sqr.c -o Source/cs_sqr.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_dl_sqr.c -o Source/cs_dl_sqr.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_ci_sqr.c -o Source/cs_ci_sqr.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_l_score_comp.c -o Utility/cholmod_l_score_comp.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_set_empty.c -o Utility/cholmod_set_empty.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_cl_sqr.c -o Source/cs_cl_sqr.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_l_set_empty.c -o Utility/cholmod_l_set_empty.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_symperm.c -o Source/cs_symperm.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_sort.c -o Utility/cholmod_sort.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_dl_symperm.c -o Source/cs_dl_symperm.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_l_sort.c -o Utility/cholmod_l_sort.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_ci_symperm.c -o Source/cs_ci_symperm.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_sparse_to_dense.c -o Utility/cholmod_sparse_to_dense.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_cl_symperm.c -o Source/cs_cl_symperm.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_l_sparse_to_dense.c -o Utility/cholmod_l_sparse_to_dense.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_sparse_to_triplet.c -o Utility/cholmod_sparse_to_triplet.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_tdfs.c -o Source/cs_tdfs.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_dl_tdfs.c -o Source/cs_dl_tdfs.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_ci_tdfs.c -o Source/cs_ci_tdfs.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_l_sparse_to_triplet.c -o Utility/cholmod_l_sparse_to_triplet.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_speye.c -o Utility/cholmod_speye.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_cl_tdfs.c -o Source/cs_cl_tdfs.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_transpose.c -o Source/cs_transpose.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_l_speye.c -o Utility/cholmod_l_speye.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_spzeros.c -o Utility/cholmod_spzeros.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_dl_transpose.c -o Source/cs_dl_transpose.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_ci_transpose.c -o Source/cs_ci_transpose.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_l_spzeros.c -o Utility/cholmod_l_spzeros.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_start.c -o Utility/cholmod_start.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_cl_transpose.c -o Source/cs_cl_transpose.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_updown.c -o Source/cs_updown.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_dl_updown.c -o Source/cs_dl_updown.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_l_start.c -o Utility/cholmod_l_start.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_ci_updown.c -o Source/cs_ci_updown.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_cl_updown.c -o Source/cs_cl_updown.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_transpose.c -o Utility/cholmod_transpose.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_l_transpose.c -o Utility/cholmod_l_transpose.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_transpose_sym.c -o Utility/cholmod_transpose_sym.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_usolve.c -o Source/cs_usolve.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_dl_usolve.c -o Source/cs_dl_usolve.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_l_transpose_sym.c -o Utility/cholmod_l_transpose_sym.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_ci_usolve.c -o Source/cs_ci_usolve.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_cl_usolve.c -o Source/cs_cl_usolve.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_transpose_unsym.c -o Utility/cholmod_transpose_unsym.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_util.c -o Source/cs_util.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_l_transpose_unsym.c -o Utility/cholmod_l_transpose_unsym.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_dl_util.c -o Source/cs_dl_util.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_triplet_to_sparse.c -o Utility/cholmod_triplet_to_sparse.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_ci_util.c -o Source/cs_ci_util.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_cl_util.c -o Source/cs_cl_util.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_utsolve.c -o Source/cs_utsolve.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_dl_utsolve.c -o Source/cs_dl_utsolve.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_ci_utsolve.c -o Source/cs_ci_utsolve.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_l_triplet_to_sparse.c -o Utility/cholmod_l_triplet_to_sparse.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cs_cl_utsolve.c -o Source/cs_cl_utsolve.o cc -I./Include -I../SuiteSparse_config -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Source/cxsparse_version.c -o Source/cxsparse_version.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_version.c -o Utility/cholmod_version.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_l_version.c -o Utility/cholmod_l_version.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_xtype.c -o Utility/cholmod_xtype.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_l_xtype.c -o Utility/cholmod_l_xtype.o rm -f CXSparse.a /usr/local/bin/ar -cr CXSparse.a Source/cs_add.o Source/cs_dl_add.o Source/cs_ci_add.o Source/cs_cl_add.o Source/cs_amd.o Source/cs_dl_amd.o Source/cs_ci_amd.o Source/cs_cl_amd.o Source/cs_chol.o Source/cs_dl_chol.o Source/cs_ci_chol.o Source/cs_cl_chol.o Source/cs_cholsol.o Source/cs_dl_cholsol.o Source/cs_ci_cholsol.o Source/cs_cl_cholsol.o Source/cs_compress.o Source/cs_dl_compress.o Source/cs_ci_compress.o Source/cs_cl_compress.o Source/cs_convert.o Source/cs_counts.o Source/cs_dl_counts.o Source/cs_ci_counts.o Source/cs_cl_counts.o Source/cs_cumsum.o Source/cs_dl_cumsum.o Source/cs_ci_cumsum.o Source/cs_cl_cumsum.o Source/cs_dfs.o Source/cs_dl_dfs.o Source/cs_ci_dfs.o Source/cs_cl_dfs.o Source/cs_dmperm.o Source/cs_dl_dmperm.o Source/cs_ci_dmperm.o Source/cs_cl_dmperm.o Source/cs_droptol.o Source/cs_dl_droptol.o Source/cs_ci_droptol.o Source/cs_cl_droptol.o Source/cs_dropzeros.o Source/cs_dl_dropzeros.o Source/cs_ci_dropzeros.o Source/cs_cl_dropzeros.o Source/cs_dupl.o Source/cs_dl_dupl.o Source/cs_ci_dupl.o Source/cs_cl_dupl.o Source/cs_entry.o Source/cs_dl_entry.o Source/cs_ci_entry.o Source/cs_cl_entry.o Source/cs_ereach.o Source/cs_dl_ereach.o Source/cs_ci_ereach.o Source/cs_cl_ereach.o Source/cs_etree.o Source/cs_dl_etree.o Source/cs_ci_etree.o Source/cs_cl_etree.o Source/cs_fkeep.o Source/cs_dl_fkeep.o Source/cs_ci_fkeep.o Source/cs_cl_fkeep.o Source/cs_gaxpy.o Source/cs_dl_gaxpy.o Source/cs_ci_gaxpy.o Source/cs_cl_gaxpy.o Source/cs_happly.o Source/cs_dl_happly.o Source/cs_ci_happly.o Source/cs_cl_happly.o Source/cs_house.o Source/cs_dl_house.o Source/cs_ci_house.o Source/cs_cl_house.o Source/cs_ipvec.o Source/cs_dl_ipvec.o Source/cs_ci_ipvec.o Source/cs_cl_ipvec.o Source/cs_leaf.o Source/cs_dl_leaf.o Source/cs_ci_leaf.o Source/cs_cl_leaf.o Source/cs_load.o Source/cs_dl_load.o Source/cs_ci_load.o Source/cs_cl_load.o Source/cs_lsolve.o Source/cs_dl_lsolve.o Source/cs_ci_lsolve.o Source/cs_cl_lsolve.o Source/cs_ltsolve.o Source/cs_dl_ltsolve.o Source/cs_ci_ltsolve.o Source/cs_cl_ltsolve.o Source/cs_lu.o Source/cs_dl_lu.o Source/cs_ci_lu.o Source/cs_cl_lu.o Source/cs_lusol.o Source/cs_dl_lusol.o Source/cs_ci_lusol.o Source/cs_cl_lusol.o Source/cs_malloc.o Source/cs_dl_malloc.o Source/cs_ci_malloc.o Source/cs_cl_malloc.o Source/cs_maxtrans.o Source/cs_dl_maxtrans.o Source/cs_ci_maxtrans.o Source/cs_cl_maxtrans.o Source/cs_multiply.o Source/cs_dl_multiply.o Source/cs_ci_multiply.o Source/cs_cl_multiply.o Source/cs_norm.o Source/cs_dl_norm.o Source/cs_ci_norm.o Source/cs_cl_norm.o Source/cs_permute.o Source/cs_dl_permute.o Source/cs_ci_permute.o Source/cs_cl_permute.o Source/cs_pinv.o Source/cs_dl_pinv.o Source/cs_ci_pinv.o Source/cs_cl_pinv.o Source/cs_post.o Source/cs_dl_post.o Source/cs_ci_post.o Source/cs_cl_post.o Source/cs_print.o Source/cs_dl_print.o Source/cs_ci_print.o Source/cs_cl_print.o Source/cs_pvec.o Source/cs_dl_pvec.o Source/cs_ci_pvec.o Source/cs_cl_pvec.o Source/cs_qr.o Source/cs_dl_qr.o Source/cs_ci_qr.o Source/cs_cl_qr.o Source/cs_qrsol.o Source/cs_dl_qrsol.o Source/cs_ci_qrsol.o Source/cs_cl_qrsol.o Source/cs_randperm.o Source/cs_dl_randperm.o Source/cs_ci_randperm.o Source/cs_cl_randperm.o Source/cs_reach.o Source/cs_dl_reach.o Source/cs_ci_reach.o Source/cs_cl_reach.o Source/cs_scatter.o Source/cs_dl_scatter.o Source/cs_ci_scatter.o Source/cs_cl_scatter.o Source/cs_scc.o Source/cs_dl_scc.o Source/cs_ci_scc.o Source/cs_cl_scc.o Source/cs_schol.o Source/cs_dl_schol.o Source/cs_ci_schol.o Source/cs_cl_schol.o Source/cs_spsolve.o Source/cs_dl_spsolve.o Source/cs_ci_spsolve.o Source/cs_cl_spsolve.o Source/cs_sqr.o Source/cs_dl_sqr.o Source/cs_ci_sqr.o Source/cs_cl_sqr.o Source/cs_symperm.o Source/cs_dl_symperm.o Source/cs_ci_symperm.o Source/cs_cl_symperm.o Source/cs_tdfs.o Source/cs_dl_tdfs.o Source/cs_ci_tdfs.o Source/cs_cl_tdfs.o Source/cs_transpose.o Source/cs_dl_transpose.o Source/cs_ci_transpose.o Source/cs_cl_transpose.o Source/cs_updown.o Source/cs_dl_updown.o Source/cs_ci_updown.o Source/cs_cl_updown.o Source/cs_usolve.o Source/cs_dl_usolve.o Source/cs_ci_usolve.o Source/cs_cl_usolve.o Source/cs_util.o Source/cs_dl_util.o Source/cs_ci_util.o Source/cs_cl_util.o Source/cs_utsolve.o Source/cs_dl_utsolve.o Source/cs_ci_utsolve.o Source/cs_cl_utsolve.o Source/cxsparse_version.o /usr/local/bin/ranlib CXSparse.a cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_zeros.c -o Utility/cholmod_zeros.o gmake[4]: Leaving directory '/tmp/RtmpET1FvR/R.INSTALL1737b42b56282/Matrix/src/SuiteSparse/CXSparse' cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Utility/cholmod_l_zeros.c -o Utility/cholmod_l_zeros.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c MatrixOps/cholmod_drop.c -o MatrixOps/cholmod_drop.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c MatrixOps/cholmod_l_drop.c -o MatrixOps/cholmod_l_drop.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c MatrixOps/cholmod_horzcat.c -o MatrixOps/cholmod_horzcat.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c MatrixOps/cholmod_l_horzcat.c -o MatrixOps/cholmod_l_horzcat.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c MatrixOps/cholmod_norm.c -o MatrixOps/cholmod_norm.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c MatrixOps/cholmod_l_norm.c -o MatrixOps/cholmod_l_norm.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c MatrixOps/cholmod_scale.c -o MatrixOps/cholmod_scale.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c MatrixOps/cholmod_l_scale.c -o MatrixOps/cholmod_l_scale.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c MatrixOps/cholmod_sdmult.c -o MatrixOps/cholmod_sdmult.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c MatrixOps/cholmod_l_sdmult.c -o MatrixOps/cholmod_l_sdmult.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c MatrixOps/cholmod_ssmult.c -o MatrixOps/cholmod_ssmult.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c MatrixOps/cholmod_l_ssmult.c -o MatrixOps/cholmod_l_ssmult.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c MatrixOps/cholmod_submatrix.c -o MatrixOps/cholmod_submatrix.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c MatrixOps/cholmod_l_submatrix.c -o MatrixOps/cholmod_l_submatrix.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c MatrixOps/cholmod_symmetry.c -o MatrixOps/cholmod_symmetry.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c MatrixOps/cholmod_l_symmetry.c -o MatrixOps/cholmod_l_symmetry.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c MatrixOps/cholmod_vertcat.c -o MatrixOps/cholmod_vertcat.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c MatrixOps/cholmod_l_vertcat.c -o MatrixOps/cholmod_l_vertcat.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Modify/cholmod_rowadd.c -o Modify/cholmod_rowadd.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Modify/cholmod_l_rowadd.c -o Modify/cholmod_l_rowadd.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Modify/cholmod_rowdel.c -o Modify/cholmod_rowdel.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Modify/cholmod_l_rowdel.c -o Modify/cholmod_l_rowdel.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Modify/cholmod_updown.c -o Modify/cholmod_updown.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Modify/cholmod_l_updown.c -o Modify/cholmod_l_updown.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Partition/cholmod_camd.c -o Partition/cholmod_camd.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Partition/cholmod_l_camd.c -o Partition/cholmod_l_camd.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Partition/cholmod_ccolamd.c -o Partition/cholmod_ccolamd.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Partition/cholmod_l_ccolamd.c -o Partition/cholmod_l_ccolamd.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Partition/cholmod_csymamd.c -o Partition/cholmod_csymamd.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Partition/cholmod_l_csymamd.c -o Partition/cholmod_l_csymamd.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Partition/cholmod_metis.c -o Partition/cholmod_metis.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Partition/cholmod_l_metis.c -o Partition/cholmod_l_metis.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Partition/cholmod_metis_wrapper.c -o Partition/cholmod_metis_wrapper.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Partition/cholmod_nesdis.c -o Partition/cholmod_nesdis.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Partition/cholmod_l_nesdis.c -o Partition/cholmod_l_nesdis.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Supernodal/cholmod_super_numeric.c -o Supernodal/cholmod_super_numeric.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Supernodal/cholmod_l_super_numeric.c -o Supernodal/cholmod_l_super_numeric.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Supernodal/cholmod_super_solve.c -o Supernodal/cholmod_super_solve.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Supernodal/cholmod_l_super_solve.c -o Supernodal/cholmod_l_super_solve.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Supernodal/cholmod_super_symbolic.c -o Supernodal/cholmod_super_symbolic.o cc -I./Include -I../SuiteSparse_config -I../AMD/Include -I../COLAMD/Include -I../CAMD/Include -I../CCOLAMD/Include -I. -I./SuiteSparse_metis/include -I./SuiteSparse_metis/GKlib -I./SuiteSparse_metis/libmetis -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DNPRINT -DNTIMER -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fpic -fvisibility=hidden -c Supernodal/cholmod_l_super_symbolic.c -o Supernodal/cholmod_l_super_symbolic.o rm -f CHOLMOD.a /usr/local/bin/ar -cr CHOLMOD.a Check/cholmod_check.o Check/cholmod_l_check.o Check/cholmod_read.o Check/cholmod_l_read.o Check/cholmod_write.o Check/cholmod_l_write.o Cholesky/cholmod_amd.o Cholesky/cholmod_l_amd.o Cholesky/cholmod_analyze.o Cholesky/cholmod_l_analyze.o Cholesky/cholmod_colamd.o Cholesky/cholmod_l_colamd.o Cholesky/cholmod_etree.o Cholesky/cholmod_l_etree.o Cholesky/cholmod_factorize.o Cholesky/cholmod_l_factorize.o Cholesky/cholmod_postorder.o Cholesky/cholmod_l_postorder.o Cholesky/cholmod_rcond.o Cholesky/cholmod_l_rcond.o Cholesky/cholmod_resymbol.o Cholesky/cholmod_l_resymbol.o Cholesky/cholmod_rowcolcounts.o Cholesky/cholmod_l_rowcolcounts.o Cholesky/cholmod_rowfac.o Cholesky/cholmod_l_rowfac.o Cholesky/cholmod_solve.o Cholesky/cholmod_l_solve.o Cholesky/cholmod_spsolve.o Cholesky/cholmod_l_spsolve.o Utility/cholmod_aat.o Utility/cholmod_l_aat.o Utility/cholmod_add.o Utility/cholmod_l_add.o Utility/cholmod_add_size_t.o Utility/cholmod_l_add_size_t.o Utility/cholmod_alloc_factor.o Utility/cholmod_l_alloc_factor.o Utility/cholmod_alloc_work.o Utility/cholmod_l_alloc_work.o Utility/cholmod_allocate_dense.o Utility/cholmod_l_allocate_dense.o Utility/cholmod_allocate_factor.o Utility/cholmod_l_allocate_factor.o Utility/cholmod_allocate_sparse.o Utility/cholmod_l_allocate_sparse.o Utility/cholmod_allocate_triplet.o Utility/cholmod_l_allocate_triplet.o Utility/cholmod_allocate_work.o Utility/cholmod_l_allocate_work.o Utility/cholmod_band.o Utility/cholmod_l_band.o Utility/cholmod_band_nnz.o Utility/cholmod_l_band_nnz.o Utility/cholmod_calloc.o Utility/cholmod_l_calloc.o Utility/cholmod_change_factor.o Utility/cholmod_l_change_factor.o Utility/cholmod_clear_flag.o Utility/cholmod_l_clear_flag.o Utility/cholmod_copy.o Utility/cholmod_l_copy.o Utility/cholmod_copy_dense.o Utility/cholmod_l_copy_dense.o Utility/cholmod_copy_dense2.o Utility/cholmod_l_copy_dense2.o Utility/cholmod_copy_factor.o Utility/cholmod_l_copy_factor.o Utility/cholmod_copy_sparse.o Utility/cholmod_l_copy_sparse.o Utility/cholmod_copy_triplet.o Utility/cholmod_l_copy_triplet.o Utility/cholmod_cumsum.o Utility/cholmod_l_cumsum.o Utility/cholmod_dbound.o Utility/cholmod_l_dbound.o Utility/cholmod_defaults.o Utility/cholmod_l_defaults.o Utility/cholmod_dense_nnz.o Utility/cholmod_l_dense_nnz.o Utility/cholmod_dense_to_sparse.o Utility/cholmod_l_dense_to_sparse.o Utility/cholmod_divcomplex.o Utility/cholmod_l_divcomplex.o Utility/cholmod_ensure_dense.o Utility/cholmod_l_ensure_dense.o Utility/cholmod_error.o Utility/cholmod_l_error.o Utility/cholmod_eye.o Utility/cholmod_l_eye.o Utility/cholmod_factor_to_sparse.o Utility/cholmod_l_factor_to_sparse.o Utility/cholmod_finish.o Utility/cholmod_l_finish.o Utility/cholmod_free.o Utility/cholmod_l_free.o Utility/cholmod_free_dense.o Utility/cholmod_l_free_dense.o Utility/cholmod_free_factor.o Utility/cholmod_l_free_factor.o Utility/cholmod_free_sparse.o Utility/cholmod_l_free_sparse.o Utility/cholmod_free_triplet.o Utility/cholmod_l_free_triplet.o Utility/cholmod_free_work.o Utility/cholmod_l_free_work.o Utility/cholmod_hypot.o Utility/cholmod_l_hypot.o Utility/cholmod_malloc.o Utility/cholmod_l_malloc.o Utility/cholmod_maxrank.o Utility/cholmod_l_maxrank.o Utility/cholmod_memdebug.o Utility/cholmod_mult_size_t.o Utility/cholmod_l_mult_size_t.o Utility/cholmod_mult_uint64_t.o Utility/cholmod_nnz.o Utility/cholmod_l_nnz.o Utility/cholmod_ones.o Utility/cholmod_l_ones.o Utility/cholmod_pack_factor.o Utility/cholmod_l_pack_factor.o Utility/cholmod_ptranspose.o Utility/cholmod_l_ptranspose.o Utility/cholmod_realloc.o Utility/cholmod_l_realloc.o Utility/cholmod_realloc_multiple.o Utility/cholmod_l_realloc_multiple.o Utility/cholmod_reallocate_column.o Utility/cholmod_l_reallocate_column.o Utility/cholmod_reallocate_factor.o Utility/cholmod_l_reallocate_factor.o Utility/cholmod_reallocate_sparse.o Utility/cholmod_l_reallocate_sparse.o Utility/cholmod_reallocate_triplet.o Utility/cholmod_l_reallocate_triplet.o Utility/cholmod_sbound.o Utility/cholmod_l_sbound.o Utility/cholmod_score_comp.o Utility/cholmod_l_score_comp.o Utility/cholmod_set_empty.o Utility/cholmod_l_set_empty.o Utility/cholmod_sort.o Utility/cholmod_l_sort.o Utility/cholmod_sparse_to_dense.o Utility/cholmod_l_sparse_to_dense.o Utility/cholmod_sparse_to_triplet.o Utility/cholmod_l_sparse_to_triplet.o Utility/cholmod_speye.o Utility/cholmod_l_speye.o Utility/cholmod_spzeros.o Utility/cholmod_l_spzeros.o Utility/cholmod_start.o Utility/cholmod_l_start.o Utility/cholmod_transpose.o Utility/cholmod_l_transpose.o Utility/cholmod_transpose_sym.o Utility/cholmod_l_transpose_sym.o Utility/cholmod_transpose_unsym.o Utility/cholmod_l_transpose_unsym.o Utility/cholmod_triplet_to_sparse.o Utility/cholmod_l_triplet_to_sparse.o Utility/cholmod_version.o Utility/cholmod_l_version.o Utility/cholmod_xtype.o Utility/cholmod_l_xtype.o Utility/cholmod_zeros.o Utility/cholmod_l_zeros.o MatrixOps/cholmod_drop.o MatrixOps/cholmod_l_drop.o MatrixOps/cholmod_horzcat.o MatrixOps/cholmod_l_horzcat.o MatrixOps/cholmod_norm.o MatrixOps/cholmod_l_norm.o MatrixOps/cholmod_scale.o MatrixOps/cholmod_l_scale.o MatrixOps/cholmod_sdmult.o MatrixOps/cholmod_l_sdmult.o MatrixOps/cholmod_ssmult.o MatrixOps/cholmod_l_ssmult.o MatrixOps/cholmod_submatrix.o MatrixOps/cholmod_l_submatrix.o MatrixOps/cholmod_symmetry.o MatrixOps/cholmod_l_symmetry.o MatrixOps/cholmod_vertcat.o MatrixOps/cholmod_l_vertcat.o Modify/cholmod_rowadd.o Modify/cholmod_l_rowadd.o Modify/cholmod_rowdel.o Modify/cholmod_l_rowdel.o Modify/cholmod_updown.o Modify/cholmod_l_updown.o Partition/cholmod_camd.o Partition/cholmod_l_camd.o Partition/cholmod_ccolamd.o Partition/cholmod_l_ccolamd.o Partition/cholmod_csymamd.o Partition/cholmod_l_csymamd.o Partition/cholmod_metis.o Partition/cholmod_l_metis.o Partition/cholmod_metis_wrapper.o Partition/cholmod_nesdis.o Partition/cholmod_l_nesdis.o Supernodal/cholmod_super_numeric.o Supernodal/cholmod_l_super_numeric.o Supernodal/cholmod_super_solve.o Supernodal/cholmod_l_super_solve.o Supernodal/cholmod_super_symbolic.o Supernodal/cholmod_l_super_symbolic.o /usr/local/bin/ranlib CHOLMOD.a gmake[4]: Leaving directory '/tmp/RtmpET1FvR/R.INSTALL1737b42b56282/Matrix/src/SuiteSparse/CHOLMOD' cc -shared -L/wrkdirs/usr/ports/math/R/work/R-4.4.3/lib -Wl,-rpath=/usr/local/lib/gcc13 -L/usr/local/lib/gcc13 -L/usr/local/lib -fstack-protector-strong -o Matrix.so Csparse.o attrib.o bind.o cholmod-common.o cholmod-etc.o coerce.o cs-etc.o dense.o determinant.o expm.o factor.o idz.o init.o kappa.o matmult.o objects.o perm.o solve.o sparse.o subassign.o subscript.o utils-R.o utils.o validity.o vector.o SuiteSparse/CHOLMOD/CHOLMOD.a SuiteSparse/CCOLAMD/CCOLAMD.a SuiteSparse/CAMD/CAMD.a SuiteSparse/COLAMD/COLAMD.a SuiteSparse/AMD/AMD.a SuiteSparse/CXSparse/CXSparse.a SuiteSparse/SuiteSparse_config/SuiteSparse_config.a -L/wrkdirs/usr/ports/math/R/work/R-4.4.3/lib -lRlapack -L/wrkdirs/usr/ports/math/R/work/R-4.4.3/lib -lRblas -L/usr/local/lib/gcc13/gcc/x86_64-portbld-freebsd14.2/13.3.0 -L/usr/local/x86_64-portbld-freebsd14.2/lib -lgfortran -lm -lssp_nonshared -lquadmath -L/wrkdirs/usr/ports/math/R/work/R-4.4.3/lib -lR gmake[3]: Leaving directory '/tmp/RtmpET1FvR/R.INSTALL1737b42b56282/Matrix/src' installing to /wrkdirs/usr/ports/math/R/work/R-4.4.3/library/Matrix/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading Creating a generic function for ‘chol2inv’ from ‘base’ in package ‘Matrix’ (from the saved implicit definition) Creating a generic function for ‘chol2inv’ from package ‘base’ in package ‘Matrix’ Creating a generic function for ‘diag’ from package ‘base’ in package ‘Matrix’ Creating a generic function for ‘zapsmall’ from package ‘base’ in package ‘Matrix’ Creating a generic function for ‘drop’ from package ‘base’ in package ‘Matrix’ in method for ‘coerce’ with signature ‘"matrix.csc","dgCMatrix"’: no definition for class “matrix.csc†in method for ‘coerce’ with signature ‘"matrix.csr","dgRMatrix"’: no definition for class “matrix.csr†in method for ‘coerce’ with signature ‘"matrix.coo","dgTMatrix"’: no definition for class “matrix.coo†in method for ‘coerce’ with signature ‘"matrix.csr","dgCMatrix"’: no definition for class “matrix.csr†in method for ‘coerce’ with signature ‘"matrix.coo","dgCMatrix"’: no definition for class “matrix.coo†in method for ‘coerce’ with signature ‘"matrix.csc","CsparseMatrix"’: no definition for class “matrix.csc†in method for ‘coerce’ with signature ‘"matrix.csc","RsparseMatrix"’: no definition for class “matrix.csc†in method for ‘coerce’ with signature ‘"matrix.csc","TsparseMatrix"’: no definition for class “matrix.csc†in method for ‘coerce’ with signature ‘"matrix.csr","CsparseMatrix"’: no definition for class “matrix.csr†in method for ‘coerce’ with signature ‘"matrix.csr","RsparseMatrix"’: no definition for class “matrix.csr†in method for ‘coerce’ with signature ‘"matrix.csr","TsparseMatrix"’: no definition for class “matrix.csr†in method for ‘coerce’ with signature ‘"matrix.coo","CsparseMatrix"’: no definition for class “matrix.coo†in method for ‘coerce’ with signature ‘"matrix.coo","RsparseMatrix"’: no definition for class “matrix.coo†in method for ‘coerce’ with signature ‘"matrix.coo","TsparseMatrix"’: no definition for class “matrix.coo†in method for ‘coerce’ with signature ‘"matrix.csc","sparseMatrix"’: no definition for class “matrix.csc†in method for ‘coerce’ with signature ‘"matrix.csr","sparseMatrix"’: no definition for class “matrix.csr†in method for ‘coerce’ with signature ‘"matrix.coo","sparseMatrix"’: no definition for class “matrix.coo†in method for ‘coerce’ with signature ‘"matrix.csc","Matrix"’: no definition for class “matrix.csc†in method for ‘coerce’ with signature ‘"matrix.csr","Matrix"’: no definition for class “matrix.csr†in method for ‘coerce’ with signature ‘"matrix.coo","Matrix"’: no definition for class “matrix.coo†in method for ‘coerce’ with signature ‘"dgCMatrix","matrix.csc"’: no definition for class “matrix.csc†in method for ‘coerce’ with signature ‘"dgRMatrix","matrix.csr"’: no definition for class “matrix.csr†in method for ‘coerce’ with signature ‘"dgTMatrix","matrix.coo"’: no definition for class “matrix.coo†in method for ‘coerce’ with signature ‘"Matrix","matrix.csc"’: no definition for class “matrix.csc†in method for ‘coerce’ with signature ‘"Matrix","matrix.csr"’: no definition for class “matrix.csr†in method for ‘coerce’ with signature ‘"Matrix","matrix.coo"’: no definition for class “matrix.coo†in method for ‘coerce’ with signature ‘"graphAM","TsparseMatrix"’: no definition for class “graphAM†in method for ‘coerce’ with signature ‘"graphNEL","TsparseMatrix"’: no definition for class “graphNEL†in method for ‘coerce’ with signature ‘"graph","CsparseMatrix"’: no definition for class “graph†in method for ‘coerce’ with signature ‘"graph","RsparseMatrix"’: no definition for class “graph†in method for ‘coerce’ with signature ‘"graph","TsparseMatrix"’: no definition for class “graph†in method for ‘coerce’ with signature ‘"graph","sparseMatrix"’: no definition for class “graph†in method for ‘coerce’ with signature ‘"graph","Matrix"’: no definition for class “graph†in method for ‘coerce’ with signature ‘"TsparseMatrix","graphNEL"’: no definition for class “graphNEL†in method for ‘coerce’ with signature ‘"Matrix","graphNEL"’: no definition for class “graphNEL†in method for ‘coerce’ with signature ‘"Matrix","graph"’: no definition for class “graph†Creating a generic function for ‘colSums’ from package ‘base’ in package ‘Matrix’ Creating a generic function for ‘colMeans’ from package ‘base’ in package ‘Matrix’ Creating a generic function for ‘rowSums’ from package ‘base’ in package ‘Matrix’ Creating a generic function for ‘rowMeans’ from package ‘base’ in package ‘Matrix’ Creating a generic function for ‘diag<-’ from package ‘base’ in package ‘Matrix’ Creating a generic function for ‘unname’ from package ‘base’ in package ‘Matrix’ Creating a generic function for ‘norm’ from package ‘base’ in package ‘Matrix’ Creating a generic function for ‘rcond’ from ‘base’ in package ‘Matrix’ (from the saved implicit definition) Creating a generic function for ‘rcond’ from package ‘base’ in package ‘Matrix’ Creating a generic function for ‘cov2cor’ from package ‘stats’ in package ‘Matrix’ Creating a generic function for ‘qr.Q’ from package ‘base’ in package ‘Matrix’ Creating a generic function for ‘qr.R’ from package ‘base’ in package ‘Matrix’ Creating a generic function for ‘qr.X’ from package ‘base’ in package ‘Matrix’ Creating a generic function for ‘qr.coef’ from package ‘base’ in package ‘Matrix’ Creating a generic function for ‘qr.fitted’ from package ‘base’ in package ‘Matrix’ Creating a generic function for ‘qr.resid’ from package ‘base’ in package ‘Matrix’ Creating a generic function for ‘qr.qty’ from package ‘base’ in package ‘Matrix’ Creating a generic function for ‘qr.qy’ from package ‘base’ in package ‘Matrix’ Creating a generic function for ‘toeplitz’ from ‘stats’ in package ‘Matrix’ (from the saved implicit definition) Creating a generic function for ‘toeplitz’ from package ‘stats’ in package ‘Matrix’ Creating a generic function for ‘which’ from package ‘base’ in package ‘Matrix’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (Matrix) begin installing recommended package survival begin installing recommended package mgcv * installing *source* package ‘survival’ ... ** package ‘survival’ successfully unpacked and MD5 sums checked ** using non-staged installation ** libs using C compiler: ‘FreeBSD clang version 18.1.6 (https://github.com/llvm/llvm-project.git llvmorg-18.1.6-0-g1118c2e05e67)’ gmake[3]: Entering directory '/tmp/RtmpwYJyru/R.INSTALL183d254f32549/survival/src' cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c agexact.c -o agexact.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c agfit4.c -o agfit4.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c agfit5.c -o agfit5.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c agmart.c -o agmart.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c agmart3.c -o agmart3.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c agscore2.c -o agscore2.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c agscore3.c -o agscore3.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c agsurv4.c -o agsurv4.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c agsurv5.c -o agsurv5.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c cdecomp.c -o cdecomp.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c chinv2.c -o chinv2.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c chinv3.c -o chinv3.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c cholesky2.c -o cholesky2.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c cholesky3.c -o cholesky3.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c cholesky5.c -o cholesky5.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c chsolve2.c -o chsolve2.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c chsolve3.c -o chsolve3.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c chsolve5.c -o chsolve5.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c collapse.c -o collapse.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c concordance1.c -o concordance1.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c concordance3.c -o concordance3.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c concordance5.c -o concordance5.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c cox_Rcallback.c -o cox_Rcallback.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c coxcount1.c -o coxcount1.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c coxdetail.c -o coxdetail.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c coxexact.c -o coxexact.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c coxfit5.c -o coxfit5.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c coxfit6.c -o coxfit6.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c coxmart.c -o coxmart.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c coxmart2.c -o coxmart2.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c coxph_wtest.c -o coxph_wtest.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c coxsafe.c -o coxsafe.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c coxscho.c -o coxscho.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c coxscore2.c -o coxscore2.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c coxsurv1.c -o coxsurv1.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c coxsurv2.c -o coxsurv2.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c coxsurv3.c -o coxsurv3.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c coxsurv4.c -o coxsurv4.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c dmatrix.c -o dmatrix.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c doloop.c -o doloop.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c fastkm.c -o fastkm.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c finegray.c -o finegray.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c gchol.c -o gchol.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c init.c -o init.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c multicheck.c -o multicheck.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c norisk.c -o norisk.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c pyears1.c -o pyears1.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c pyears2.c -o pyears2.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c pyears3b.c -o pyears3b.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c pystep.c -o pystep.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c residcsum.c -o residcsum.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c survConcordance.c -o survConcordance.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c survdiff2.c -o survdiff2.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c survfit4.c -o survfit4.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c survfitaj.c -o survfitaj.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c survfitkm.c -o survfitkm.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c survfitresid.c -o survfitresid.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c survpenal.c -o survpenal.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c survreg6.c -o survreg6.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c survreg7.c -o survreg7.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c survregc1.c -o survregc1.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c survregc2.c -o survregc2.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c survsplit.c -o survsplit.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c tmerge.c -o tmerge.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c twoclust.c -o twoclust.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c zph1.c -o zph1.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c zph2.c -o zph2.o cc -shared -L/wrkdirs/usr/ports/math/R/work/R-4.4.3/lib -Wl,-rpath=/usr/local/lib/gcc13 -L/usr/local/lib/gcc13 -L/usr/local/lib -fstack-protector-strong -o survival.so agexact.o agfit4.o agfit5.o agmart.o agmart3.o agscore2.o agscore3.o agsurv4.o agsurv5.o cdecomp.o chinv2.o chinv3.o cholesky2.o cholesky3.o cholesky5.o chsolve2.o chsolve3.o chsolve5.o collapse.o concordance1.o concordance3.o concordance5.o cox_Rcallback.o coxcount1.o coxdetail.o coxexact.o coxfit5.o coxfit6.o coxmart.o coxmart2.o coxph_wtest.o coxsafe.o coxscho.o coxscore2.o coxsurv1.o coxsurv2.o coxsurv3.o coxsurv4.o dmatrix.o doloop.o fastkm.o finegray.o gchol.o init.o multicheck.o norisk.o pyears1.o pyears2.o pyears3b.o pystep.o residcsum.o survConcordance.o survdiff2.o survfit4.o survfitaj.o survfitkm.o survfitresid.o survpenal.o survreg6.o survreg7.o survregc1.o survregc2.o survsplit.o tmerge.o twoclust.o zph1.o zph2.o -L/wrkdirs/usr/ports/math/R/work/R-4.4.3/lib -lR gmake[3]: Leaving directory '/tmp/RtmpwYJyru/R.INSTALL183d254f32549/survival/src' installing to /wrkdirs/usr/ports/math/R/work/R-4.4.3/library/survival/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (survival) begin installing recommended package boot * installing *source* package ‘boot’ ... ** package ‘boot’ successfully unpacked and MD5 sums checked ** using non-staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (boot) * installing *source* package ‘mgcv’ ... ** package ‘mgcv’ successfully unpacked and MD5 sums checked ** using non-staged installation ** libs using C compiler: ‘FreeBSD clang version 18.1.6 (https://github.com/llvm/llvm-project.git llvmorg-18.1.6-0-g1118c2e05e67)’ gmake[3]: Entering directory '/tmp/RtmpiWd58J/R.INSTALL183d41825cae1/mgcv/src' cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c coxph.c -o coxph.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c davies.c -o davies.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c discrete.c -o discrete.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c gdi.c -o gdi.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c init.c -o init.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c magic.c -o magic.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c mat.c -o mat.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c matrix.c -o matrix.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c mgcv.c -o mgcv.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c misc.c -o misc.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c mvn.c -o mvn.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c ncv.c -o ncv.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c qp.c -o qp.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c soap.c -o soap.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c sparse-smooth.c -o sparse-smooth.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c sparse.c -o sparse.o cc -I"/wrkdirs/usr/ports/math/R/work/R-4.4.3/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c tprs.c -o tprs.o cc -shared -L/wrkdirs/usr/ports/math/R/work/R-4.4.3/lib -Wl,-rpath=/usr/local/lib/gcc13 -L/usr/local/lib/gcc13 -L/usr/local/lib -fstack-protector-strong -o mgcv.so coxph.o davies.o discrete.o gdi.o init.o magic.o mat.o matrix.o mgcv.o misc.o mvn.o ncv.o qp.o soap.o sparse-smooth.o sparse.o tprs.o -L/wrkdirs/usr/ports/math/R/work/R-4.4.3/lib -lRlapack -L/wrkdirs/usr/ports/math/R/work/R-4.4.3/lib -lRblas -L/usr/local/lib/gcc13/gcc/x86_64-portbld-freebsd14.2/13.3.0 -L/usr/local/x86_64-portbld-freebsd14.2/lib -lgfortran -lm -lssp_nonshared -lquadmath -fopenmp -L/wrkdirs/usr/ports/math/R/work/R-4.4.3/lib -lR gmake[3]: Leaving directory '/tmp/RtmpiWd58J/R.INSTALL183d41825cae1/mgcv/src' installing to /wrkdirs/usr/ports/math/R/work/R-4.4.3/library/mgcv/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (mgcv) gmake[2]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/Recommended' gmake[1]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/src/library/Recommended' =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> R-4.4.3 depends on executable: cmake - not found ===> Installing existing package /packages/All/cmake-core-3.31.6.pkg [142amd64-current-job-04] Installing cmake-core-3.31.6... [142amd64-current-job-04] `-- Installing jsoncpp-1.9.6_1... [142amd64-current-job-04] `-- Extracting jsoncpp-1.9.6_1: .......... done [142amd64-current-job-04] `-- Installing libuv-1.50.0... [142amd64-current-job-04] `-- Extracting libuv-1.50.0: .......... done [142amd64-current-job-04] `-- Installing rhash-1.4.4_1... [142amd64-current-job-04] `-- Extracting rhash-1.4.4_1: .......... done [142amd64-current-job-04] Extracting cmake-core-3.31.6: .......... done ===> R-4.4.3 depends on executable: cmake - found ===> Returning to build of R-4.4.3 ===> R-4.4.3 depends on executable: gmake - found ===> R-4.4.3 depends on executable: gfortran13 - found ===> R-4.4.3 depends on package: ghostscript10>=10.02.0 - found ===> R-4.4.3 depends on file: /usr/local/libdata/pkgconfig/ice.pc - found ===> R-4.4.3 depends on file: /usr/local/libdata/pkgconfig/sm.pc - found ===> R-4.4.3 depends on file: /usr/local/libdata/pkgconfig/x11.pc - found ===> R-4.4.3 depends on file: /usr/local/libdata/pkgconfig/xext.pc - found ===> R-4.4.3 depends on file: /usr/local/libdata/pkgconfig/xmu.pc - found ===> R-4.4.3 depends on file: /usr/local/libdata/pkgconfig/xscrnsaver.pc - found ===> R-4.4.3 depends on file: /usr/local/libdata/pkgconfig/xt.pc - found ===> R-4.4.3 depends on executable: indexinfo - found =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for R-4.4.3 ===> Generating temporary packing list mkdir /wrkdirs/usr/ports/math/R/work/stage/usr/local/lib/R gmake[1]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/m4' gmake[1]: Nothing to be done for 'install-strip'. gmake[1]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/m4' gmake[1]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/tools' gmake[1]: Nothing to be done for 'install-strip'. gmake[1]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/tools' gmake[1]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc' installing doc ... mkdir /wrkdirs/usr/ports/math/R/work/stage/usr/local/share/doc/R gmake[2]: Entering directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/html' installing doc/html ... mkdir 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(/usr/local/share/texmf-dist/tex/latex/inconsolata/t1zi4.fd) (/usr/local/share/texmf-dist/tex/latex/amsfonts/umsa.fd) (/usr/local/share/texmf-dist/tex/latex/amsfonts/umsb.fd) (/usr/local/share/texmf-dist/tex/latex/jknapltx/ursfs.fd) [3{/usr/local/share/texmf-dist/fonts/enc/dvips/inconsolata/i4-t1-0.enc}] [4] Underfull \hbox (badness 6252) in paragraph at lines 149--157 []\T1/ptm/m/n/10 a small pos-i-tive floating-point num-ber []\T1/zi4/m/n/10 x [ ]\T1/ptm/m/n/10 such that []\T1/zi4/m/n/10 1 - x != 1[]\T1/ptm/m/n/10 . It Underfull \hbox (badness 10000) in paragraph at lines 149--157 \T1/ptm/m/n/10 equals []\T1/zi4/m/n/10 double.base ^ double.neg.ulp.digits []\T 1/ptm/m/n/10 if []\T1/zi4/m/n/10 double.base Underfull \hbox (badness 10000) in paragraph at lines 149--157 []\T1/ptm/m/n/10 is 2 or []\T1/zi4/m/n/10 double.rounding []\T1/ptm/m/n/10 is 0 ; oth-er-wise, it is []\T1/zi4/m/n/10 (double.base Underfull \hbox (badness 10000) in paragraph at lines 149--157 \T1/zi4/m/n/10 ^ double.neg.ulp.digits) / 2[]\T1/ptm/m/n/10 . Nor-mally []\T1/z i4/m/n/10 1.110223e-16[]\T1/ptm/m/n/10 . As Underfull \hbox (badness 4995) in paragraph at lines 149--157 []\T1/zi4/m/n/10 double.neg.ulp.digits []\T1/ptm/m/n/10 is bounded be-low by [] \T1/zi4/m/n/10 -(double.digits + 3)[]\T1/ptm/m/n/10 , [5] [6] [7] Underfull \hbox (badness 1178) in paragraph at lines 337--340 []\T1/ptm/m/n/10 character string, the pre-ferred set-ting for [][][]\T1/zi4/m/ n/10 options[][][]("pkgType")[]\T1/ptm/m/n/10 . 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This reads the [122] Underfull \hbox (badness 2261) in paragraph at lines 7741--7746 \T1/zi4/m/n/10 / / github . com / astrand / xclip$[][]\T1/ptm/m/n/10 ) or []\T1 /zi4/m/n/10 xsel []\T1/ptm/m/n/10 ([][]$\T1/zi4/m/n/10 https : / / www . vergen et . net / ~conrad / software / [123] [124] Underfull \vbox (badness 10000) has occurred while \output is active [125] [126] [127] [128] [129] [130] [131] [132] [133] Underfull \hbox (badness 2096) in paragraph at lines 8474--8478 \T1/zi4/m/n/10 status _ codes$[][] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / List _ of _ FTP _ server _ return _ codes$ [][]\T1/ptm/m/n/10 . [134] [135] Underfull \hbox (badness 2351) in paragraph at lines 8589--8592 [][][]\T1/zi4/m/n/10 split[][][] []\T1/ptm/m/n/10 for split-ting a vari-able ac -cord-ing to a group fac-tor; [][][]\T1/zi4/m/n/10 factor[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 tabulate[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 t able[][][][]\T1/ptm/m/n/10 , [136] [137] [138] [139] [140] Underfull \hbox (badness 4479) in paragraph at lines 8906--8917 [][][]\T1/zi4/m/n/10 I[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 plot.data.f rame[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 print.data.frame[][][][]\T1/p tm/m/n/10 , [][][]\T1/zi4/m/n/10 row.names[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi 4/m/n/10 names[][][] []\T1/ptm/m/n/10 (for the col-umn names), [141] [142] [143] [144] [145] [146] Underfull \hbox (badness 1629) in paragraph at lines 9334--9346 []\T1/ptm/m/n/10 A few times have spe-cific is-sues. First, the leap sec-onds a re ig-nored, and real times Underfull \hbox (badness 2875) in paragraph at lines 9334--9346 []\T1/zi4/m/n/10 NA[]\T1/ptm/m/n/10 , and hence []\T1/zi4/m/n/10 as.POSIXct("19 69-12-31 23:59:59", tz = "UTC") []\T1/ptm/m/n/10 will give []\T1/zi4/m/n/10 "19 69-12-31 [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157] [158] [159] Underfull \hbox (badness 1178) in paragraph at lines 10200--10204 []\T1/ptm/m/n/10 If true, [][][]\T1/zi4/m/n/10 list[][][][]\T1/ptm/m/n/10 s and atomic vec-tors with non-[][][]\T1/zi4/m/n/10 NA[][][] []\T1/ptm/m/n/10 names (see [][][]\T1/zi4/m/n/10 names[][][][]\T1/ptm/m/n/10 ) are de- [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] [183] [184] [185] [186] [187] [188] [189] [190] [191] [192] [193] [194] [195] Underfull \hbox (badness 2744) in paragraph at lines 12540--12542 []\T1/ptm/m/n/10 Changing the cur-rent en-cod-ing from a run-ning R ses-sion ma y lead to con-fu-sion (see [196] [197] [198] [199] [200] [201] [202] [203] Underfull \vbox (badness 10000) has occurred while \output is active [204] [205] [206] [207] [208] [209] [210] [211] [212] [213] [214] [215] [216] [217] [218] [219] [220] [221] [222] [223] [224] [225] [226] [227] [228] Underfull \hbox (badness 2253) in paragraph at lines 14746--14748 []\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is done: see Underfull \hbox (badness 1490) in paragraph at lines 14781--14784 []\T1/ptm/m/n/10 Junction points and sym-bolic links are fol-lowed, so in-for-m a-tion is given about the [229] Underfull \hbox (badness 1565) in paragraph at lines 14863--14867 [][][]\T1/zi4/m/n/10 Sys.readlink[][][] []\T1/ptm/m/n/10 to find out about sym- bolic links, [][][]\T1/zi4/m/n/10 files[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m /n/10 file.access[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 list.files[][][] []\T1/ptm/m/n/10 , and [230] Underfull \hbox (badness 4927) in paragraph at lines 14914--14916 []\T1/ptm/m/n/10 It can also be used for en-vi-ron-ment paths such as []\T1/zi4 /m/n/10 PATH []\T1/ptm/m/n/10 and []\T1/zi4/m/n/10 R_LIBS []\T1/ptm/m/n/10 with []\T1/zi4/m/n/10 fsep = [231] [232] [233] Underfull \hbox (badness 1466) in paragraph at lines 15065--15068 []\T1/ptm/m/n/10 character vec-tors, con-tain-ing file names or paths. For []\T 1/zi4/m/n/10 file.copy []\T1/ptm/m/n/10 and [234] Underfull \hbox (badness 10000) in paragraph at lines 15196--15200 [][][]\T1/zi4/m/n/10 file.info[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 fil e.access[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 file.path[][][][]\T1/ptm/ m/n/10 , [][][]\T1/zi4/m/n/10 file.show[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m /n/10 list.files[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 unlink[][][][]\T1 /ptm/m/n/10 , [][][]\T1/zi4/m/n/10 basename[][][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 15207--15210 [][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][ ] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wik i / [235] [236] [237] [238] [239] Underfull \hbox (badness 3965) in paragraph at lines 15504--15508 []\T1/ptm/m/n/10 This is the same com-pu-ta-tion as for the em-pir-i-cal dis-tr i-bu-tion func-tion, and in-deed, [240] [241] [242] [243] [244] [245] [246] [247] Underfull \hbox (badness 5260) in paragraph at lines 16006--16006 []\T1/zi4/m/n/10 big.mark[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 big.interval[]\T1/ ptm/m/n/10 , []\T1/zi4/m/n/10 small.mark[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 sma ll.interval[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 decimal.mark[]\T1/ptm/m/n/10 , [248] [249] [250] [251] Underfull \hbox (badness 4429) in paragraph at lines 16296--16299 []\T1/ptm/m/n/10 an atomic nu-mer-i-cal or char-ac-ter ob-ject, pos-si-bly [][] []\T1/zi4/m/n/10 complex[][][] []\T1/ptm/m/n/10 only for [252] [253] Underfull \hbox (badness 10000) in paragraph at lines 16403--16405 []\T1/ptm/m/n/10 This works via []\T1/zi4/m/n/10 prettyNum()[]\T1/ptm/m/n/10 , which calls []\T1/zi4/m/n/10 .format.zeros(*, [254] Underfull \hbox (badness 2035) in paragraph at lines 16476--16480 []\T1/ptm/m/n/10 The de-fault for []\T1/zi4/m/n/10 decimal.mark []\T1/ptm/m/n/1 0 in []\T1/zi4/m/n/10 formatC() []\T1/ptm/m/n/10 was changed in \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.2.0: for use within [255] Underfull \vbox (badness 10000) has occurred while \output is active [256] [257] [258] [259] [260] [261] [262] [263] [264] Underfull \hbox (badness 2452) in paragraph at lines 17099--17103 []\T1/zi4/m/n/10 gctorture2 []\T1/ptm/m/n/10 can also be in-voked via en-vi-ron -ment vari-ables at the start of the \T1/phv/m/n/10 R \T1/ptm/m/n/10 ses- Underfull \hbox (badness 1147) in paragraph at lines 17099--17103 \T1/ptm/m/n/10 sion. []\T1/zi4/m/n/10 R_GCTORTURE []\T1/ptm/m/n/10 cor-re-spond s to the []\T1/zi4/m/n/10 step []\T1/ptm/m/n/10 ar-gu-ment, []\T1/zi4/m/n/10 R_ GCTORTURE_WAIT []\T1/ptm/m/n/10 to []\T1/zi4/m/n/10 wait[]\T1/ptm/m/n/10 , and [265] [266] [267] Underfull \hbox (badness 1092) in paragraph at lines 17273--17278 [][][]\T1/zi4/m/n/10 library.dynam[][][][]\T1/ptm/m/n/10 , or can be found af-t er the DLL has been loaded us-ing [268] [269] [270] Underfull \hbox (badness 6741) in paragraph at lines 17526--17530 \T1/ptm/m/n/10 Additionally, the list will have an ad-di-tional class, be-ing [ ]\T1/zi4/m/n/10 CRoutine[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 CallRoutine[]\T1/pt m/m/n/10 , [271] [272] [273] [274] [275] [276] [277] [278] [279] [280] [281] Underfull \vbox (badness 3803) has occurred while \output is active [282] Underfull \vbox (badness 10000) has occurred while \output is active [283] [284] [285] [286] [287] [288] [289] [290] [291] [292] Underfull \hbox (badness 1769) in paragraph at lines 18999--19002 []\T1/ptm/m/n/10 a char-ac-ter vec-tor, or an ob-ject to be con-verted to a cha r-ac-ter vec-tor [293] [294] [295] [296] [297] Underfull \hbox (badness 10000) in paragraph at lines 19308--19310 []\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/zi4/m/n/10 https : / / ww w . unicode . org / reports / tr35 / Underfull \hbox (badness 2088) in paragraph at lines 19314--19323 []\T1/ptm/m/n/10 For the spec-i-fi-ca-tions of `real' ICU lo-cales, see [][]$\T 1/zi4/m/n/10 https : / / unicode-[]org . github . io / icu / [298] [299] [300] [301] [302] [303] [304] [305] [306] [307] Underfull \hbox (badness 1442) in paragraph at lines 19922--19924 []\T1/ptm/m/n/10 the choice of de-fault graph-ics de-vice launched when needed and by [][][]\T1/zi4/m/n/10 dev.new[][][][]\T1/ptm/m/n/10 : see [308] Underfull \hbox (badness 2452) in paragraph at lines 20018--20044 [][][]\T1/zi4/m/n/10 as.character[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 as.complex[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 as.double[][][][]\T1/pt m/m/n/10 , [][][]\T1/zi4/m/n/10 as.integer[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi 4/m/n/10 as.logical[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 as.raw[][][][] \T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 as.vector[][][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 5726) in paragraph at lines 20018--20044 [][][]\T1/zi4/m/n/10 as.call[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 as.en vironment[][][] [][]is.array[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 is.ma trix[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 is.na[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 anyNA[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 is.nan [][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 is.finite[][][] [309] [310] [311] [312] [313] [314] Underfull \hbox (badness 1248) in paragraph at lines 20416--20419 []\T1/zi4/m/n/10 is.atomic []\T1/ptm/m/n/10 is true for the [][]atomic[][][] ty pes ([]\T1/zi4/m/n/10 "logical"[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 "integer"[]\ T1/ptm/m/n/10 , []\T1/zi4/m/n/10 "numeric"[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 " complex"[]\T1/ptm/m/n/10 , [315] [316] [317] [318] [319] Underfull \hbox (badness 4739) in paragraph at lines 20683--20685 []\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere d, see [320] [321] [322] [323] [324] Underfull \vbox (badness 10000) has occurred while \output is active [325] [326] [327] [328] [329] [330] [331] [332] [333] [334] [335] [336] [337] [338] Underfull \hbox (badness 2469) in paragraph at lines 21851--21856 []\T1/ptm/m/n/10 In late 2017 a []\T1/zi4/m/n/10 libcurl []\T1/ptm/m/n/10 in-st al-la-tion was seen di-vided into two li-braries, []\T1/zi4/m/n/10 libcurl []\T 1/ptm/m/n/10 and [339] Underfull \hbox (badness 1675) in paragraph at lines 21938--21947 []\T1/ptm/m/n/10 At startup, the li-brary search path is ini-tial-ized from the en-vi-ron-ment vari-ables []\T1/zi4/m/n/10 R_LIBS[]\T1/ptm/m/n/10 , Underfull \hbox (badness 3189) in paragraph at lines 21948--21961 []\T1/ptm/m/n/10 First, []\T1/zi4/m/n/10 .Library.site []\T1/ptm/m/n/10 is ini- tial-ized from []\T1/zi4/m/n/10 R_LIBS_SITE[]\T1/ptm/m/n/10 . If this is un-set or empty, the [340] Underfull \hbox (badness 10000) in paragraph at lines 21996--21999 []\T1/zi4/m/n/10 LOCALAPPDATA []\T1/ptm/m/n/10 (usu-ally []\T1/zi4/m/n/10 C:\Us ers\username\AppData\Local[]\T1/ptm/m/n/10 ) on Win-dows is a hid- Underfull \hbox (badness 4752) in paragraph at lines 21996--21999 \T1/ptm/m/n/10 den di-rec-tory and may not be viewed by some soft-ware. It may be opened by [341] [342] Underfull \hbox (badness 1014) in paragraph at lines 22130--22135 []\T1/ptm/m/n/10 Normally []\T1/zi4/m/n/10 library []\T1/ptm/m/n/10 re-turns (i n-vis-i-bly) the list of at-tached pack-ages, but []\T1/zi4/m/n/10 TRUE []\T1/p tm/m/n/10 or []\T1/zi4/m/n/10 FALSE []\T1/ptm/m/n/10 if [343] [344] [345] [346] [347] [348] [349] [350] [351] [352] [353] [354] [355] Underfull \hbox (badness 1264) in paragraph at lines 22977--22985 []\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways be sup-ported: Underfull \hbox (badness 4441) in paragraph at lines 23012--23015 []\T1/ptm/m/n/10 Note that set-ting cat-e-gory []\T1/zi4/m/n/10 "LC_ALL" []\T1/ ptm/m/n/10 sets only cat-e-gories []\T1/zi4/m/n/10 "LC_COLLATE"[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 "LC_CTYPE"[]\T1/ptm/m/n/10 , [356] [357] [358] [359] [360] [361] [362] [363] [364] [365] [366] [367] [368] Underfull \hbox (badness 5231) in paragraph at lines 23830--23832 []\T1/ptm/m/n/10 The al-go-rithm used by []\T1/zi4/m/n/10 make.unique []\T1/ptm /m/n/10 has the prop-erty that []\T1/zi4/m/n/10 make.unique(c(A, B)) == [369] [370] [371] [372] [373] [374] [375] [376] [377] [378] [379] [380] [381] [382] [383] [384] [385] Underfull \hbox (badness 6380) in paragraph at lines 24940--24946 [][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Data _ compress ion$[][] \T1/ptm/m/n/10 for back-ground on data com-pres- Underfull \hbox (badness 1472) in paragraph at lines 24940--24946 [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Bzip2$[][]\T1/ptm /m/n/10 , and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / XZ _ Utils$[][] [386] [387] [388] [389] [390] [391] [392] [393] [394] Underfull \hbox (badness 2790) in paragraph at lines 25453--25456 []\T1/zi4/m/n/10 packageStartupMessage []\T1/ptm/m/n/10 is a vari-ant whose mes -sages can be sup-pressed sep-a-rately by Underfull \hbox (badness 1571) in paragraph at lines 25453--25456 []\T1/zi4/m/n/10 suppressPackageStartupMessages[]\T1/ptm/m/n/10 . (They are sti ll mes-sages, so can be sup-pressed by [395] [396] [397] [398] [399] Underfull \hbox (badness 1194) in paragraph at lines 25781--25784 []\T1/ptm/m/n/10 The de-fault method for []\T1/zi4/m/n/10 anyNA []\T1/ptm/m/n/1 0 han-dles atomic vec-tors with-out a class and []\T1/zi4/m/n/10 NULL[]\T1/ptm/ m/n/10 . It calls [400] [401] [402] Underfull \hbox (badness 2368) in paragraph at lines 25988--25994 []\T1/ptm/m/n/10 For an [][][]\T1/zi4/m/n/10 environment[][][] env[]\T1/ptm/m/n /10 , []\T1/zi4/m/n/10 names(env) []\T1/ptm/m/n/10 gives the names of the cor-r e-spond-ing list, i.e., [403] [404] [405] [406] [407] [408] Underfull \hbox (badness 10000) in paragraph at lines 26378--26381 []\T1/ptm/m/n/10 optional [][][]\T1/zi4/m/n/10 logical[][][] []\T1/ptm/m/n/10 e ven-tu-ally to be passed to []\T1/zi4/m/n/10 print()[]\T1/ptm/m/n/10 , used by [409] [410] [411] [412] [413] [414] [415] [416] [417] [418] Underfull \hbox (badness 10000) in paragraph at lines 27006--27008 []\T1/zi4/m/n/10 isNamespaceLoaded(pkg) []\T1/ptm/m/n/10 is equiv-a-lent to but more ef-fi-cient than []\T1/zi4/m/n/10 pkg %in% [419] [420] [421] [422] [423] [424] [425] Underfull \hbox (badness 2443) in paragraph at lines 27497--27505 \T1/ptm/m/n/10 suit-able char-ac-ter vec-tors as above, or nu-meric ver-sion ob -jects. For [426] [427] [428] [429] [430] [431] [432] Underfull \hbox (badness 1881) in paragraph at lines 27927--27930 []\T1/ptm/m/n/10 integer value con-trol-ling the print-ing of lan-guage con-str ucts which are Underfull \hbox (badness 6220) in paragraph at lines 27952--27954 []\T1/ptm/m/n/10 Extra command-line ar-gu-ment(s) for non-default meth-ods: see [433] [434] Underfull \hbox (badness 2142) in paragraph at lines 28093--28097 []\T1/ptm/m/n/10 the de-fault pa-per for-mat used by [][][]\T1/zi4/m/n/10 posts cript[][][][]\T1/ptm/m/n/10 ; set by en-vi-ron-ment vari-able Underfull \hbox (badness 1968) in paragraph at lines 28150--28155 []\T1/ptm/m/n/10 the com-mand used by [][][]\T1/zi4/m/n/10 postscript[][][] []\ T1/ptm/m/n/10 for print-ing; set by en-vi-ron-ment vari-able [435] [436] [437] [438] Underfull \hbox (badness 10000) in paragraph at lines 28446--28452 []\T1/ptm/m/n/10 The URL of a Bio-con-duc-tor mir-ror for use by [][][]\T1/zi4/ m/n/10 setRepositories[][][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 28446--28452 \T1/ptm/m/n/10 e.g. the de-fault `[]\T1/zi4/m/n/10 "https://bioconductor.org"[] \T1/ptm/m/n/10 ' or the Eu-ro-pean mir-ror Underfull \hbox (badness 10000) in paragraph at lines 28446--28452 \T1/ptm/m/n/10 `[]\T1/zi4/m/n/10 "https://bioconductor.statistik.tu-dortmund.de "[]\T1/ptm/m/n/10 '. Can be set by Underfull \hbox (badness 5878) in paragraph at lines 28459--28462 []\T1/ptm/m/n/10 default Cc: ad-dress used by [][][]\T1/zi4/m/n/10 create.post[ ][][] []\T1/ptm/m/n/10 (and hence [][][]\T1/zi4/m/n/10 bug.report[][][] []\T1/p tm/m/n/10 and Underfull \hbox (badness 2689) in paragraph at lines 28485--28487 []\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na l HTTP server, see Underfull \hbox (badness 10000) in paragraph at lines 28531--28536 []\T1/ptm/m/n/10 Used by [][][]\T1/zi4/m/n/10 install.packages[][][] []\T1/ptm/ m/n/10 (and in-di-rectly [439] Underfull \hbox (badness 2529) in paragraph at lines 28537--28548 \T1/ptm/m/n/10 in-di-rectly [][][]\T1/zi4/m/n/10 update.packages[][][][]\T1/ptm /m/n/10 ) on plat-forms which sup-port bi-nary pack-ages. Pos-si- Underfull \hbox (badness 2512) in paragraph at lines 28537--28548 \T1/ptm/m/n/10 ble val-ues are []\T1/zi4/m/n/10 "never"[]\T1/ptm/m/n/10 , []\T1 /zi4/m/n/10 "interactive" []\T1/ptm/m/n/10 (which means ask in in-ter-ac-tive u se and Underfull \hbox (badness 7203) in paragraph at lines 28549--28552 []\T1/ptm/m/n/10 default email-ing method used by [][][]\T1/zi4/m/n/10 create.p ost[][][] []\T1/ptm/m/n/10 and hence [][][]\T1/zi4/m/n/10 bug.report[][][] []\T 1/ptm/m/n/10 and [440] [441] [442] [443] [444] Underfull \vbox (badness 10000) has occurred while \output is active [445] Underfull \hbox (badness 10000) in paragraph at lines 28967--28971 \T1/ptm/m/n/10 el-e-ment []\T1/zi4/m/n/10 A[c(arrayindex.x, arrayindex.y)] = FU N(X[arrayindex.x], Y[arrayindex.y], [446] [447] Underfull \hbox (badness 10000) in paragraph at lines 29114--29117 []\T1/zi4/m/n/10 str2expression(s) []\T1/ptm/m/n/10 and []\T1/zi4/m/n/10 str2la ng(s) []\T1/ptm/m/n/10 re-turn spe-cial ver-sions of []\T1/zi4/m/n/10 parse(tex t=s, [448] Underfull \hbox (badness 7925) in paragraph at lines 29195--29199 []\T1/ptm/m/n/10 for a [][][]\T1/zi4/m/n/10 character[][][] []\T1/ptm/m/n/10 ve c-tor []\T1/zi4/m/n/10 s[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 str2expression(s) [ ]\T1/ptm/m/n/10 cor-re-sponds to Underfull \hbox (badness 1253) in paragraph at lines 29195--29199 [][][]\T1/zi4/m/n/10 parse[][][](text = s, keep.source=FALSE)[]\T1/ptm/m/n/10 , which is al-ways of type ([][][]\T1/zi4/m/n/10 typeof[][][][]\T1/ptm/m/n/10 ) and [][][]\T1/zi4/m/n/10 class[][][] Underfull \hbox (badness 2521) in paragraph at lines 29200--29209 []\T1/ptm/m/n/10 for a [][][]\T1/zi4/m/n/10 character[][][] []\T1/ptm/m/n/10 st ring []\T1/zi4/m/n/10 s[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 str2lang(s) []\T1/pt m/m/n/10 cor-re-sponds to [][][]\T1/zi4/m/n/10 parse[][][](text = s, [449] [450] [451] [452] [453] [454] [455] [456] [457] [458] [459] [460] [461] [462] [463] [464] Underfull \hbox (badness 2726) in paragraph at lines 30214--30217 []\T1/ptm/m/n/10 character string (or []\T1/zi4/m/n/10 NULL[]\T1/ptm/m/n/10 ) i n-di-cat-ing [][][]\T1/zi4/m/n/10 NA[][][] []\T1/ptm/m/n/10 val-ues in printed out-put, see [465] [466] [467] [468] [469] [470] [471] [472] [473] [474] [475] [476] [477] [478] [479] [480] [481] [482] [483] Underfull \vbox (badness 3803) has occurred while \output is active [484] [485] [486] [487] [488] [489] [490] [491] [492] Underfull \hbox (badness 1533) in paragraph at lines 32024--32027 []\T1/ptm/m/n/10 As with all com-piled code, mis-specifying these func-tions ca n crash \T1/phv/m/n/10 R\T1/ptm/m/n/10 . Do in-clude the [493] [494] [495] Underfull \hbox (badness 1163) in paragraph at lines 32195--32206 []\T1/ptm/m/n/10 If all com-po-nents are dif-fer-ent (and no []\T1/zi4/m/n/10 N A[]\T1/ptm/m/n/10 s), the ranks are well de-fined, with val-ues in [496] [497] [498] [499] [500] [501] [502] Underfull \vbox (badness 3803) has occurred while \output is active [503] [504] Underfull \hbox (badness 6300) in paragraph at lines 32741--32743 []\T1/ptm/m/n/10 The sec-tion `Pro-cess-ing doc-u-men-ta-tion files' in the `Wr it-ing R Ex-ten-sions' man-ual: [505] [506] [507] [508] [509] [510] [511] [512] [513] [514] [515] [516] [517] [518] [519] [520] [521] Underfull \hbox (badness 10000) in paragraph at lines 33864--33868 []\T1/zi4/m/n/10 regexpr []\T1/ptm/m/n/10 and []\T1/zi4/m/n/10 gregexpr []\T1/p tm/m/n/10 sup-port `named cap-ture'. If groups are named, e.g., Underfull \hbox (badness 1221) in paragraph at lines 33864--33868 []\T1/zi4/m/n/10 "(?[A-Z][a-z]+)" []\T1/ptm/m/n/10 then the po-si-tions of the matches are also re-turned by name. Underfull \hbox (badness 3557) in paragraph at lines 33885--33887 []\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/zi4/m/n/10 https : / / pubs . opengroup . org / onlinepubs / 9699919799 / Underfull \hbox (badness 1122) in paragraph at lines 33888--33892 []\T1/ptm/m/n/10 The []\T1/zi4/m/n/10 pcre2pattern []\T1/ptm/m/n/10 or []\T1/zi 4/m/n/10 pcrepattern man []\T1/ptm/m/n/10 page (found as part of [][]$\T1/zi4/m /n/10 https : / / www . pcre . org / [522] [523] Underfull \vbox (badness 10000) has occurred while \output is active [524] [525] [526] [527] [528] [529] [530] [531] Underfull \hbox (badness 1655) in paragraph at lines 34490--34492 []\T1/ptm/m/n/10 a vec-tor (atomic, not a list) for []\T1/zi4/m/n/10 rle()[]\T1 /ptm/m/n/10 ; an ob-ject of class []\T1/zi4/m/n/10 "rle" []\T1/ptm/m/n/10 for [532] [533] [534] [535] [536] [537] [538] [539] [540] [541] [542] [543] [544] [545] [546] [547] [548] [549] [550] Underfull \hbox (badness 2261) in paragraph at lines 35693--35698 []\T1/ptm/m/n/10 If []\T1/zi4/m/n/10 strip.white []\T1/ptm/m/n/10 is of length 1, it ap-plies to all fields; oth-er-wise, if [551] [552] [553] [554] [555] [556] [557] [558] [559] [560] [561] [562] [563] [564] [565] [566] Underfull \hbox (badness 3668) in paragraph at lines 36728--36732 []\T1/zi4/m/n/10 getAllConnections []\T1/ptm/m/n/10 re-turns a se-quence of in- te-ger con-nec-tion de-scrip-tors for use with [567] Underfull \hbox (badness 10000) in paragraph at lines 36819--36830 \T1/zi4/m/n/10 / / learn . microsoft . com / en-[]us / cpp / c-[]language / par sing-[]c-[]command-[]line-[]arguments ? [568] [569] [570] [571] [572] [573] [574] [575] [576] [577] [578] [579] [580] [581] [582] [583] [584] [585] [586] [587] [588] [589] [590] [591] [592] Underfull \hbox (badness 10000) in paragraph at lines 38451--38453 [][][]$\T1/zi4/m/n/10 https : / / pubs . opengroup . org / onlinepubs / 9699919 799 / functions / snprintf . html$[][] \T1/ptm/m/n/10 for [593] [594] [595] [596] [597] [598] [599] Underfull \hbox (badness 2913) in paragraph at lines 38869--38873 \T1/ptm/m/n/10 ber of nested \T1/phv/m/n/10 R \T1/ptm/m/n/10 ex-pres-sions cur- rently un-der eval-u-a-tion, ex-ceeds the limit set by [600] [601] [602] Underfull \hbox (badness 1072) in paragraph at lines 39115--39119 []\T1/ptm/m/n/10 On front-ends which sup-port it, the com-mands his-tory is rea d from the file spec-i-fied by [603] Underfull \hbox (badness 10000) in paragraph at lines 39120--39124 []\T1/ptm/m/n/10 The command-line op-tion `[]\T1/zi4/m/n/10 --vanilla[]\T1/ptm/ m/n/10 ' im-plies `[]\T1/zi4/m/n/10 --no-site-file[]\T1/ptm/m/n/10 ', `[]\T1/zi 4/m/n/10 --no-init-file[]\T1/ptm/m/n/10 ', Underfull \hbox (badness 10000) in paragraph at lines 39160--39166 []\T1/ptm/m/n/10 On sys-tems with sub-architectures (mainly Win-dows), the file s `\T1/zi4/m/n/10 Renviron.site\T1/ptm/m/n/10 ' Underfull \hbox (badness 10000) in paragraph at lines 39160--39166 \T1/ptm/m/n/10 and `\T1/zi4/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' are looked for first in architecture-specific di-rec-to-ries, Underfull \hbox (badness 1320) in paragraph at lines 39160--39166 \T1/ptm/m/n/10 e.g. `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/zi4/m/n/10 /etc/i386/R environ.site\T1/ptm/m/n/10 '. And e.g. `\T1/zi4/m/n/10 .Renviron.i386\T1/ptm/m/ n/10 ' will be used in Underfull \hbox (badness 3009) in paragraph at lines 39175--39182 []\T1/ptm/m/n/10 On Unix ver-sions of \T1/phv/m/n/10 R \T1/ptm/m/n/10 there is also a file `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/zi4/m/n/10 /etc/Renviron\T1/pt m/m/n/10 ' which is read Underfull \hbox (badness 1038) in paragraph at lines 39175--39182 \T1/ptm/m/n/10 very early in the start-up pro-cess-ing. It con-tains en-vi-ron- ment vari-ables set by \T1/phv/m/n/10 R \T1/ptm/m/n/10 in the Underfull \hbox (badness 2573) in paragraph at lines 39175--39182 \T1/ptm/m/n/10 con-fig-ure pro-cess. Val-ues in that file can be over-rid-den i n site or user en-vi-ron-ment Underfull \hbox (badness 1917) in paragraph at lines 39175--39182 \T1/ptm/m/n/10 files: do not change `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/zi4/m/ n/10 /etc/Renviron\T1/ptm/m/n/10 ' it-self. Note that this is dis-tinct from [604] [605] [606] [607] Underfull \hbox (badness 2644) in paragraph at lines 39410--39414 []\T1/ptm/m/n/10 alternative to []\T1/zi4/m/n/10 exprs []\T1/ptm/m/n/10 or []\T 1/zi4/m/n/10 ...[]\T1/ptm/m/n/10 : an `expression-like' ob-ject, typ-i-cally an [608] [609] [610] Underfull \hbox (badness 1389) in paragraph at lines 39573--39580 []\T1/ptm/m/n/10 a char-ac-ter string. The de-fault for the []\T1/zi4/m/n/10 fo rmat []\T1/ptm/m/n/10 meth-ods is []\T1/zi4/m/n/10 "%Y-%m-%d [611] [612] [613] [614] [615] [616] [617] [618] [619] [620] [621] [622] [623] [624] [625] [626] [627] [628] [629] [630] [631] Underfull \hbox (badness 1158) in paragraph at lines 40939--40941 []\T1/ptm/m/n/10 integer code used in []\T1/zi4/m/n/10 quantile(*, type=quantil e.type) []\T1/ptm/m/n/10 for the de-fault [632] [633] [634] [635] [636] [637] [638] [639] [640] [641] Underfull \hbox (badness 1137) in paragraph at lines 41539--41545 []\T1/ptm/m/n/10 This ex-pands tilde (see [][]tilde ex-pan-sion[][][]) and wild -cards in file paths. For pre-cise de-tails Underfull \hbox (badness 4967) in paragraph at lines 41557--41562 []\T1/ptm/m/n/10 If a file-name starts with []\T1/zi4/m/n/10 . []\T1/ptm/m/n/10 this may need to be matched ex-plic-itly: for ex-am-ple [642] [643] Underfull \hbox (badness 1616) in paragraph at lines 41677--41682 []\T1/zi4/m/n/10 system("id") []\T1/ptm/m/n/10 is much more portable on Unix-al ikes, pro-vided only the POSIX op-tions [644] [645] [646] [647] Underfull \vbox (badness 3803) has occurred while \output is active [648] [649] [650] [651] [652] Underfull \hbox (badness 1472) in paragraph at lines 42224--42227 []\T1/ptm/m/n/10 logical. If []\T1/zi4/m/n/10 TRUE[]\T1/ptm/m/n/10 , func-tions keep their source in-clud-ing com-ments, see [653] [654] [655] LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/n' instead on input line 42436. [656] [657] [658] [659] [660] [661] [662] [663] [664] [665] [666] [667] Underfull \hbox (badness 10000) in paragraph at lines 43175--43179 []\T1/ptm/m/n/10 On 64-bit plat-forms []\T1/zi4/m/sl/10 bin []\T1/ptm/m/n/10 ca n have $\OT1/cmr/m/n/10 2[]$ \T1/ptm/m/n/10 or more el-e-ments (i.e., []\T1/zi4 /m/sl/10 length(bin) > [668] [669] [670] [671] [672] Underfull \hbox (badness 10000) in paragraph at lines 43534--43537 [][][]\T1/zi4/m/sl/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [][]$https : / / developer . r-[]project . org / [673] [674] [675] Underfull \hbox (badness 10000) in paragraph at lines 43718--43722 [][][]\T1/zi4/m/sl/10 addTaskCallback[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/s l/10 removeTaskCallback[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 taskCallb ackManager[][][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/sl/10 https : / / developer . [676] [677] [678] [679] [680] [681] [682] [683] [684] [685] Underfull \hbox (badness 10000) in paragraph at lines 44366--44369 [][][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / wiki / Time _ zone$[] [] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/sl/10 https : / / data . iana . org / time -[]zones / [686] [687] [688] [689] [690] [691] Underfull \vbox (badness 10000) has occurred while \output is active [692] [693] [694] [695] [696] [697] [698] [699] Underfull \hbox (badness 1990) in paragraph at lines 45282--45290 []\T1/zi4/m/sl/10 try []\T1/ptm/m/n/10 eval-u-ates an ex-pres-sion and traps an y er-rors that oc-cur dur-ing the eval-u-a-tion. If Underfull \hbox (badness 4846) in paragraph at lines 45282--45290 \T1/ptm/m/n/10 an er-ror oc-curs then the er-ror mes-sage is printed to the [][ ][]\T1/zi4/m/sl/10 stderr[][][] []\T1/ptm/m/n/10 con-nec-tion un-less [700] [701] [702] [703] [704] [705] [706] [707] [708] [709] [710] [711] [712] [713] [714] [715] [716] [717] [718] [719] [720] [721] Underfull \hbox (badness 1014) in paragraph at lines 46719--46722 []\T1/ptm/m/n/10 logical, in-di-cat-ing if the warn-ing should be out-put im-me -di-ately, even if [722] [723] Underfull \hbox (badness 2401) in paragraph at lines 46852--46856 []\T1/ptm/m/n/10 See the de-scrip-tion of [][][]\T1/zi4/m/sl/10 options[][][](" warn") []\T1/ptm/m/n/10 for the cir-cum-stances un-der which there is a [724] [725] Underfull \hbox (badness 3492) in paragraph at lines 46978--46980 []\T1/zi4/m/sl/10 weekdays []\T1/ptm/m/n/10 and []\T1/zi4/m/sl/10 months []\T1/ ptm/m/n/10 re-turn a char-ac-ter vec-tor of names in the lo-cale in use, i.e., [726] [727] Underfull \hbox (badness 2111) in paragraph at lines 47064--47069 \T1/ptm/m/n/10 If [][][]\T1/zi4/m/sl/10 names[][][](.dimnames) []\T1/ptm/m/n/10 is not empty, these are used as col-umn names. [728] [729] [730] Underfull \hbox (badness 4001) in paragraph at lines 47312--47314 []\T1/ptm/m/n/10 Thomas Lum-ley (2003) \T1/ptm/m/it/10 Stan-dard non-stan-dard eval-u-a-tion rules\T1/ptm/m/n/10 . [][]$\T1/zi4/m/sl/10 https : / / developer . [731] [732] [733] [734] [735] [736] [737] Underfull \hbox (badness 5417) in paragraph at lines 47713--47717 []\T1/zi4/m/sl/10 .packages() []\T1/ptm/m/n/10 re-turns the names of the cur-re ntly at-tached pack-ages \T1/ptm/m/it/10 in-vis-i-bly \T1/ptm/m/n/10 whereas [738] Underfull \hbox (badness 10000) in paragraph at lines 47774--47778 []\T1/zi4/m/sl/10 .standard_regexps []\T1/ptm/m/n/10 re-turns a list of `stan-d ard' reg-exps, in-clud-ing el-e-ments named [739]) (./compiler-pkg.tex [740] Chapter 2. [741] [742] [743] [744]) (./datasets-pkg.tex Chapter 3. [745] [746] [747] [748] [749] [750] [751] [752] [753] [754] [755] [756] [757] [758] [759] [760] [761] Underfull \hbox (badness 1097) in paragraph at lines 1034--1038 []\T1/ptm/m/n/10 MacDonell, W.R. (1902). On crim-i-nal an-thro-pom-e-try and th e iden-ti-fi-ca-tion of crim-i-nals. [762] [763] [764] [765] [766] [767] [768] [769] [770] [771] [772] [773] [774] [775] [776] [777] [778] [779] [780] [781] [782] [783] [784] [785] [786] [787] [788] [789] [790] [791] [792] [793] [794] [795] [796] [797] [798] [799] [800] [801] [802] [803] Overfull \hbox (2.27475pt too wide) in paragraph at lines 3524--3524 []\T1/zi4/m/n/9 ## From https://pubs.usgs.gov/gip/Elevations-Distances/elvadis t.html#Geographic%20Centers[] [804] [805] [806] [807] [808] [809] [810] [811] [812] [813] [814] [815] [816] [817] [818] [819] [820] [821] [822] [823] [824] [825] [826] [827]) (./graphics-pkg.tex [828] Chapter 4. [829] [830] [831] [832] [833] [834] [835] [836] [837] [838] [839] Underfull \vbox (badness 3803) has occurred while \output is active [840] [841] [842] [843] [844] [845] Overfull \hbox (12.71341pt too wide) in paragraph at lines 1037--1037 [] \T1/zi4/m/n/9 main = "barplot(Freq ~ Class + Survived, *)", ylab = " # {passengers}", legend.text = TRUE)[] [846] [847] [848] [849] [850] [851] Underfull \hbox (badness 4634) in paragraph at lines 1410--1413 [][][]\T1/zi4/m/sl/10 boxplot.default[][][] []\T1/ptm/m/n/10 which al-ready wor ks nowa-days with data.frames; [][][]\T1/zi4/m/sl/10 boxplot.formula[][][][]\T1 /ptm/m/n/10 , [852] [853] [854] [855] [856] [857] [858] [859] [860] [861] [862] [863] [864] [865] [866] [867] [868] Underfull \hbox (badness 1728) in paragraph at lines 2388--2390 []\T1/ptm/m/n/10 a string in-di-cat-ing the x-axis style; use []\T1/zi4/m/sl/10 "n" []\T1/ptm/m/n/10 to sup-press and see also [869] Underfull \hbox (badness 1009) in paragraph at lines 2481--2488 \T1/ptm/m/n/10 be in as-cend-ing or-der. (The rest of this de-scrip-tion does n ot ap-ply to [870] [871] [872] [873] [874] [875] [876] [877] [878] [879] [880] [881] [882] [883] [884] [885] [886] [887] [888] [889] [890] [891] [892] Underfull \vbox (badness 10000) has occurred while \output is active [893] Underfull \vbox (badness 10000) has occurred while \output is active [894] [895] [896] [897] [898] [899] Underfull \vbox (badness 3803) has occurred while \output is active [900] [901] [902] [903] [904] [905] [906] Underfull \hbox (badness 3229) in paragraph at lines 4733--4738 []\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing if log-a-rith-mic axes are to be used, see [907] [908] [909] [910] [911] Underfull \hbox (badness 1107) in paragraph at lines 5233--5239 []\T1/ptm/m/n/10 is []\T1/zi4/m/sl/10 par("cin")/par("pin") []\T1/ptm/m/n/10 sc aled to user co-or-di-nates. Note that []\T1/zi4/m/sl/10 c([][]strwidth[][][](c h), [912] [913] Underfull \hbox (badness 10000) in paragraph at lines 5362--5365 [914 ] Underfull \hbox (badness 10000) in paragraph at lines 5423--5425 [915 ] [916] [917] [918] [919] [920] [921] [922] [923] [924] [925] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.plot}) ha s been already used, duplicate ignored \relax l.6097 \aliasA{plot}{plot.default}{plot} [926] [927] [928] [929] [930] [931] [932] [933] [934] [935] [936] [937] [938] [939] Overfull \hbox (31.57222pt too wide) in paragraph at lines 6997--6998 [][] [940 ] [941] Underfull \vbox (badness 3803) has occurred while \output is active [942] [943] [944] [945] [946] [947] [948] [949] [950] [951] [952] [953] [954] [955] [956] [957] [958] [959] [960] [961] [962] [963] [964] [965] [966] [967] [968] [969] [970] [971] [972] [973] [974] Underfull \hbox (badness 4954) in paragraph at lines 9109--9111 []\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color []\T1/zi4/m /sl/10 par(c("font.sub", Underfull \hbox (badness 1019) in paragraph at lines 9111--9113 []\T1/ptm/m/n/10 X axis la-bel us-ing font, size and color []\T1/zi4/m/sl/10 pa r(c("font.lab", "cex.lab", [975] [976] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.units}) h as been already used, duplicate ignored \relax l.9191 \HeaderA{units}{Graphical Units}{units} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.units.1}) has been already used, duplicate ignored \relax l.9191 \HeaderA{units}{Graphical Units}{units} [977] [978] [979] [980]) (./grDevices-pkg.tex Chapter 5. [981] [982] [983] [984] [985] Underfull \hbox (badness 2221) in paragraph at lines 282--286 []\T1/ptm/m/n/10 numeric vec-tor of length 3, []\T1/zi4/m/sl/10 c(mi, ma, n.)[] \T1/ptm/m/n/10 , with iden-ti-cal mean-ing to Underfull \hbox (badness 10000) in paragraph at lines 297--302 []\T1/ptm/m/n/10 Apart from that, [][][]\T1/zi4/m/sl/10 axisTicks[][][]() []\T1 /ptm/m/n/10 just calls the C func-tion []\T1/zi4/m/sl/10 CreateAtVector() []\T1 /ptm/m/n/10 in [986] [987] [988] [989] [990] [991] [992] [993] [994] Underfull \hbox (badness 1424) in paragraph at lines 901--903 [][][]\T1/zi4/m/sl/10 NA[][][] []\T1/ptm/m/n/10 (as in-te-ger or char-ac-ter) a nd []\T1/zi4/m/sl/10 "NA" []\T1/ptm/m/n/10 mean trans-par-ent, which can also b e spec-i-fied as [995] [996] [997] [998] [999] [1000] Underfull \hbox (badness 5175) in paragraph at lines 1229--1231 []\T1/ptm/m/n/10 There is cur-rently no doc-u-men-ta-tion about the al-go-rithm . The source code is in [1001] [1002] Underfull \hbox (badness 2512) in paragraph at lines 1348--1350 []\T1/ptm/m/n/10 For the white points [][]$\T1/zi4/m/sl/10 https : / / web . ar chive . org / web / 20190613001950 / http : / / efg2 . com / [1003] [1004] [1005] [1006] [1007] Underfull \hbox (badness 1490) in paragraph at lines 1648--1653 \T1/ptm/m/n/10 by [][][]\T1/zi4/m/sl/10 rasterImage[][][] []\T1/ptm/m/n/10 and [][][]\T1/zi4/m/sl/10 grid.raster[][][][]\T1/ptm/m/n/10 ? Pos-si-ble val-ues [] \T1/zi4/m/sl/10 "no"[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 "yes" []\T1/ptm/m/n/10 and Underfull \hbox (badness 3302) in paragraph at lines 1661--1665 []\T1/ptm/m/n/10 character: Does the de-vice sup-port pat-tern fills? One or mo re of [1008] [1009] [1010] [1011] [1012] [1013] Underfull \hbox (badness 1325) in paragraph at lines 2076--2086 []\T1/zi4/m/sl/10 "png48"[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 "pngmono"[]\T1/pt m/m/n/10 , []\T1/zi4/m/sl/10 "pnggray"[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 "png alpha"[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 "bmp16"[]\T1/ptm/m/n/10 , []\T1/zi4/ m/sl/10 "bmp16m" "bmp256"[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 "bmp32b"[]\T1/ptm /m/n/10 , [1014] [1015] Underfull \hbox (badness 10000) in paragraph at lines 2188--2190 []\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the set-ting of [1016] [1017] [1018] Underfull \hbox (badness 6758) in paragraph at lines 2376--2379 []\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript doc-u-men-ta-tion) are [1019] [1020] [1021] [1022] [1023] [1024] [1025] [1026] [1027] [1028] [1029] [1030] Underfull \hbox (badness 10000) in paragraph at lines 3132--3133 [1031] [1032] [1033] [1034] [1035] [1036] [1037] [1038] [1039] [1040] [1041] [1042] Underfull \vbox (badness 3803) has occurred while \output is active [1043] [1044] [1045] [1046] Underfull \vbox (badness 10000) has occurred while \output is active [1047] [1048] [1049] [1050] Underfull \hbox (badness 1418) in paragraph at lines 4410--4417 \T1/ptm/m/n/10 it is one of []\T1/zi4/m/sl/10 "AvantGarde"[]\T1/ptm/m/n/10 , [] \T1/zi4/m/sl/10 "Bookman"[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 "Courier"[]\T1/pt m/m/n/10 , []\T1/zi4/m/sl/10 "Helvetica"[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 "H elvetica-Narrow"[]\T1/ptm/m/n/10 , [1051] [1052] [1053] [1054] [1055] [1056] [1057] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.symbol}) has been already used, duplicate ignored \relax l.4875 \aliasA{symbol}{plotmath}{symbol} [1058] [1059] [1060] [1061] Underfull \vbox (badness 3803) has occurred while \output is active [1062] [1063] Underfull \hbox (badness 1584) in paragraph at lines 5268--5270 []\T1/ptm/m/n/10 For type []\T1/zi4/m/sl/10 "cairo"[]\T1/ptm/m/n/10 , the []\T1 /zi4/m/sl/10 symbolfamily []\T1/ptm/m/n/10 ar-gu-ment can be sup-plied. See Underfull \hbox (badness 1067) in paragraph at lines 5272--5279 \T1/ptm/m/n/10 The lat-ter will only be avail-able if the sys-tem was com-piled with sup- [1064] [1065] [1066] [1067] Underfull \hbox (badness 1377) in paragraph at lines 5574--5579 []\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the color model: cur-rently al-lowed val-ues [1068] [1069] Underfull \hbox (badness 1377) in paragraph at lines 5678--5683 []\T1/ptm/m/n/10 Color mod-els pro-vided for back-wards com-pat-i-bil-ity are [ ]\T1/zi4/m/sl/10 "rgb" []\T1/ptm/m/n/10 (which is RGB+gray) and [1070] Underfull \hbox (badness 7344) in paragraph at lines 5747--5749 []\T1/ptm/m/n/10 Support for Com-puter Mod-ern fonts is based on a con-tri-bu-t ion by Brian D'Urso [1071] [1072] Underfull \hbox (badness 2035) in paragraph at lines 5886--5895 []\T1/ptm/m/n/10 Mappings for a num-ber of stan-dard Adobe fonts (and URW equiv -a-lents) are also pro- Underfull \hbox (badness 10000) in paragraph at lines 5886--5895 \T1/ptm/m/n/10 vided: []\T1/zi4/m/sl/10 "AvantGarde"[]\T1/ptm/m/n/10 , []\T1/zi 4/m/sl/10 "Bookman"[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 "Courier"[]\T1/ptm/m/n/ 10 , []\T1/zi4/m/sl/10 "Helvetica"[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 "Helveti ca-Narrow"[]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 5886--5895 []\T1/zi4/m/sl/10 "NewCenturySchoolbook"[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 "P alatino" []\T1/ptm/m/n/10 and []\T1/zi4/m/sl/10 "Times"[]\T1/ptm/m/n/10 ; []\T1 /zi4/m/sl/10 "URWGothic"[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 "URWBookman"[]\T1/ ptm/m/n/10 , [1073] Underfull \hbox (badness 10000) in paragraph at lines 5953--5958 []\T1/zi4/m/sl/10 BousungEG-Light-GB []\T1/ptm/m/n/10 can be found at [][]$\T1/ zi4/m/sl/10 https : / / ftp . gnu . org / pub / non-[]gnu / [1074] [1075] [1076] Underfull \hbox (badness 1546) in paragraph at lines 6093--6101 []\T1/ptm/m/n/10 arguments []\T1/zi4/m/sl/10 onefile[]\T1/ptm/m/n/10 , []\T1/zi 4/m/sl/10 family[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 title[]\T1/ptm/m/n/10 , [] \T1/zi4/m/sl/10 fonts[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 encoding[]\T1/ptm/m/n /10 , []\T1/zi4/m/sl/10 bg[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 fg[]\T1/ptm/m/n/ 10 , []\T1/zi4/m/sl/10 width[]\T1/ptm/m/n/10 , [1077] [1078] [1079] [1080] [1081] [1082] Underfull \hbox (badness 6625) in paragraph at lines 6537--6540 []\T1/ptm/m/n/10 Murrell, P., Ooms, J., Al-laire, J.J. (2015), "Record-ing and Re-play-ing the Graph- [1083] [1084] Underfull \hbox (badness 10000) in paragraph at lines 6641--6644 []\T1/zi4/m/sl/10 rgb2hsv []\T1/ptm/m/n/10 trans-forms col-ors from RGB space ( red/green/blue) into HSV space [1085] [1086] [1087] [1088] Overfull \hbox (9.73488pt too wide) in paragraph at lines 6878--6878 []\T1/zi4/m/n/9 ## but now, x in [-0.5, 20] -- "too far" ==> "wrap around" pro blem (without \TS1/zi4/m/n/9 '\T1/zi4/m/n/9 continuous=TRUE\TS1/zi4/m/n/9 '\T1/ zi4/m/n/9 ):[] [1089] [1090] [1091] [1092] [1093] [1094] [1095] [1096] [1097] [1098] Underfull \hbox (badness 1189) in paragraph at lines 7507--7509 []\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used . One of [1099] Underfull \hbox (badness 10000) in paragraph at lines 7612--7614 []\T1/zi4/m/sl/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" []\T1/ptm/m/n/10 for C JK lan-guages and [1100] [1101] [1102] [1103] [1104] Underfull \hbox (badness 3780) in paragraph at lines 7927--7933 []\T1/ptm/m/n/10 the font fam-ily to be used. This must be one of []\T1/zi4/m/s l/10 "AvantGarde"[]\T1/ptm/m/n/10 , [1105] [1106] [1107] [1108] [1109] [1110]) (./grid-pkg.tex Chapter 6. [1111] [1112] [1113] [1114] [1115] [1116] [1117] [1118] [1119] Underfull \hbox (badness 2680) in paragraph at lines 551--554 []\T1/ptm/m/n/10 Note that []\T1/zi4/m/sl/10 preDrawDetails []\T1/ptm/m/n/10 an d []\T1/zi4/m/sl/10 postDrawDetails []\T1/ptm/m/n/10 are also called in the cal -cu-la-tion of [1120] [1121] [1122] [1123] [1124] [1125] [1126] [1127] [1128] [1129] [1130] Underfull \hbox (badness 4279) in paragraph at lines 1188--1197 [][][]\T1/ptm/m/n/10 Grid[][][], [][][]\T1/zi4/m/sl/10 pushViewport[][][][]\T1/ ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 popViewport[][][][]\T1/ptm/m/n/10 , [][][]\T 1/zi4/m/sl/10 downViewport[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 seekVi ewport[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 upViewport[][][][]\T1/ptm/ m/n/10 , [][][]\T1/zi4/m/sl/10 unit[][][][]\T1/ptm/m/n/10 , [1131] [1132] [1133] [1134] [1135] [1136] [1137] [1138] [1139] [1140] [1141] [1142] [1143] [1144] [1145] [1146] [1147] [1148] [1149] [1150] [1151] [1152] [1153] [1154] [1155] [1156] [1157] [1158] [1159] [1160] [1161] [1162] Underfull \hbox (badness 10000) in paragraph at lines 3103--3105 []\T1/ptm/m/n/10 A func-tion that re-turns an affine trans-for-ma-tion ma-trix; see [1163] [1164] [1165] [1166] [1167] [1168] [1169] [1170] [1171] [1172] [1173] [1174] [1175] [1176] [1177] [1178] Underfull \vbox (badness 10000) has occurred while \output is active [1179] [1180] [1181] [1182] [1183] [1184] [1185] [1186] [1187] [1188] [1189] [1190] [1191] [1192] Underfull \hbox (badness 1067) in paragraph at lines 4842--4845 []\T1/ptm/m/n/10 Both func-tions cre-ate a seg-ments grob (a graph-i-cal ob-jec t de-scrib-ing seg-ments), but only [1193] [1194] [1195] [1196] [1197] [1198] Underfull \hbox (badness 7256) in paragraph at lines 5193--5195 []\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject s are co-erced by [1199] [1200] [1201] [1202] [1203] [1204] [1205] Underfull \hbox (badness 2142) in paragraph at lines 5647--5651 []\T1/ptm/m/n/10 ob-jects. For []\T1/zi4/m/sl/10 gridGTreeCoords []\T1/ptm/m/n/ 10 a list of ei-ther []\T1/zi4/m/sl/10 "GridGrobCoords" []\T1/ptm/m/n/10 or [1206] [1207] Underfull \hbox (badness 4699) in paragraph at lines 5729--5734 []\T1/ptm/m/n/10 Either a []\T1/zi4/m/sl/10 "GridGrobCoords" []\T1/ptm/m/n/10 o b-ject (a list of lists with com-po-nents []\T1/zi4/m/sl/10 x []\T1/ptm/m/n/10 and []\T1/zi4/m/sl/10 y[]\T1/ptm/m/n/10 ) or a [1208] [1209] [1210] [1211] [1212] [1213] [1214] [1215] [1216] [1217] [1218] [1219] [1220] [1221] [1222] [1223] [1224] [1225] [1226] [1227] [1228] [1229] [1230] [1231] [1232] [1233] [1234] [1235] [1236] [1237] [1238] [1239]) (./methods-pkg.tex [1240] Chapter 7. [1241] [1242] [1243] [1244] [1245] [1246] [1247] [1248] Underfull \vbox (badness 10000) has occurred while \output is active [1249] Underfull \vbox (badness 10000) has occurred while \output is active [1250] [1251] [1252] [1253] [1254] [1255] [1256] [1257] [1258] [1259] Underfull \hbox (badness 2237) in paragraph at lines 1384--1386 []\T1/ptm/m/n/10 The class []\T1/zi4/m/sl/10 "className" []\T1/ptm/m/n/10 ex-te nds []\T1/zi4/m/sl/10 "character" []\T1/ptm/m/n/10 and has a slot []\T1/zi4/m/s l/10 "package"[]\T1/ptm/m/n/10 , also of class [1260] [1261] [1262] [1263] [1264] [1265] [1266] [1267] [1268] Underfull \hbox (badness 10000) in paragraph at lines 1980--1985 []\T1/ptm/m/n/10 The ar-gu-ment to []\T1/zi4/m/sl/10 insertSource []\T1/ptm/m/n /10 can be an ob-ject of class Underfull \hbox (badness 1038) in paragraph at lines 1980--1985 \T1/ptm/m/n/10 file name is passed to []\T1/zi4/m/sl/10 insertSource []\T1/ptm/ m/n/10 it calls []\T1/zi4/m/sl/10 evalSource []\T1/ptm/m/n/10 to ob-tain the [1269] [1270] [1271] Underfull \hbox (badness 2213) in paragraph at lines 2212--2217 []\T1/ptm/m/n/10 To re-strict the search to classes in a par-tic-u-lar pack-age , use []\T1/zi4/m/sl/10 where = [1272] [1273] [1274] [1275] [1276] Underfull \hbox (badness 10000) in paragraph at lines 2572--2575 []\T1/ptm/m/n/10 As you might ex-pect [][][]\T1/zi4/m/sl/10 setGeneric[][][] [] \T1/ptm/m/n/10 and [][][]\T1/zi4/m/sl/10 setGroupGeneric[][][] []\T1/ptm/m/n/10 cre-ate ob-jects of class [1277] [1278] Underfull \hbox (badness 1132) in paragraph at lines 2712--2716 []\T1/ptm/m/n/10 In []\T1/zi4/m/sl/10 getGenerics[]\T1/ptm/m/n/10 , if []\T1/zi 4/m/sl/10 TRUE[]\T1/ptm/m/n/10 , the []\T1/zi4/m/sl/10 package []\T1/ptm/m/n/10 slot of the re-turned re-sult is in [1279] Underfull \hbox (badness 1033) in paragraph at lines 2748--2753 \T1/ptm/m/n/10 In ad-di-tion, []\T1/zi4/m/sl/10 removeGeneric []\T1/ptm/m/n/10 re-moves the func-tion it-self; []\T1/zi4/m/sl/10 removeMethods []\T1/ptm/m/n/1 0 re-stores the [1280] [1281] [1282] [1283] [1284] [1285] [1286] Underfull \hbox (badness 1102) in paragraph at lines 3305--3307 []\T1/zi4/m/sl/10 getPackageName []\T1/ptm/m/n/10 re-turns the character-string name of the pack-age (with-out the ex-tra-ne-ous [1287] [1288] [1289] [1290] [1291] Underfull \hbox (badness 10000) in paragraph at lines 3642--3651 []\T1/ptm/m/n/10 The [1292] [1293] Underfull \hbox (badness 10000) in paragraph at lines 3762--3763 [] \T1/zi4/m/sl/10 Pos <- setClass("Pos", slots = c(latitude = "numeric", longi tude = "numeric", [1294] Underfull \hbox (badness 10000) in paragraph at lines 3846--3847 []\T1/zi4/m/sl/10 Currency <- setClass("Currency", slots = c(unit = "character" ), contains = [1295] [1296] [1297] [1298] [1299] [1300] [1301] [1302] [1303] [1304] Underfull \hbox (badness 1769) in paragraph at lines 4477--4483 []\T1/ptm/m/n/10 class [][][]\T1/zi4/m/sl/10 MethodsList[][][] []\T1/ptm/m/n/10 for the ob-jects defin-ing sets of meth-ods as-so-ci-ated with a par-tic-u-lar Underfull \hbox (badness 1939) in paragraph at lines 4477--4483 []\T1/zi4/m/sl/10 MethodDefinition[]\T1/ptm/m/n/10 , or an ex-ten-sion. Class [ ][][]\T1/zi4/m/sl/10 MethodWithNext[][][] []\T1/ptm/m/n/10 for an ex-ten-sion u sed by [1305] [1306] [1307] [1308] [1309] [1310] [1311] [1312] [1313] [1314] Underfull \vbox (badness 10000) has occurred while \output is active [1315] [1316] [1317] Underfull \hbox (badness 4036) in paragraph at lines 5442--5445 []\T1/ptm/m/n/10 Object of class []\T1/zi4/m/sl/10 "PossibleMethod" []\T1/ptm/m /n/10 the method to use in re-sponse to a [1318] [1319] Underfull \hbox (badness 3803) in paragraph at lines 5517--5519 []\T1/ptm/m/n/10 arguments to spec-ify prop-er-ties of the new ob-ject, to be p assed to [1320] [1321] [1322] Underfull \hbox (badness 1087) in paragraph at lines 5748--5753 []\T1/ptm/m/n/10 In ad-di-tion, the cur-rently avail-able gener-ics with meth-o ds for this class are found (us-ing [1323] [1324] [1325] [1326] [1327] [1328] [1329] [1330] [1331] Underfull \hbox (badness 1675) in paragraph at lines 6455--6461 []\T1/ptm/m/n/10 can be con-verted ex-plic-itly as []\T1/zi4/m/sl/10 externalRe fMethod(f)[]\T1/ptm/m/n/10 , which re-turns an ob-ject of class [1332] [1333] [1334] [1335] Underfull \vbox (badness 10000) has occurred while \output is active [1336] [1337] [1338] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.S4}) has been already used, duplicate ignored \relax l.6976 \aliasA{S4}{S3Part}{S4} [1339] [1340] [1341] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Complex}) has been already used, duplicate ignored \relax l.7232 \aliasA{Complex}{S4groupGeneric}{Complex} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Logic}) h as been already used, duplicate ignored \relax l.7234 \aliasA{Logic}{S4groupGeneric}{Logic} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Math}) ha s been already used, duplicate ignored \relax l.7235 \aliasA{Math}{S4groupGeneric}{Math} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Ops}) has been already used, duplicate ignored \relax l.7237 \aliasA{Ops}{S4groupGeneric}{Ops} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Summary}) has been already used, duplicate ignored \relax l.7238 \aliasA{Summary}{S4groupGeneric}{Summary} [1342] Underfull \hbox (badness 2050) in paragraph at lines 7299--7303 []\T1/ptm/m/n/10 The mem-bers of the group de-fined by a par-tic-u-lar generic can be ob-tained by call-ing [1343] [1344] [1345] Underfull \hbox (badness 1286) in paragraph at lines 7487--7489 []\T1/ptm/m/n/10 for []\T1/zi4/m/sl/10 .selectSuperClasses() []\T1/ptm/m/n/10 o nly, a [][][]\T1/zi4/m/sl/10 list[][][] []\T1/ptm/m/n/10 of class ex-ten-sions, typ-i-cally [1346] [1347] [1348] [1349] [1350] [1351] [1352] [1353] [1354] [1355] [1356] [1357] [1358] [1359] [1360] [1361] [1362] [1363] [1364] [1365] [1366] [1367] [1368] [1369] [1370] [1371] [1372] Underfull \vbox (badness 10000) has occurred while \output is active [1373] [1374] [1375] [1376] [1377] [1378] [1379] [1380] [1381] [1382] [1383] [1384] [1385] [1386] Underfull \hbox (badness 1158) in paragraph at lines 10494--10497 []\T1/ptm/m/n/10 Chambers, John M. (2009) \T1/ptm/m/it/10 Class In-her-i-tance in R [][]$\T1/zi4/m/sl/10 https : / / johnmchambers . su . domains / [1387] Underfull \hbox (badness 1852) in paragraph at lines 10572--10576 []\T1/ptm/m/n/10 Each of the classes ex-tends the cor-re-spond-ing un-traced cl ass, from the data part; e.g., [1388] [1389] [1390] [1391]) (./parallel-pkg.tex [1392] Chapter 8. Underfull \hbox (badness 5490) in paragraph at lines 14--16 []\T1/ptm/m/n/10 There is sup-port for mul-ti-ple RNG streams with the `[]\T1/z i4/m/sl/10 "L\TS1/zi4/m/n/10 '\T1/zi4/m/sl/10 Ecuyer-CMRG"[]\T1/ptm/m/n/10 ' [] []RNG[][][]: see [1393] [1394] [1395] [1396] [1397] Underfull \hbox (badness 1320) in paragraph at lines 300--303 []\T1/ptm/m/n/10 It has meth-ods to do so for Linux, ma-cOS, FreeBSD, OpenBSD, So-laris and Win-dows. [1398] [1399] [1400] [1401] [1402] [1403] [1404] [1405] [1406] [1407] [1408] [1409] [1410] [1411] [1412] [1413] [1414] Underfull \hbox (badness 3386) in paragraph at lines 1400--1403 []\T1/ptm/m/n/10 An in-te-ger vec-tor of length 7 as given by []\T1/zi4/m/sl/10 .Random.seed []\T1/ptm/m/n/10 when the [1415] [1416]) (./splines-pkg.tex Chapter 9. Underfull \hbox (badness 10000) in paragraph at lines 22--24 []\T1/ptm/m/n/10 Douglas M. Bates \T1/zi4/m/sl/10 \T1/ptm /m/n/10 and William N. Ven-ables [1417] [1418] [1419] [1420] [1421] [1422] [1423] [1424] [1425] [1426] [1427] [1428] [1429] [1430] [1431] [1432]) (./stats-pkg.tex Chapter 10. [1433] [1434] [1435] [1436] [1437] [1438] [1439] [1440] [1441] [1442] [1443] [1444] [1445] [1446] Underfull \hbox (badness 1412) in paragraph at lines 901--903 []\T1/ptm/m/n/10 A fit-ted model ob-ject, for ex-am-ple from []\T1/zi4/m/sl/10 lm []\T1/ptm/m/n/10 or []\T1/zi4/m/sl/10 aov[]\T1/ptm/m/n/10 , or a for-mula fo r [1447] [1448] [1449] [1450] [1451] [1452] [1453] [1454] Underfull \hbox (badness 2503) in paragraph at lines 1389--1392 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of []\T1/zi4/m/sl/10 "two.sided"[]\T1/ptm/m/n/10 , [1455] [1456] [1457] [1458] [1459] [1460] [1461] [1462] [1463] [1464] [1465] [1466] [1467] [1468] [1469] [1470] [1471] [1472] [1473] [1474] [1475] [1476] [1477] [1478] [1479] [1480] [1481] [1482] [1483] [1484] [1485] [1486] [1487] [1488] Underfull \hbox (badness 2503) in paragraph at lines 3561--3564 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of []\T1/zi4/m/sl/10 "two.sided"[]\T1/ptm/m/n/10 , [1489] [1490] Package amsmath Warning: Foreign command \atopwithdelims; (amsmath) \frac or \genfrac should be used instead (amsmath) on input line 3674. [1491] [1492] [1493] [1494] [1495] [1496] [1497] [1498] [1499] [1500] [1501] [1502] [1503] [1504] [1505] [1506] [1507] [1508] Underfull \hbox (badness 3989) in paragraph at lines 4820--4827 []\T1/ptm/m/n/10 a nu-meric vec-tor of length 2, equal to say $\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 g[]; g[]\OT1/cmr/m/n/10 )$\T1/ptm/m/n/10 , where $\OML/cmm/m/ it/10 g[] \OT1/cmr/m/n/10 = [1509] [1510] [1511] [1512] [1513] [1514] [1515] [1516] [1517] [1518] Underfull \hbox (badness 2556) in paragraph at lines 5474--5477 []\T1/ptm/m/n/10 character; par-tially matched to []\T1/zi4/m/sl/10 "circular"[ ]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 "open"[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 "filter"[]\T1/ptm/m/n/10 . For [1519] [1520] [1521] [1522] [1523] [1524] [1525] Underfull \hbox (badness 2503) in paragraph at lines 5886--5890 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of []\T1/zi4/m/sl/10 "two.sided"[]\T1/ptm/m/n/10 , [1526] [1527] [1528] [1529] [1530] [1531] [1532] [1533] [1534] [1535] [1536] [1537] [1538] Underfull \hbox (badness 7081) in paragraph at lines 6678--6681 []\T1/ptm/m/n/10 Objects of class []\T1/zi4/m/sl/10 "hclust" []\T1/ptm/m/n/10 c an be con-verted to class []\T1/zi4/m/sl/10 "dendrogram" []\T1/ptm/m/n/10 us-in g method Underfull \hbox (badness 10000) in paragraph at lines 6682--6684 []\T1/zi4/m/sl/10 rev.dendrogram []\T1/ptm/m/n/10 sim-ply re-turns the den-dro- gram []\T1/zi4/m/sl/10 x []\T1/ptm/m/n/10 with re-versed nodes, see also [1539] [1540] [1541] [1542] [1543] [1544] Underfull \vbox (badness 10000) has occurred while \output is active [1545] [1546] [1547] Underfull \vbox (badness 10000) has occurred while \output is active [1548] [1549] [1550] [1551] [1552] Underfull \hbox (badness 10000) in paragraph at lines 7578--7581 []\T1/ptm/m/n/10 optionally, the dis-tance method used; re-sult-ing from [][][] \T1/zi4/m/sl/10 dist[][][]()[]\T1/ptm/m/n/10 , the [1553] [1554] [1555] [1556] [1557] [1558] Underfull \vbox (badness 3803) has occurred while \output is active [1559] [1560] [1561] [1562] [1563] [1564] [1565] [1566] [1567] [1568] [1569] [1570] [1571] [1572] [1573] [1574] Underfull \vbox (badness 3803) has occurred while \output is active [1575] [1576] [1577] [1578] [1579] [1580] Underfull \hbox (badness 2626) in paragraph at lines 9275--9278 []\T1/ptm/m/n/10 Either []\T1/zi4/m/sl/10 "convolution" []\T1/ptm/m/n/10 or []\ T1/zi4/m/sl/10 "recursive" []\T1/ptm/m/n/10 (and can be ab-bre-vi-ated). If [1581] Underfull \hbox (badness 2503) in paragraph at lines 9382--9386 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of []\T1/zi4/m/sl/10 "two.sided"[]\T1/ptm/m/n/10 , [1582] [1583] [1584] [1585] [1586] [1587] [1588] [1589] [1590] [1591] [1592] [1593] [1594] [1595] [1596] [1597] [1598] [1599] [1600] [1601] [1602] Underfull \hbox (badness 4518) in paragraph at lines 10730--10735 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1603] [1604] [1605] [1606] [1607] Underfull \hbox (badness 2142) in paragraph at lines 11092--11095 []\T1/ptm/m/n/10 positive con-ver-gence tol-er-ance $\OML/cmm/m/it/10 ^^O$\T1/p tm/m/n/10 ; the it-er-a-tions con-verge when $\OMS/cmsy/m/n/10 j\OML/cmm/m/it/1 0 dev \OMS/cmsy/m/n/10 ^^@ Underfull \hbox (badness 1253) in paragraph at lines 11111--11114 []\T1/ptm/m/n/10 When []\T1/zi4/m/sl/10 trace []\T1/ptm/m/n/10 is true, calls t o [][][]\T1/zi4/m/sl/10 cat[][][] []\T1/ptm/m/n/10 pro-duce the out-put for eac h IWLS it-er-a-tion. Hence, [1608] Underfull \hbox (badness 1708) in paragraph at lines 11173--11177 []\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter- na-tives are: [1609] [1610] [1611] [1612] [1613] [1614] Underfull \hbox (badness 1694) in paragraph at lines 11569--11572 []\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these de-fault to [1615] [1616] [1617] [1618] [1619] [1620] [1621] [1622] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.hat}) has been already used, duplicate ignored \relax l.12050 \aliasA{hat}{influence.measures}{hat} [1623] [1624] Underfull \hbox (badness 1484) in paragraph at lines 12195--12197 []\T1/ptm/m/n/10 The func-tion []\T1/zi4/m/sl/10 hat() []\T1/ptm/m/n/10 ex-ists mainly for S (ver-sion 2) com-pat-i-bil-ity; we rec-om-mend us-ing [1625] [1626] [1627] [1628] [1629] [1630] [1631] [1632] [1633] [1634] Underfull \hbox (badness 10000) in paragraph at lines 12782--12784 []\T1/ptm/m/n/10 tolerance even-tu-ally passed to [][][]\T1/zi4/m/sl/10 solve.d efault[][][] []\T1/ptm/m/n/10 when []\T1/zi4/m/sl/10 SSinit = [1635] [1636] [1637] [1638] [1639] Underfull \hbox (badness 2894) in paragraph at lines 13124--13128 []\T1/ptm/m/n/10 logical or in-te-ger num-ber, cur-rently only used in the de-f ault method [1640] [1641] [1642] [1643] [1644] [1645] [1646] Underfull \hbox (badness 1496) in paragraph at lines 13552--13558 []\T1/ptm/m/n/10 Gunar Schröer and Di-et-rich Tren-kler (1995). Ex-act and Ran- dom-iza-tion Dis-tri-bu-tions of [1647] [1648] [1649] [1650] [1651] [1652] Underfull \hbox (badness 4518) in paragraph at lines 13955--13960 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1653] [1654] [1655] [1656] [1657] [1658] [1659] [1660] [1661] [1662] Underfull \hbox (badness 4518) in paragraph at lines 14617--14622 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1663] [1664] [1665] Underfull \hbox (badness 6412) in paragraph at lines 14757--14761 []\T1/ptm/m/n/10 Only for the (de-fault) case []\T1/zi4/m/sl/10 (surface = "int erpolate", statistics = Underfull \hbox (badness 1199) in paragraph at lines 14764--14766 []\T1/ptm/m/n/10 the num-ber of it-er-a-tions used in ro-bust fit-ting, i.e. on ly if []\T1/zi4/m/sl/10 family []\T1/ptm/m/n/10 is [1666] [1667] [1668] [1669] [1670] [1671] [1672] [1673] [1674] [1675] [1676] [1677] [1678] [1679] [1680] [1681] [1682] [1683] Underfull \hbox (badness 2503) in paragraph at lines 15841--15845 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of []\T1/zi4/m/sl/10 "two.sided"[]\T1/ptm/m/n/10 , [1684] [1685] [1686] [1687] [1688] [1689] [1690] [1691] Underfull \hbox (badness 10000) in paragraph at lines 16354--16360 []\T1/zi4/m/sl/10 model.extract(m, "offset") []\T1/ptm/m/n/10 and []\T1/zi4/m/s l/10 model.extract(m, "response") []\T1/ptm/m/n/10 are equiv-a-lent to Underfull \hbox (badness 1867) in paragraph at lines 16354--16360 []\T1/zi4/m/sl/10 model.offset(m) []\T1/ptm/m/n/10 and []\T1/zi4/m/sl/10 model. response(m) []\T1/ptm/m/n/10 re-spec-tively. []\T1/zi4/m/sl/10 model.offset []\ T1/ptm/m/n/10 sums any terms [1692] [1693] [1694] [1695] [1696] [1697] [1698] [1699] [1700] [1701] [1702] [1703] [1704] [1705] [1706] [1707] [1708] [1709] [1710] [1711] [1712] [1713] [1714] [1715] [1716] [1717] [1718] Underfull \hbox (badness 1158) in paragraph at lines 18012--18015 []\T1/ptm/m/n/10 the ex-pres-sion that was passed to []\T1/zi4/m/sl/10 nls []\T 1/ptm/m/n/10 as the data ar-gu-ment. The ac- [1719] [1720] Underfull \vbox (badness 10000) has occurred while \output is active [1721] Underfull \vbox (badness 10000) has occurred while \output is active [1722] [1723] [1724] [1725] [1726] [1727] [1728] [1729] [1730] [1731] [1732] [1733] [1734] [1735] Underfull \hbox (badness 1377) in paragraph at lines 19055--19060 []\T1/ptm/m/n/10 A vec-tor of scal-ing val-ues for the pa-ram-e-ters. Op-ti-miz a-tion is per-formed on Underfull \hbox (badness 1735) in paragraph at lines 19060--19063 []\T1/ptm/m/n/10 A vec-tor of step sizes for the finite-difference ap-prox-i-ma -tion to the gra-di-ent, on Underfull \hbox (badness 2343) in paragraph at lines 19073--19077 []\T1/ptm/m/n/10 Relative con-ver-gence tol-er-ance. The al-go-rithm stops if i t is un-able to re-duce Underfull \hbox (badness 3471) in paragraph at lines 19073--19077 \T1/ptm/m/n/10 the value by a fac-tor of []\T1/zi4/m/sl/10 reltol * (abs(val) + reltol) []\T1/ptm/m/n/10 at a step. De-faults to Underfull \hbox (badness 2662) in paragraph at lines 19081--19085 []\T1/ptm/m/n/10 The fre-quency of re-ports for the []\T1/zi4/m/sl/10 "BFGS"[]\ T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 "L-BFGS-B" []\T1/ptm/m/n/10 and []\T1/zi4/m/s l/10 "SANN" []\T1/ptm/m/n/10 meth-ods if [1736] [1737] [1738] Underfull \vbox (badness 10000) has occurred while \output is active [1739] Overfull \hbox (15.73795pt too wide) in paragraph at lines 19306--19306 []\T1/zi4/m/n/9 ## 1-D minimization: "Brent" or optimize() being preferred.. b ut NM may be ok and "unavoidable",[] Overfull \hbox (3.75941pt too wide) in paragraph at lines 19309--19309 []\T1/zi4/m/n/9 system.time(ro <- optim(1, function(x) (x-pi)^2, control=list( warn.1d.NelderMead = FALSE)))[] [1740] [1741] [1742] [1743] [1744] [1745] [1746] Underfull \hbox (badness 1337) in paragraph at lines 19771--19774 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1747] [1748] [1749] [1750] [1751] [1752] [1753] [1754] [1755] Underfull \hbox (badness 10000) in paragraph at lines 20240--20246 \T1/zi4/m/sl/10 legend = "Cook\TS1/zi4/m/n/10 '\T1/zi4/m/sl/10 s distance", lty = cook.lty, col = cook.col, text.col [1756] [1757] [1758] [1759] [1760] [1761] [1762] Underfull \hbox (badness 1194) in paragraph at lines 20667--20670 []\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting of the con-fi-dence [1763] [1764] [1765] [1766] [1767] [1768] Underfull \hbox (badness 2503) in paragraph at lines 21045--21048 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of []\T1/zi4/m/sl/10 "two.sided"[]\T1/ptm/m/n/10 , Underfull \hbox (badness 3919) in paragraph at lines 21072--21074 []\T1/ptm/m/n/10 the char-ac-ter string []\T1/zi4/m/sl/10 "Exact Poisson test" []\T1/ptm/m/n/10 or []\T1/zi4/m/sl/10 "Comparison of Poisson [1769] [1770] [1771] [1772] [1773] [1774] [1775] [1776] [1777] [1778] [1779] [1780] [1781] [1782] [1783] [1784] [1785] [1786] Underfull \hbox (badness 10000) in paragraph at lines 22150--22156 []\T1/ptm/m/n/10 For time-series pre-dic-tion, [][][]\T1/zi4/m/sl/10 predict.ar [][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 predict.Arima[][][][]\T1/ptm/m/n /10 , [][][]\T1/zi4/m/sl/10 predict.arima0[][][][]\T1/ptm/m/n/10 , [1787] [1788] [1789] [1790] [1791] [1792] [1793] [1794] [1795] [1796] [1797] [1798] [1799] [1800] [1801] [1802] [1803] [1804] [1805] [1806] [1807] [1808] [1809] [1810] [1811] Underfull \hbox (badness 1337) in paragraph at lines 23626--23632 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1812] [1813] [1814] [1815] [1816] [1817] [1818] [1819] Underfull \hbox (badness 1436) in paragraph at lines 24116--24119 \T1/ptm/m/n/10 per-cent-ages. In \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions up t o 4.0.x, this had been set to []\T1/zi4/m/sl/10 max(2, [1820] Underfull \hbox (badness 10000) in paragraph at lines 24254--24255 []\T1/ptm/m/n/10 Wikipedia: [][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . o rg / wiki / Quantile # Estimating _ quantiles _ from _ a _ [1821] [1822] [1823] [1824] [1825] [1826] [1827] [1828] [1829] [1830] [1831] [1832] [1833] [1834] [1835] [1836] Underfull \hbox (badness 1824) in paragraph at lines 25224--25230 []\T1/ptm/m/n/10 Here, all the NAs in []\T1/zi4/m/sl/10 x []\T1/ptm/m/n/10 are first re-placed by al-ter- Underfull \hbox (badness 1033) in paragraph at lines 25224--25230 \T1/ptm/m/n/10 nat-ing $\OMS/cmsy/m/n/10 ^^F\OML/cmm/m/it/10 B$ \T1/ptm/m/n/10 where $\OML/cmm/m/it/10 B$ \T1/ptm/m/n/10 is a ``Big'' num-ber (with $\OT1/cmr/ m/n/10 2\OML/cmm/m/it/10 B < M\OMS/cmsy/m/n/10 ^^C$\T1/ptm/m/n/10 , where [1837] Underfull \hbox (badness 10000) in paragraph at lines 25245--25248 []\T1/ptm/m/n/10 Apart from the end val-ues, the re-sult []\T1/zi4/m/sl/10 y = runmed(x, k) []\T1/ptm/m/n/10 sim-ply has []\T1/zi4/m/sl/10 y[j] = [1838] [1839] [1840] [1841] [1842] [1843] [1844] [1845] [1846] Underfull \hbox (badness 2165) in paragraph at lines 25820--25825 []\T1/ptm/m/n/10 Each of the fol-low-ing are []\T1/zi4/m/sl/10 "selfStart" []\T 1/ptm/m/n/10 mod-els (with ex-am-ples) [][][]\T1/zi4/m/sl/10 SSasymp[][][][]\T1 /ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 SSasympOff[][][][]\T1/ptm/m/n/10 , [1847] [1848] [1849] [1850] Underfull \hbox (badness 1867) in paragraph at lines 26030--26032 []\T1/ptm/m/n/10 potentially fur-ther ar-gu-ments passed to and from meth-ods. Passed to Underfull \hbox (badness 10000) in paragraph at lines 26046--26050 []\T1/ptm/m/n/10 where []\T1/zi4/m/sl/10 NN <- [][]nobs[][][](object, use.fallb ack = use.fallback) []\T1/ptm/m/n/10 and []\T1/zi4/m/sl/10 PP <- [1851] [1852] [1853] [1854] [1855] [1856] [1857] [1858] [1859] [1860] [1861] [1862] [1863] [1864] [1865] [1866] [1867] [1868] [1869] [1870] [1871] [1872] [1873] [1874] [1875] Underfull \vbox (badness 10000) has occurred while \output is active [1876] [1877] Underfull \hbox (badness 3514) in paragraph at lines 27698--27703 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/zi4/m/sl/10 inp ut[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1878] [1879] [1880] [1881] Overfull \hbox (2.23795pt too wide) in paragraph at lines 27932--27932 [] \T1/zi4/m/n/9 quote({f(t[0.5]) == frac(phi[1],2)}~{} %=>% {}~~{t[0.5] == frac(log(2), e^{phi[2]})}),[] Underfull \hbox (badness 3514) in paragraph at lines 27968--27974 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/zi4/m/sl/10 inp ut[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1882] Overfull \hbox (14.22568pt too wide) in paragraph at lines 28028--28028 [] \T1/zi4/m/n/9 control = list(scaleOffset=1, printEval=TRUE, tol= 1e-11, nDcentral=TRUE), trace=TRUE)[] [1883] [1884] [1885] [1886] Underfull \hbox (badness 3514) in paragraph at lines 28201--28206 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/zi4/m/sl/10 inp ut[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1887] Underfull \hbox (badness 3514) in paragraph at lines 28288--28293 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/zi4/m/sl/10 inp ut[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1888] Underfull \hbox (badness 3514) in paragraph at lines 28353--28358 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/zi4/m/sl/10 inp ut[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1889] [1890] Underfull \hbox (badness 3514) in paragraph at lines 28447--28452 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/zi4/m/sl/10 inp ut[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1891] [1892] Underfull \hbox (badness 6691) in paragraph at lines 28539--28544 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/zi4/m/sl/10 x[] \T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1893] [1894] [1895] [1896] [1897] [1898] [1899] [1900] Underfull \hbox (badness 4024) in paragraph at lines 29026--29029 []\T1/ptm/m/n/10 the span (in lags) of the loess win-dow for trend ex-trac-tion , which [1901] [1902] [1903] [1904] [1905] [1906] [1907] [1908] [1909] [1910] Underfull \hbox (badness 5431) in paragraph at lines 29629--29631 []\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above []\T1 /zi4/m/sl/10 cov.unscaled[]\T1/ptm/m/n/10 , if [1911] [1912] [1913] Underfull \hbox (badness 5431) in paragraph at lines 29839--29842 []\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above []\T1 /zi4/m/sl/10 cov.unscaled[]\T1/ptm/m/n/10 , if [1914] [1915] [1916] [1917] [1918] [1919] Underfull \hbox (badness 1337) in paragraph at lines 30154--30158 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1920] [1921] Underfull \hbox (badness 1127) in paragraph at lines 30291--30294 []\T1/ptm/m/n/10 non-centrality pa-ram-e-ter $\OML/cmm/m/it/10 ^^N$\T1/ptm/m/n/ 10 ; cur-rently ex-cept for []\T1/zi4/m/sl/10 rt()[]\T1/ptm/m/n/10 , ac-cu-rate only for [1922] [1923] [1924] Underfull \hbox (badness 1616) in paragraph at lines 30497--30500 []\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial resid-u-als, when [1925] [1926] [1927] [1928] [1929] [1930] [1931] [1932] [1933] [1934] [1935] [1936] [1937] [1938] [1939] [1940] [1941] [1942] [1943] [1944] [1945] Underfull \hbox (badness 3557) in paragraph at lines 31724--31728 []\T1/ptm/m/n/10 Setting []\T1/zi4/m/sl/10 extendInt []\T1/ptm/m/n/10 to a non- []\T1/zi4/m/sl/10 "no" []\T1/ptm/m/n/10 string, means search-ing for the cor-re ct []\T1/zi4/m/sl/10 interval = [1946] [1947] [1948] Underfull \vbox (badness 10000) has occurred while \output is active [1949] [1950] [1951] Underfull \hbox (badness 1337) in paragraph at lines 32091--32095 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1952] [1953] [1954] [1955] [1956] [1957] [1958] [1959] [1960] Underfull \hbox (badness 1337) in paragraph at lines 32619--32623 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1961] [1962] [1963] Overfull \hbox (0.71648pt too wide) in paragraph at lines 32827--32827 []\T1/zi4/m/n/9 wilcox.test( 4:2, 3:1, paired=TRUE) # Warning: canno t compute exact p-value with ties[] [1964] [1965] [1966] Overfull \hbox (19.71954pt too wide) in paragraph at lines 32988--32988 [] \T1/zi4/m/sl/10 frequency = NULL, deltat = NULL, extend = FALSE, ts.ep s = getOption("ts.eps"), ...)[] [1967] [1968] [1969] [1970] [1971]) (./stats4-pkg.tex [1972] Chapter 11. [1973] [1974] [1975] Underfull \vbox (badness 10000) has occurred while \output is active [1976] Underfull \vbox (badness 10000) has occurred while \output is active [1977] [1978] [1979] [1980] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.show.Rdas h.methods}) has been already used, duplicate ignored \relax l.503 ...Package \pkg{stats4}}{show.Rdash.methods} [1981] [1982] [1983]) (./tcltk-pkg.tex [1984] Chapter 12. [1985] [1986] [1987] [1988] [1989] [1990] [1991] Underfull \vbox (badness 10000) has occurred while \output is active [1992] Underfull \vbox (badness 10000) has occurred while \output is active [1993] Underfull \hbox (badness 1546) in paragraph at lines 672--679 []\T1/zi4/m/sl/10 tcl []\T1/ptm/m/n/10 pro-vides a generic in-ter-face to call- ing any Tk or Tcl com-mand by sim-ply run-ning [1994] [1995] [1996] [1997] [1998] Underfull \vbox (badness 10000) has occurred while \output is active [1999] [2000] [2001] [2002] [2003] [2004] [2005] [2006]) (./tools-pkg.tex Chapter 13. [2007] LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined (Font) using `T1/zi4/m/n' instead on input line 72. [2008] Underfull \hbox (badness 3039) in paragraph at lines 167--170 []\T1/zi4/m/sl/10 assertWarning() []\T1/ptm/m/n/10 as-serts that a warn-ing wil l be sig-nalled, but \T1/ptm/m/it/10 not \T1/ptm/m/n/10 an er-ror, whereas [2009] [2010] Underfull \hbox (badness 1308) in paragraph at lines 288--301 []\T1/ptm/m/n/10 At a min-i-mum, the en-vi-ron-ment should con-tain rou-tines t o ren-der each of the 12 types Underfull \hbox (badness 4967) in paragraph at lines 288--301 \T1/ptm/m/n/10 of bib-li-o-graphic en-try sup-ported by [][][]\T1/zi4/m/sl/10 b ibentry[][][] []\T1/ptm/m/n/10 as well as sev-eral other rou-tines de- Underfull \hbox (badness 10000) in paragraph at lines 288--301 []\T1/zi4/m/sl/10 formatIncollection[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 format InProceedings[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 formatManual[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 formatMastersthesis[]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 288--301 []\T1/zi4/m/sl/10 formatMisc[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 formatPhdthesi s[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 formatProceedings[]\T1/ptm/m/n/10 , []\T1 /zi4/m/sl/10 formatTechreport []\T1/ptm/m/n/10 and [2011] [2012] Underfull \hbox (badness 3039) in paragraph at lines 392--394 []\T1/zi4/m/sl/10 NULL []\T1/ptm/m/n/10 or char-ac-ter; name of vi-gnette en-gi ne to use. Over-rides any [2013] Underfull \hbox (badness 1142) in paragraph at lines 464--468 \T1/ptm/m/n/10 If given, vi-gnette source files are by de-fault looked for in s ub-di-rec-tory [2014] [2015] [2016] [2017] [2018] [2019] [2020] [2021] [2022] [2023] [2024] [2025] [2026] Underfull \hbox (badness 1014) in paragraph at lines 1220--1222 []\T1/ptm/m/n/10 a log-i-cal in-di-cat-ing whether to also sum-ma-rize the re-v erse de-pen-den-cies Underfull \hbox (badness 7238) in paragraph at lines 1226--1228 []\T1/ptm/m/n/10 a char-ac-ter string giv-ing the path to the di-rec-tory of a pre-vi-ous [2027] Underfull \hbox (badness 10000) in paragraph at lines 1263--1266 []\T1/ptm/m/n/10 Results and tim-ings can con-ve-niently be sum-ma-rized us-ing Overfull \hbox (15.52087pt too wide) in paragraph at lines 1263--1266 []\T1/zi4/m/sl/10 summarize_check_packages_in_dir_results []\T1/ptm/m/n/10 and []\T1/zi4/m/sl/10 summarize_check_packages_in_dir_timings[]\T1/ptm/m/n/10 , [2028] [2029] [2030] [2031] [2032] [2033] Underfull \hbox (badness 10000) in paragraph at lines 1637--1640 []\T1/ptm/m/n/10 Internal func-tions []\T1/zi4/m/sl/10 CRAN_aliases_db[]\T1/ptm /m/n/10 , []\T1/zi4/m/sl/10 CRAN_archive_db[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 CRAN_current_db []\T1/ptm/m/n/10 and [2034] [2035] Underfull \hbox (badness 4096) in paragraph at lines 1756--1764 \T1/zi4/m/sl/10 "Imports", "LinkingTo", "Suggests", "Enhances")[]\T1/ptm/m/n/10 . Char-ac-ter string Underfull \hbox (badness 1082) in paragraph at lines 1766--1768 []\T1/ptm/m/n/10 a char-ac-ter vec-tor of \T1/phv/m/n/10 R \T1/ptm/m/n/10 li-br ary trees, or []\T1/zi4/m/sl/10 NULL []\T1/ptm/m/n/10 for all known trees (see [2036] [2037] [2038] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.GSC}) has been already used, duplicate ignored \relax l.1967 \aliasA{GSC}{find\_gs\_cmd}{GSC} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.R.Rul.GSC MD}) has been already used, duplicate ignored \relax l.1968 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD} [2039] [2040] [2041] [2042] [2043] [2044] [2045] [2046] Underfull \hbox (badness 3386) in paragraph at lines 2442--2445 []\T1/ptm/m/n/10 The de-fault method of []\T1/zi4/m/sl/10 as.Rconcordance []\T1 /ptm/m/n/10 searches for strings match-ing the pat-tern of [2047] [2048] Underfull \hbox (badness 4096) in paragraph at lines 2582--2590 \T1/zi4/m/sl/10 "Imports", "LinkingTo", "Suggests", "Enhances")[]\T1/ptm/m/n/10 . Char-ac-ter string [2049] [2050] [2051] [2052] [2053] [2054] [2055] [2056] [2057] [2058] [2059] [2060] [2061] [2062] [2063] Underfull \hbox (badness 1424) in paragraph at lines 3516--3518 []\T1/zi4/m/sl/10 NULL []\T1/ptm/m/n/10 or a named (by top-ics) char-ac-ter vec -tor of links, as re-turned by [2064] [2065] [2066] [2067] [2068] [2069] [2070] [2071] [2072] [2073] [2074] Underfull \hbox (badness 10000) in paragraph at lines 4232--4234 []\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run , [2075] [2076] [2077] Underfull \hbox (badness 10000) in paragraph at lines 4388--4391 []\T1/ptm/m/n/10 Where sup-ported ([]\T1/zi4/m/sl/10 texi2dvi []\T1/ptm/m/n/10 5.0 and later; []\T1/zi4/m/sl/10 texify.exe []\T1/ptm/m/n/10 from MiK-TeX), op- tion [2078] [2079] [2080] [2081] [2082] Underfull \hbox (badness 1796) in paragraph at lines 4745--4750 []\T1/ptm/m/n/10 Users should ex-pect sig-nif-i-cantly smaller speedups over [] \T1/zi4/m/sl/10 write_PACKAGES []\T1/ptm/m/n/10 in the []\T1/zi4/m/sl/10 type = = [2083] [2084] Underfull \hbox (badness 1838) in paragraph at lines 4831--4837 []\T1/ptm/m/n/10 The re-main-ing steps are done only if file `\T1/zi4/m/sl/10 p o/\T1/ptm/m/sl/10 pkgname\T1/zi4/m/sl/10 .pot\T1/ptm/m/n/10 ' al-ready ex-ists. The Underfull \hbox (badness 10000) in paragraph at lines 4831--4837 \T1/ptm/m/n/10 `\T1/zi4/m/sl/10 src/*.{c,cc,cpp,m,mm}\T1/ptm/m/n/10 ' files in the pack-age are ex-am-ined to cre-ate a file [2085] [2086] [2087] [2088] Underfull \hbox (badness 2197) in paragraph at lines 5112--5122 []\T1/ptm/m/n/10 The de-fault cor-re-sponds to the fields needed by [][][]\T1/z i4/m/sl/10 available.packages[][][][]\T1/ptm/m/n/10 : [2089] Underfull \hbox (badness 1571) in paragraph at lines 5178--5182 []\T1/ptm/m/n/10 For a re-mote repos-i-tory there is a trade-off be-tween down- load speed and time spent by [2090] [2091] [2092] [2093]) (./utils-pkg.tex [2094] Chapter 14. [2095] Underfull \hbox (badness 2556) in paragraph at lines 47--52 []\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `[] \T1/zi4/m/sl/10 insertions[]\T1/ptm/m/n/10 ', [2096] [2097] [2098] [2099] [2100] [2101] [2102] [2103] [2104] [2105] Underfull \hbox (badness 10000) in paragraph at lines 728--734 []\T1/ptm/m/n/10 Functions []\T1/zi4/m/sl/10 aspell_package_Rd_files[]\T1/ptm/m /n/10 , []\T1/zi4/m/sl/10 aspell_package_vignettes[]\T1/ptm/m/n/10 , Underfull \hbox (badness 3343) in paragraph at lines 728--734 []\T1/zi4/m/sl/10 aspell_package_R_files []\T1/ptm/m/n/10 and []\T1/zi4/m/sl/10 aspell_package_C_files []\T1/ptm/m/n/10 per-form spell check-ing on the [2106] [2107] [2108] Underfull \hbox (badness 3861) in paragraph at lines 934--939 []\T1/ptm/m/n/10 Where pro-vided by the repos-i-tory, fields []\T1/zi4/m/sl/10 "OS_type"[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 "License"[]\T1/ptm/m/n/10 , []\T1 /zi4/m/sl/10 "License_is_FOSS"[]\T1/ptm/m/n/10 , [2109] [2110] [2111] Underfull \hbox (badness 10000) in paragraph at lines 1139--1141 []\T1/ptm/m/n/10 logical in-di-cat-ing if biben-tries should be sorted, us-ing [2112] [2113] [2114] Underfull \vbox (badness 10000) has occurred while \output is active [2115] [2116] [2117] [2118] [2119] Underfull \hbox (badness 1371) in paragraph at lines 1666--1668 []\T1/ptm/m/n/10 additional named ar-gu-ments such as []\T1/zi4/m/sl/10 method []\T1/ptm/m/n/10 and []\T1/zi4/m/sl/10 ccaddress []\T1/ptm/m/n/10 to pass to [2120] [2121] [2122] [2123] [2124] [2125] [2126] [2127] [2128] [2129] [2130] [2131] Underfull \hbox (badness 2057) in paragraph at lines 2386--2388 []\T1/ptm/m/n/10 None for []\T1/zi4/m/sl/10 chooseCRANmirror()[]\T1/ptm/m/n/10 , this func-tion is in-voked for its side ef-fect of up-dat-ing [2132] Underfull \hbox (badness 2150) in paragraph at lines 2461--2468 []\T1/ptm/m/n/10 If the ob-ject re-turned by []\T1/zi4/m/sl/10 citation() []\T1 /ptm/m/n/10 con-tains only one ref-er-ence, the as-so-ci-ated print Underfull \hbox (badness 1400) in paragraph at lines 2461--2468 \T1/ptm/m/n/10 method shows both a text ver-sion and a Bib-TeX en-try for it. I f a pack-age has more [2133] [2134] [2135] Underfull \vbox (badness 3803) has occurred while \output is active [2136] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.clipboard }) has been already used, duplicate ignored \relax l.2738 ... the Clipboard in MS Windows}{clipboard} [2137] [2138] [2139] [2140] [2141] [2142] [2143] [2144] [2145] [2146] [2147] [2148] [2149] [2150] [2151] [2152] [2153] [2154] [2155] [2156] [2157] Underfull \hbox (badness 6842) in paragraph at lines 4048--4053 []\T1/ptm/m/n/10 Support for method []\T1/zi4/m/sl/10 "libcurl" []\T1/ptm/m/n/1 0 was op-tional on Win-dows prior to \T1/phv/m/n/10 R \T1/ptm/m/n/10 4.2.0: use [2158] Underfull \hbox (badness 1430) in paragraph at lines 4111--4115 []\T1/ptm/m/n/10 The level of de-tail pro-vided dur-ing trans-fer can be set by the []\T1/zi4/m/sl/10 quiet []\T1/ptm/m/n/10 ar-gu-ment and the [2159] Underfull \hbox (badness 1184) in paragraph at lines 4182--4198 []\T1/ptm/m/n/10 On Win-dows with []\T1/zi4/m/sl/10 method = "libcurl"[]\T1/ptm /m/n/10 , the CA root cer-tifi-cates are pro-vided by the OS Underfull \hbox (badness 1019) in paragraph at lines 4182--4198 \T1/ptm/m/n/10 con-tain-ing `[]\T1/zi4/m/sl/10 "Schannel"[]\T1/ptm/m/n/10 '. If it does not, for ver-i-fi-ca-tion to be on the en-vi-ron-ment vari- Underfull \hbox (badness 1668) in paragraph at lines 4182--4198 \T1/ptm/m/n/10 able []\T1/zi4/m/sl/10 CURL_CA_BUNDLE []\T1/ptm/m/n/10 must be s et to a path to a cer-tifi-cate bun-dle file, usu-ally named [2160] [2161] Underfull \hbox (badness 10000) in paragraph at lines 4332--4334 []\T1/ptm/m/n/10 additional ar-gu-ments to be passed to [][][]\T1/zi4/m/sl/10 d ownload.file[][][] []\T1/ptm/m/n/10 and [2162] [2163] [2164] [2165] [2166] [2167] [2168] [2169] [2170] [2171] [2172] [2173] [2174] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.format}) has been already used, duplicate ignored \relax l.5111 ...mat Unordered and Ordered Lists}{format} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.format.1} ) has been already used, duplicate ignored \relax l.5111 ...mat Unordered and Ordered Lists}{format} [2175] [2176] [2177] [2178] [2179] [2180] [2181] [2182] Underfull \hbox (badness 1622) in paragraph at lines 5634--5638 []\T1/ptm/m/n/10 This func-tion will search for Win-dows han-dles, for pass-ing to ex-ter-nal GUIs or to the [2183] [2184] [2185] [2186] [2187] [2188] Underfull \hbox (badness 1448) in paragraph at lines 6019--6024 []\T1/ptm/m/n/10 External pointer ob-jects are com-pared as ref-er-ence ob-ject s, cor-re-spond-ing to call-ing [2189] [2190] [2191] [2192] [2193] [2194] [2195] [2196] Underfull \hbox (badness 1371) in paragraph at lines 6567--6569 []\T1/ptm/m/n/10 additional named ar-gu-ments such as []\T1/zi4/m/sl/10 method []\T1/ptm/m/n/10 and []\T1/zi4/m/sl/10 ccaddress []\T1/ptm/m/n/10 to pass to [2197] [2198] Underfull \hbox (badness 1502) in paragraph at lines 6656--6662 []\T1/ptm/m/n/10 a char-ac-ter string to be matched in the help page `key-words '. `Key- Underfull \hbox (badness 2103) in paragraph at lines 6656--6662 \T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are listed in file [2199] [2200] Underfull \hbox (badness 10000) in paragraph at lines 6833--6842 []\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de x, Underfull \hbox (badness 3354) in paragraph at lines 6833--6842 \T1/ptm/m/n/10 `\T1/ptm/m/sl/10 R_DOC_DIR\T1/zi4/m/sl/10 /html/packages.html\T1 /ptm/m/n/10 ', which can be re-made by [][][]\T1/zi4/m/sl/10 make.packages.html [][][]()[]\T1/ptm/m/n/10 . [2201] Underfull \hbox (badness 2150) in paragraph at lines 6895--6898 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion to search. See [2202] [2203] Underfull \hbox (badness 3118) in paragraph at lines 7034--7036 []\T1/ptm/m/n/10 For de-tails of the lock-ing which is done, see the sec-tion ` Lock-ing' in the help for [2204] [2205] [2206] Underfull \hbox (badness 1325) in paragraph at lines 7213--7217 []\T1/ptm/m/n/10 a ma-trix as re-turned by [][][]\T1/zi4/m/sl/10 available.pack ages[][][] []\T1/ptm/m/n/10 list-ing pack-ages avail-able [2207] Underfull \hbox (badness 1424) in paragraph at lines 7306--7309 []\T1/ptm/m/n/10 logical: if true, re-duce the amount of out-put. This is \T1/p tm/m/it/10 not \T1/ptm/m/n/10 passed to [2208] Underfull \hbox (badness 3219) in paragraph at lines 7378--7385 []\T1/ptm/m/n/10 An al-ter-na-tive (and the cur-rent de-fault) is []\T1/zi4/m/s l/10 "both" []\T1/ptm/m/n/10 which means `use bi-nary if avail- Underfull \hbox (badness 5175) in paragraph at lines 7378--7385 \T1/ptm/m/n/10 able and cur-rent, oth-er-wise try source'. The ac-tion if there are source pack-ages Underfull \hbox (badness 1342) in paragraph at lines 7378--7385 \T1/ptm/m/n/10 which are pre-ferred but may con-tain code which needs to be com -piled is con-trolled by Underfull \hbox (badness 1596) in paragraph at lines 7378--7385 [][][]\T1/zi4/m/sl/10 getOption[][][]("install.packages.compile.from.source")[] \T1/ptm/m/n/10 . []\T1/zi4/m/sl/10 type = "both" []\T1/ptm/m/n/10 will be silen tly Underfull \hbox (badness 2932) in paragraph at lines 7386--7389 []\T1/ptm/m/n/10 Using pack-ages with []\T1/zi4/m/sl/10 type = "source" []\T1/p tm/m/n/10 al-ways works pro-vided the pack-age con-tains no [2209] [2210] Underfull \hbox (badness 1024) in paragraph at lines 7515--7518 []\T1/ptm/m/n/10 For other repos-i-to-ries, us-ing []\T1/zi4/m/sl/10 available. packages(filters = "OS_type")[\T1/ptm/m/sl/10 pkgname\T1/zi4/m/sl/10 , ] []\T1/ ptm/m/n/10 will Underfull \hbox (badness 10000) in paragraph at lines 7548--7553 [][][]\T1/zi4/m/sl/10 update.packages[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/s l/10 available.packages[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 download. packages[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 installed.packages[][][] []\T1/ptm/m/n/10 , [2211] Underfull \hbox (badness 5133) in paragraph at lines 7607--7611 []\T1/ptm/m/n/10 a char-ac-ter vec-tor giv-ing the fields to ex-tract from each pack-age's [2212] [2213] [2214] [2215] [2216] [2217] [2218] [2219] [2220] [2221] [2222] Underfull \hbox (badness 10000) in paragraph at lines 8271--8273 []\T1/ptm/m/n/10 typically the re-sult of []\T1/zi4/m/sl/10 methods(..)[]\T1/pt m/m/n/10 , an \T1/phv/m/n/10 R \T1/ptm/m/n/10 ob-ject of S3 class [2223] [2224] [2225] [2226] [2227] [2228] [2229] [2230] [2231] [2232] [2233] [2234] [2235] Underfull \hbox (badness 2310) in paragraph at lines 9058--9063 []\T1/ptm/m/n/10 If a `\T1/zi4/m/sl/10 DESCRIPTION\T1/ptm/m/n/10 ' file for the given pack-age is found and can suc-cess-fully be read, [2236] [2237] [2238] [2239] [2240] [2241] [2242] [2243] [2244] Underfull \hbox (badness 1248) in paragraph at lines 9629--9633 []\T1/zi4/m/sl/10 R CMD build []\T1/ptm/m/n/10 builds \T1/phv/m/n/10 R \T1/ptm/ m/n/10 source tar-balls. The name(s) of the pack-ages are taken from the [2245] Underfull \hbox (badness 1789) in paragraph at lines 9707--9709 []\T1/ptm/m/n/10 See `Writ-ing R Ex-ten-sions' and the `R for Win-dows FAQ' for more dis-cus-sion of the [2246] [2247] [2248] [2249] Underfull \hbox (badness 2600) in paragraph at lines 9931--9934 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the name of the help topic; de-faults to [2250] [2251] [2252] [2253] [2254] [2255] [2256] [2257] [2258] Underfull \hbox (badness 1097) in paragraph at lines 10568--10571 []\T1/ptm/m/n/10 The name []\T1/zi4/m/sl/10 "clipboard" []\T1/ptm/m/n/10 may al so be used on Win-dows, in which case [2259] [2260] Underfull \hbox (badness 3000) in paragraph at lines 10704--10709 [][][]\T1/zi4/m/sl/10 scan[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 type.c onvert[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 read.fwf[][][] []\T1/ptm/m /n/10 for read-ing \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ixed \T1/ptm/m/it/10 w\T1/pt m/m/n/10 idth \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ormatted in-put; [][][]\T1/zi4/m/ sl/10 read.table[][][][]\T1/ptm/m/n/10 ; [2261] [2262] [2263] [2264] [2265] [2266] [2267] [2268] [2269] Underfull \hbox (badness 2134) in paragraph at lines 11299--11304 [][][]\T1/zi4/m/sl/10 scan[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 type.c onvert[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 read.fwf[][][] []\T1/ptm/m /n/10 for read-ing \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ixed \T1/ptm/m/it/10 w\T1/pt m/m/n/10 idth \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ormatted in-put; [][][]\T1/zi4/m/ sl/10 write.table[][][][]\T1/ptm/m/n/10 ; [2270] Underfull \hbox (badness 10000) in paragraph at lines 11355--11360 []\T1/ptm/m/n/10 The `hive' con-tain-ing the key. The ab-bre-vi-a-tions are for Underfull \hbox (badness 10000) in paragraph at lines 11355--11360 []\T1/zi4/m/sl/10 HKEY_LOCAL_MACHINE[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 HKEY_C LASSES_ROOT[]\T1/ptm/m/n/10 . []\T1/zi4/m/sl/10 HKEY_CURRENT_USER[]\T1/ptm/m/n/ 10 , [2271] [2272] [2273] [2274] [2275] [2276] [2277] [2278] Underfull \hbox (badness 1824) in paragraph at lines 11853--11857 \T1/zi4/m/sl/10 / / en . wikipedia . org / w / index . php ? title = Roman _ nu merals & oldid = 1188781837$[][]\T1/ptm/m/n/10 . Ac-cessed [2279] [2280] [2281] [2282] [2283] [2284] [2285] Underfull \hbox (badness 4060) in paragraph at lines 12299--12302 []\T1/ptm/m/n/10 If `[]\T1/zi4/m/sl/10 --default-packages[]\T1/ptm/m/n/10 ' is not used, then []\T1/zi4/m/sl/10 Rscript []\T1/ptm/m/n/10 checks the en-vi-ron- ment vari-able Overfull \hbox (18.77168pt too wide) in paragraph at lines 12322--12322 []\T1/zi4/m/n/9 Rscript --default-packages=methods,datasets,utils,grDevices,gr aphics,stats -e \TS1/zi4/m/n/9 '\T1/zi4/m/n/9 sessionInfo()\TS1/zi4/m/n/9 '[] [2286] [2287] [2288] [2289] Underfull \hbox (badness 2150) in paragraph at lines 12577--12579 [][][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / wiki / Ctags$[][]\T1/ ptm/m/n/10 , [][]$\T1/zi4/m/sl/10 https : / / www . gnu . org / software / emac s / manual / [2290] [2291] [2292] [2293] Underfull \hbox (badness 10000) in paragraph at lines 12797--12801 []\T1/ptm/m/n/10 The de-fault for []\T1/zi4/m/sl/10 stylepath []\T1/ptm/m/n/10 is now taken from the en-vi-ron-ment vari-able Underfull \hbox (badness 10000) in paragraph at lines 12830--12836 []\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y ou can add a [2294] Underfull \hbox (badness 2762) in paragraph at lines 12845--12851 \T1/ptm/m/n/10 UTF-8 lo-cales (note that pdf-TeX as-sumes UTF-8 by de-fault sin ce 2018). Ei-ther set [2295] [2296] Underfull \hbox (badness 1009) in paragraph at lines 13020--13032 []\T1/ptm/m/n/10 Before each code chunk is eval-u-ated, zero or more hook func- tions can be ex-e-cuted. If Underfull \hbox (badness 4779) in paragraph at lines 13060--13062 []\T1/ptm/m/n/10 The file `\T1/zi4/m/sl/10 Rconsole\T1/ptm/m/n/10 ' con-fig-ure s the R GUI ([]\T1/zi4/m/sl/10 Rgui[]\T1/ptm/m/n/10 ) con-sole un-der MS Win-do ws and [2297] Underfull \hbox (badness 1077) in paragraph at lines 13090--13097 \T1/ptm/m/n/10 (strip-ping any trail-ing slash), oth-er-wise to the Win-dows `p er-sonal' di-rec-tory, oth-er-wise to [2298] [2299] [2300] [2301] [2302] [2303] Underfull \hbox (badness 3780) in paragraph at lines 13515--13521 []\T1/ptm/m/n/10 A Bio-con-duc-tor mir-ror can be se-lected by set-ting [][][]\ T1/zi4/m/sl/10 options[][][]("BioC_mirror")[]\T1/ptm/m/n/10 , e.g. via [2304] Underfull \hbox (badness 2635) in paragraph at lines 13533--13536 []\T1/ptm/m/n/10 Repository `[]\T1/zi4/m/sl/10 CRAN[]\T1/ptm/m/n/10 ' is treate d spe-cially: the value is taken from the cur-rent set-ting of [2305] [2306] [2307] Underfull \hbox (badness 2302) in paragraph at lines 13743--13745 []\T1/ptm/m/n/10 Convert file paths to the short form. This is an in-ter-face t o the Win-dows API call [2308] [2309] [2310] [2311] [2312] Underfull \hbox (badness 4441) in paragraph at lines 14042--14047 []\T1/ptm/m/n/10 logical; if []\T1/zi4/m/sl/10 TRUE []\T1/ptm/m/n/10 (de-fault) , [][][]\T1/zi4/m/sl/10 deparse[][][](control = \T1/ptm/m/sl/10 control\T1/zi4/ m/sl/10 ) []\T1/ptm/m/n/10 will not have Underfull \hbox (badness 5970) in paragraph at lines 14051--14054 []\T1/ptm/m/n/10 the page width to be used. The de-fault is the cur-rently ac-t ive [2313] [2314] [2315] [2316] [2317] [2318] [2319] Underfull \hbox (badness 2932) in paragraph at lines 14482--14489 []\T1/ptm/m/n/10 If []\T1/zi4/m/sl/10 syntax = NULL []\T1/ptm/m/n/10 (the de-fa ult) then the avail-able syn-tax ob-jects are con-sulted in turn, Underfull \hbox (badness 1688) in paragraph at lines 14482--14489 \T1/ptm/m/n/10 and se-lected if their []\T1/zi4/m/sl/10 extension []\T1/ptm/m/n /10 com-po-nent matches (as a reg-exp) the file name. Ob- [2320] [2321] [2322] [2323] Underfull \hbox (badness 6510) in paragraph at lines 14794--14798 []\T1/ptm/m/n/10 When ar-gu-ment []\T1/zi4/m/sl/10 tar []\T1/ptm/m/n/10 is set to the com-mand []\T1/zi4/m/sl/10 tar []\T1/ptm/m/n/10 on ma-cOS, en-vi-ron-men t vari-able [2324] Underfull \hbox (badness 10000) in paragraph at lines 14801--14804 [][][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / wiki / Tar _ (file _ format)$[][]\T1/ptm/m/n/10 , [][]$\T1/zi4/m/sl/10 https : / / pubs . opengroup . org / Underfull \hbox (badness 2245) in paragraph at lines 14801--14804 \T1/zi4/m/sl/10 onlinepubs / 9699919799 / utilities / pax . html # tag _ 20 _ 9 2 _ 13 _ 06$[][] \T1/ptm/m/n/10 for the way the POSIX [2325] [2326] [2327] [2328] [2329] [2330] [2331] [2332] [2333] [2334] Underfull \hbox (badness 10000) in paragraph at lines 15474--15479 []\T1/ptm/m/n/10 Arguments such as []\T1/zi4/m/sl/10 destdir []\T1/ptm/m/n/10 a nd []\T1/zi4/m/sl/10 dependencies []\T1/ptm/m/n/10 to be passed to Underfull \hbox (badness 3861) in paragraph at lines 15474--15479 [][][]\T1/zi4/m/sl/10 install.packages[][][] []\T1/ptm/m/n/10 and []\T1/zi4/m/s l/10 ignore_repo_cache[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 max_repo_cache_age [ ]\T1/ptm/m/n/10 and Underfull \hbox (badness 1052) in paragraph at lines 15480--15482 []\T1/ptm/m/n/10 character, in-di-cat-ing the type of pack-age to down-load and in-stall. See Underfull \hbox (badness 10000) in paragraph at lines 15539--15542 [][][]\T1/zi4/m/sl/10 install.packages[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/ sl/10 available.packages[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 download .packages[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 installed.packages[][][ ][]\T1/ptm/m/n/10 , [2335] [2336] [2337] [2338] [2339] [2340] [2341] [2342] [2343] [2344] [2345] [2346] [2347] [2348] [2349] [2350]) [2351] [2352] (./boot-pkg.tex Chapter 15. [2353] [2354] [2355] [2356] [2357] [2358] [2359] [2360] [2361] [2362] [2363] Underfull \hbox (badness 1297) in paragraph at lines 799--809 []\T1/ptm/m/n/10 Where random-number gen-er-a-tion is done in the worker pro-ce sses, the de-fault be-haviour Underfull \hbox (badness 1881) in paragraph at lines 826--828 []\T1/ptm/m/n/10 Davison, A.C., Hink-ley, D.V. and Schecht-man, E. (1986) Ef-fi -cient boot-strap sim-u-la-tion. [2364] [2365] Underfull \vbox (badness 10000) has occurred while \output is active [2366] [2367] [2368] Underfull \hbox (badness 2150) in paragraph at lines 1105--1111 []\T1/ptm/m/n/10 The ob-served value of the statis-tic of in-ter-est. The de-fa ult value is [2369] [2370] [2371] [2372] [2373] Underfull \hbox (badness 1571) in paragraph at lines 1445--1447 []\T1/ptm/m/n/10 Rawlings, J.O. (1988) \T1/ptm/m/it/10 Ap-plied Re-gres-sion An al-y-sis\T1/ptm/m/n/10 . Wadsworth and Brooks/Cole Statis- [2374] [2375] [2376] [2377] [2378] [2379] Underfull \hbox (badness 1005) in paragraph at lines 1800--1807 []\T1/ptm/m/n/10 The sim-u-la-tion type. Pos-si-ble types are []\T1/zi4/m/sl/10 "ordinary" []\T1/ptm/m/n/10 (case re-sam-pling), [2380] [2381] [2382] [2383] Underfull \hbox (badness 7379) in paragraph at lines 2084--2086 []\T1/ptm/m/n/10 The length of time (in months) that the res-i-dent spent at Ch an-ning House. [2384] [2385] [2386] [2387] Underfull \hbox (badness 1565) in paragraph at lines 2338--2343 []\T1/ptm/m/n/10 The ob-served value of the statis-tic of in-ter-est on the ori g-i-nal data set [2388] Underfull \hbox (badness 1881) in paragraph at lines 2432--2434 []\T1/ptm/m/n/10 Davison, A.C., Hink-ley, D.V. and Schecht-man, E. (1986) Ef-fi -cient boot-strap sim-u-la-tion. [2389] Underfull \hbox (badness 2970) in paragraph at lines 2536--2540 []\T1/ptm/m/n/10 The un-bi-ased es-ti-ma-tor uses a mul-ti-plier of []\T1/zi4/m /sl/10 n/((n-1)*(n-2)) []\T1/ptm/m/n/10 where []\T1/zi4/m/sl/10 n []\T1/ptm/m/n /10 is the sam-ple Underfull \hbox (badness 2310) in paragraph at lines 2536--2540 \T1/ptm/m/n/10 size, if []\T1/zi4/m/sl/10 unbiased []\T1/ptm/m/n/10 is []\T1/zi 4/m/sl/10 FALSE []\T1/ptm/m/n/10 then a mul-ti-plier of []\T1/zi4/m/sl/10 1/n [ ]\T1/ptm/m/n/10 is used. This is mul-ti-plied by [2390] [2391] [2392] [2393] [2394] [2395] [2396] [2397] [2398] [2399] [2400] [2401] [2402] [2403] [2404] [2405] [2406] [2407] [2408] [2409] [2410] [2411] [2412] [2413] [2414] [2415] [2416] [2417] [2418] [2419] [2420] [2421] [2422] [2423] [2424] [2425] [2426] [2427] Underfull \hbox (badness 3000) in paragraph at lines 4959--4962 []\T1/ptm/m/n/10 The in-dex of the statis-tic of in-ter-est within the out-put of a call to [2428] [2429] [2430] [2431] Underfull \hbox (badness 2293) in paragraph at lines 5238--5241 []\T1/ptm/m/n/10 An in-te-ger giv-ing the num-ber of classes to be used in the boot-strap Underfull \hbox (badness 1668) in paragraph at lines 5238--5241 \T1/ptm/m/n/10 his-togram. The de-fault is the in-te-ger be-tween 10 and 100 cl os-est to [2432] [2433] [2434] [2435] [2436] [2437] [2438] [2439] [2440] [2441] [2442] [2443] Underfull \hbox (badness 4954) in paragraph at lines 6021--6024 []\T1/ptm/m/n/10 The re-turned value is an ob-ject of class []\T1/zi4/m/sl/10 " saddle.distn"[]\T1/ptm/m/n/10 . See the help file for [2444] [2445] [2446] [2447] [2448] [2449] [2450] [2451] [2452] [2453] [2454] Underfull \hbox (badness 1596) in paragraph at lines 6742--6746 []\T1/ptm/m/n/10 A char-ac-ter string in-di-cat-ing the type of sec-ond ar-gu-m ent ex-pected by [2455] [2456] [2457] [2458] [2459] Underfull \vbox (badness 3803) has occurred while \output is active [2460] [2461] [2462] [2463] [2464]) (./class-pkg.tex Chapter 16. [2465] [2466] [2467] [2468] [2469] [2470] [2471] [2472] [2473] [2474] [2475] [2476] [2477] [2478] [2479] [2480] [2481]) (./cluster-pkg.tex [2482] Chapter 17. [2483] [2484] [2485] [2486] [2487] [2488] [2489] [2490] [2491] [2492] [2493] [2494] Underfull \hbox (badness 1412) in paragraph at lines 782--787 []\T1/ptm/m/n/10 Kaufman and Rousseeuw (see [][][]\T1/zi4/m/sl/10 agnes[][][][] \T1/ptm/m/n/10 ), orig-i-nally. Met-ric []\T1/zi4/m/sl/10 "jaccard"[]\T1/ptm/m/ n/10 : Kamil Ko-zlowski [2495] [2496] Underfull \hbox (badness 10000) in paragraph at lines 882--884 []\T1/ptm/m/n/10 list with sil-hou-ette width in-for-ma-tion for the best sam-p le, see [2497] [2498] Underfull \hbox (badness 10000) in paragraph at lines 992--994 []\T1/ptm/m/n/10 simply cor-re-sponds to the global max-i-mum, i.e., is Underfull \hbox (badness 1342) in paragraph at lines 1006--1010 []\T1/ptm/m/n/10 This, the de-fault, has been pro-posed by Mar-tin Maech-ler in 2012, [2499] [2500] Underfull \vbox (badness 3803) has occurred while \output is active [2501] [2502] [2503] [2504] [2505] Underfull \hbox (badness 10000) in paragraph at lines 1474--1477 [2506] [2507] Underfull \hbox (badness 2503) in paragraph at lines 1583--1586 []\T1/ptm/m/n/10 an ob-ject of class []\T1/zi4/m/sl/10 "hclust" []\T1/ptm/m/n/1 0 or []\T1/zi4/m/sl/10 "twins"[]\T1/ptm/m/n/10 , i.e., typ-i-cally the re-sult of [2508] Underfull \hbox (badness 4954) in paragraph at lines 1680--1682 []\T1/ptm/b/n/10 A\T1/ptm/m/n/10 symmetric bi-nary vari-able, aka []\T1/zi4/m/s l/10 "A" []\T1/ptm/m/n/10 in re-sult []\T1/zi4/m/sl/10 Types[]\T1/ptm/m/n/10 , see [2509] Underfull \hbox (badness 7667) in paragraph at lines 1694--1698 []\T1/ptm/b/n/10 I\T1/ptm/m/n/10 nterval scaled -- the \T1/ptm/b/n/10 de-fault \T1/ptm/m/n/10 for all nu-meric Underfull \hbox (badness 10000) in paragraph at lines 1694--1698 \T1/ptm/m/n/10 (incl []\T1/zi4/m/sl/10 integer[]\T1/ptm/m/n/10 ) columns of []\ T1/zi4/m/sl/10 x[]\T1/ptm/m/n/10 , aka []\T1/zi4/m/sl/10 "I" []\T1/ptm/m/n/10 i n re-sult []\T1/zi4/m/sl/10 Types[]\T1/ptm/m/n/10 , see [2510] [2511] Overfull \hbox (5.24408pt too wide) in paragraph at lines 1866--1866 []\T1/zi4/m/n/9 summary(dA123 <- daisy(flowerN)) # .. all 3 logicals treated * A*symmetric binary (w/ warning)[] Overfull \hbox (11.23795pt too wide) in paragraph at lines 1877--1877 []\T1/zi4/m/n/9 ## Still, using Euclidean/Manhattan distance for {0-1} *is* id entical to treating them as "N" :[] [2512] [2513] [2514] [2515] [2516] Underfull \hbox (badness 10000) in paragraph at lines 2212--2215 [2517] Underfull \hbox (badness 10000) in paragraph at lines 2223--2229 [][][]\T1/zi4/m/sl/10 predict.ellipsoid[][][] []\T1/ptm/m/n/10 which is also th e [][][]\T1/zi4/m/sl/10 predict[][][] []\T1/ptm/m/n/10 method for []\T1/zi4/m/s l/10 ellipsoid []\T1/ptm/m/n/10 ob-jects. [2518] [2519] [2520] Underfull \hbox (badness 6675) in paragraph at lines 2457--2459 []\T1/ptm/m/n/10 list with sil-hou-ette in-for-ma-tion of the near-est crisp cl us-ter-ing, see [2521] [2522] [2523] [2524] [2525] [2526] [2527] [2528] [2529] [2530] Underfull \hbox (badness 2980) in paragraph at lines 3059--3063 [][][]\T1/zi4/m/sl/10 agnes[][][] []\T1/ptm/m/n/10 for back-ground and ref-er-e nces; [][][]\T1/zi4/m/sl/10 pam.object[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/ sl/10 clara[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 daisy[][][][]\T1/ptm/ m/n/10 , [][][]\T1/zi4/m/sl/10 partition.object[][][][]\T1/ptm/m/n/10 , [2531] [2532] [2533] [2534] [2535] [2536] Underfull \hbox (badness 1142) in paragraph at lines 3406--3409 []\T1/ptm/m/n/10 graphical pa-ram-e-ters (see [][][]\T1/zi4/m/sl/10 par[][][][] \T1/ptm/m/n/10 ) may also be sup-plied and are passed to [2537] Underfull \hbox (badness 1142) in paragraph at lines 3525--3528 []\T1/ptm/m/n/10 graphical pa-ram-e-ters (see [][][]\T1/zi4/m/sl/10 par[][][][] \T1/ptm/m/n/10 ) may also be sup-plied and are passed to [2538] [2539] [2540] [2541] Underfull \hbox (badness 2582) in paragraph at lines 3748--3753 [][][]\T1/zi4/m/sl/10 partition.object[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/ sl/10 clusplot.partition[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 clusplot .default[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 pam[][][][]\T1/ptm/m/n/1 0 , [][][]\T1/zi4/m/sl/10 pam.object[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl /10 clara[][][][]\T1/ptm/m/n/10 , [2542] Underfull \hbox (badness 2698) in paragraph at lines 3810--3815 []\T1/ptm/m/n/10 Note that cur-rently the method func-tion sim-ply calls []\T1/ zi4/m/sl/10 plot([][]as.hclust[][][](x), ...)[]\T1/ptm/m/n/10 , which Underfull \hbox (badness 4792) in paragraph at lines 3810--3815 \T1/ptm/m/n/10 dis-patches to [][][]\T1/zi4/m/sl/10 plot.hclust[][][](..)[]\T1/ ptm/m/n/10 . If more flex-i-ble plots are needed, con-sider []\T1/zi4/m/sl/10 x x <- [2543] Underfull \hbox (badness 10000) in paragraph at lines 3883--3885 []\T1/ptm/m/n/10 Available as `\T1/zi4/m/sl/10 pluton.dat\T1/ptm/m/n/10 ' from the archive of the Uni-ver-sity of Antwer-pen, [2544] [2545] [2546] [2547] Underfull \hbox (badness 10000) in paragraph at lines 4097--4099 []\T1/ptm/m/n/10 a []\T1/zi4/m/sl/10 dissimilarity []\T1/ptm/m/n/10 ob-ject or a []\T1/zi4/m/sl/10 summary.dissimilarity []\T1/ptm/m/n/10 one for [2548] [2549] [2550] [2551] Underfull \hbox (badness 2626) in paragraph at lines 4326--4331 []\T1/ptm/m/n/10 arguments passed [][][]\T1/zi4/m/sl/10 barplot[][][]()[]\T1/pt m/m/n/10 ; note that the de-fault used to be []\T1/zi4/m/sl/10 col = [2552] Underfull \hbox (badness 1383) in paragraph at lines 4403--4408 []\T1/ptm/m/n/10 While []\T1/zi4/m/sl/10 silhouette() []\T1/ptm/m/n/10 is \T1/p tm/m/it/10 in-trin-sic \T1/ptm/m/n/10 to the [][][]\T1/zi4/m/sl/10 partition[][ ][] []\T1/ptm/m/n/10 clus-ter-ings, and hence has a (triv-ial) [2553] [2554] [2555] [2556] [2557] [2558] [2559] [2560] Underfull \hbox (badness 10000) in paragraph at lines 4844--4846 []\T1/ptm/m/n/10 Sample data set ac-com-pa-ny-ing the ref-er-ence be-low (file `\T1/zi4/m/sl/10 xclara.dat\T1/ptm/m/n/10 ' in side [2561]) (./codetools-pkg.tex [2562] Chapter 18. [2563] [2564] [2565] [2566] [2567]) (./foreign-pkg.tex [2568] Chapter 19. Underfull \hbox (badness 10000) in paragraph at lines 33--37 []\T1/ptm/m/n/10 SAS Tech-ni-cal Sup-port doc-u-ment TS-140: ``The Record Lay-o ut of Underfull \hbox (badness 10000) in paragraph at lines 33--37 \T1/ptm/m/n/10 a Data Set in SAS Trans-port (XPORT) For-mat'' avail-able as [][ ]$\T1/zi4/m/sl/10 https : Underfull \hbox (badness 10000) in paragraph at lines 33--37 \T1/zi4/m/sl/10 / / support . sas . com / content / dam / SAS / support / en / technical-[]papers / Underfull \hbox (badness 10000) in paragraph at lines 33--37 \T1/zi4/m/sl/10 record-[]layout-[]of-[]a-[]sas-[]version-[]5-[]or-[]6-[]data-[] set-[]in-[]sas-[]transport-[]xport-[]format . [2569] Underfull \hbox (badness 10000) in paragraph at lines 78--80 []\T1/ptm/m/n/10 Attribute-Relation File For-mat [][]$\T1/zi4/m/sl/10 https : / / waikato . github . io / weka-[]wiki / formats _ and _ [2570] [2571] [2572] [2573] [2574] [2575] [2576] [2577] Underfull \hbox (badness 2846) in paragraph at lines 502--511 []\T1/ptm/m/n/10 character: what to do with du-pli-cated value la-bels for dif- fer-ent lev- Underfull \hbox (badness 5417) in paragraph at lines 502--511 \T1/ptm/m/n/10 els. For []\T1/zi4/m/sl/10 "append" []\T1/ptm/m/n/10 (the de-fau lt), the first orig-i-nal value la-bel is Underfull \hbox (badness 6001) in paragraph at lines 502--511 \T1/ptm/m/n/10 kept while fur-ther du-pli-cated la-bels are re-named to []\T1/z i4/m/sl/10 paste0(label, [2578] Overfull \hbox (6.73795pt too wide) in paragraph at lines 620--620 []\T1/zi4/m/n/9 ### Expect lots of warnings as value labels (corresponding to R factor labels) are uncomplete,[] [2579] [2580] [2581] [2582] Underfull \hbox (badness 10000) in paragraph at lines 808--809 [2583] Underfull \hbox (badness 10000) in paragraph at lines 865--869 []\T1/ptm/m/n/10 SAS Tech-ni-cal Sup-port doc-u-ment TS-140: ``The Record Lay-o ut of Underfull \hbox (badness 10000) in paragraph at lines 865--869 \T1/ptm/m/n/10 a Data Set in SAS Trans-port (XPORT) For-mat'' avail-able at [][ ]$\T1/zi4/m/sl/10 https : Underfull \hbox (badness 10000) in paragraph at lines 865--869 \T1/zi4/m/sl/10 / / support . sas . com / content / dam / SAS / support / en / technical-[]papers / Underfull \hbox (badness 10000) in paragraph at lines 865--869 \T1/zi4/m/sl/10 record-[]layout-[]of-[]a-[]sas-[]version-[]5-[]or-[]6-[]data-[] set-[]in-[]sas-[]transport-[]xport-[]format . [2584] [2585] Underfull \hbox (badness 10000) in paragraph at lines 986--988 []\T1/ptm/m/n/10 Attribute-Relation File For-mat [][]$\T1/zi4/m/sl/10 https : / / waikato . github . io / weka-[]wiki / formats _ and _ [2586] [2587] [2588] [2589] Underfull \hbox (badness 10000) in paragraph at lines 1265--1271 []\T1/ptm/m/n/10 The work for this func-tion is done by []\T1/zi4/m/sl/10 forei gn:::writeForeignStata[]\T1/ptm/m/n/10 , [2590] [2591]) (./KernSmooth-pkg.tex [2592] Chapter 20. [2593] [2594] [2595] [2596] [2597] [2598] [2599] [2600] [2601] [2602] [2603]) (./lattice-pkg.tex [2604] Chapter 21. [2605] Underfull \hbox (badness 1484) in paragraph at lines 114--118 []\T1/ptm/m/n/10 Bell Lab's Trel-lis Page con-tains sev-eral doc-u-ments out-li n-ing the use of Trel-lis graph-ics; Underfull \hbox (badness 10000) in paragraph at lines 114--118 \T1/zi4/m/sl/10 20081020164041 / http : / / cm . bell-[]labs . com / cm / ms / departments / sia / project / trellis / [2606] [2607] [2608] Underfull \vbox (badness 10000) has occurred while \output is active [2609] [2610] [2611] [2612] [2613] [2614] [2615] [2616] [2617] [2618] [2619] [2620] [2621] [2622] Underfull \hbox (badness 1062) in paragraph at lines 1395--1399 \T1/ptm/m/n/10 no-ta-tion for the x and y axes re-spec-tively. See doc-u-men-ta -tion for [2623] [2624] Underfull \hbox (badness 1803) in paragraph at lines 1563--1580 [][][]\T1/zi4/m/sl/10 Lattice[][][] []\T1/ptm/m/n/10 for an overview of the pac k-age, as well as [][][]\T1/zi4/m/sl/10 barchart.table[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 print.trellis[][][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1563--1580 [][][]\T1/zi4/m/sl/10 panel.stripplot[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/s l/10 panel.superpose[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 panel.loess[ ][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 panel.average[][][][]\T1/ptm/m/n/ 10 , [][][]\T1/zi4/m/sl/10 strip.default[][][][]\T1/ptm/m/n/10 , [2625] [2626] [2627] Underfull \hbox (badness 3009) in paragraph at lines 1705--1707 []\T1/ptm/m/n/10 additional ar-gu-ments passed to [][][]\T1/zi4/m/sl/10 xyplot[ ][][][]\T1/ptm/m/n/10 , which may pass them on to Underfull \hbox (badness 6808) in paragraph at lines 1735--1739 []\T1/ptm/m/n/10 graphical ar-gu-ments, which are pro-cessed and even-tu-ally p assed to [2628] [2629] [2630] [2631] [2632] [2633] Underfull \hbox (badness 10000) in paragraph at lines 2137--2140 []\T1/ptm/m/n/10 When []\T1/zi4/m/sl/10 breaks []\T1/ptm/m/n/10 is un-spec-i-fi ed, the value of [2634] [2635] [2636] [2637] [2638] [2639] [2640] [2641] [2642] Underfull \vbox (badness 10000) has occurred while \output is active [2643] [2644] Underfull \hbox (badness 2781) in paragraph at lines 2871--2873 []\T1/ptm/m/n/10 A color ramp spec-i-fi-ca-tion, as in the []\T1/zi4/m/sl/10 co l.regions []\T1/ptm/m/n/10 ar-gu-ment in [2645] [2646] Underfull \hbox (badness 2486) in paragraph at lines 3021--3025 []\T1/ptm/m/n/10 Other use-ful ar-gu-ments are men-tioned in the help page for the de-fault panel func-tion [2647] [2648] [2649] [2650] [2651] [2652] [2653] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.parallel} ) has been already used, duplicate ignored \relax l.3506 \aliasA{parallel}{B\_08\_splom}{parallel} [2654] [2655] Underfull \hbox (badness 2368) in paragraph at lines 3644--3644 []\T1/zi4/m/sl/10 auto.key[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 prepanel[]\T1/pt m/m/n/10 , []\T1/zi4/m/sl/10 scales[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 strip[] \T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 groups[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 x lab[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 xlim[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/1 0 ylab[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 ylim[]\T1/ptm/m/n/10 , [2656] [2657] [2658] [2659] [2660] Underfull \hbox (badness 5696) in paragraph at lines 3992--3996 []\T1/ptm/m/n/10 A pos-si-ble use of this ar-gu-ment is to change the de-fault set-tings Underfull \hbox (badness 10000) in paragraph at lines 3992--3996 \T1/ptm/m/n/10 by spec-i-fy-ing []\T1/zi4/m/sl/10 lattice.options(default.theme = "col.whitebg")[]\T1/ptm/m/n/10 . Underfull \hbox (badness 2435) in paragraph at lines 3992--3996 \T1/ptm/m/n/10 For back-compatibility, this is ini-tially (when lat-tice is loa ded) set to [2661] [2662] [2663] Underfull \hbox (badness 1389) in paragraph at lines 4175--4183 \T1/ptm/m/n/10 based on HCL palettes, but cus-tomiza-tion of the palettes is al -lowed. Ear-lier be-haviour [2664] Underfull \hbox (badness 1173) in paragraph at lines 4251--4255 []\T1/ptm/m/n/10 A char-ac-ter string giv-ing the name of a com-po-nent. If un- spec-i-fied in Underfull \hbox (badness 3219) in paragraph at lines 4278--4280 []\T1/ptm/m/n/10 A log-i-cal flag, in-di-cat-ing whether a warn-ing should be i s-sued when [2665] [2666] [2667] Underfull \hbox (badness 3492) in paragraph at lines 4478--4488 []\T1/ptm/m/n/10 A color spec-i-fi-ca-tion. []\T1/zi4/m/sl/10 col []\T1/ptm/m/n /10 is used for com-po-nents []\T1/zi4/m/sl/10 "plot.symbol"[]\T1/ptm/m/n/10 , [2668] Underfull \hbox (badness 10000) in paragraph at lines 4503--4506 []\T1/ptm/m/n/10 fill color, ap-pli-ca-ble for com-po-nents []\T1/zi4/m/sl/10 p lot.symbol[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 plot.polygon[]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4506--4508 []\T1/ptm/m/n/10 border color, ap-pli-ca-ble for com-po-nents []\T1/zi4/m/sl/10 plot.polygon []\T1/ptm/m/n/10 and [2669] [2670] [2671] [2672] [2673] [2674] [2675] [2676] [2677] [2678] Underfull \hbox (badness 6157) in paragraph at lines 5232--5235 []\T1/zi4/m/sl/10 plot.shingle []\T1/ptm/m/n/10 dis-plays the ranges of shin-gl es via rect-an-gles. []\T1/zi4/m/sl/10 print.shingle []\T1/ptm/m/n/10 and [2679] [2680] [2681] [2682] [2683] [2684] [2685] [2686] Underfull \hbox (badness 10000) in paragraph at lines 5684--5687 []\T1/ptm/m/n/10 logical, spec-i-fy-ing whether the la-bels etc should be hor-i -zon-tal. Underfull \hbox (badness 5592) in paragraph at lines 5684--5687 []\T1/zi4/m/sl/10 horizontal=FALSE []\T1/ptm/m/n/10 is use-ful for strips on th e left of pan-els us-ing [2687] [2688] [2689] [2690] [2691] Underfull \hbox (badness 4805) in paragraph at lines 6045--6049 []\T1/ptm/m/n/10 logical, whether the view-port be-ing as-signed fo-cus should be high- Underfull \hbox (badness 10000) in paragraph at lines 6056--6063 []\T1/ptm/m/n/10 For []\T1/zi4/m/sl/10 panel.identify.qqmath[]\T1/ptm/m/n/10 , ex-tra pa-ram-e-ters are passed on to Underfull \hbox (badness 1226) in paragraph at lines 6056--6063 []\T1/zi4/m/sl/10 panel.identify[]\T1/ptm/m/n/10 . For []\T1/zi4/m/sl/10 panel. identify[]\T1/ptm/m/n/10 , ex-tra ar-gu-ments are treated as Underfull \hbox (badness 2418) in paragraph at lines 6056--6063 \T1/ptm/m/n/10 graph-i-cal pa-ram-e-ters and are used for la-belling. For []\T1 /zi4/m/sl/10 trellis.focus Underfull \hbox (badness 10000) in paragraph at lines 6056--6063 []\T1/ptm/m/n/10 and []\T1/zi4/m/sl/10 trellis.switchFocus[]\T1/ptm/m/n/10 , th ese are used (in com-bi-na-tion with Underfull \hbox (badness 1259) in paragraph at lines 6056--6063 [][][]\T1/zi4/m/sl/10 lattice.options[][][][]\T1/ptm/m/n/10 ) for high-light-in g the cho-sen view-port if so re-quested. [2692] [2693] [2694] [2695] Underfull \hbox (badness 4242) in paragraph at lines 6356--6361 []\T1/ptm/m/n/10 Graphical pa-ram-e-ters for the bars. By de-fault, the trel-li s pa-ram-e- Underfull \hbox (badness 2529) in paragraph at lines 6356--6361 \T1/ptm/m/n/10 ter []\T1/zi4/m/sl/10 plot.polygon []\T1/ptm/m/n/10 is used if t here is no group-ing vari-able, oth-er-wise [2696] [2697] Underfull \hbox (badness 2310) in paragraph at lines 6472--6477 []\T1/ptm/m/n/10 Creates Box and Whisker plot of []\T1/zi4/m/sl/10 x []\T1/ptm/ m/n/10 for ev-ery level of []\T1/zi4/m/sl/10 y []\T1/ptm/m/n/10 (or the other w ay round if [2698] [2699] [2700] [2701] [2702] [2703] [2704] [2705] [2706] [2707] [2708] [2709] [2710] Underfull \hbox (badness 3168) in paragraph at lines 7330--7334 []\T1/ptm/m/n/10 to know what ar-gu-ments this func-tion is passed when called. Use [2711] [2712] [2713] [2714] Underfull \hbox (badness 2012) in paragraph at lines 7601--7604 []\T1/ptm/m/n/10 Further ar-gu-ments, of-ten graph-i-cal pa-ram-e-ters, even-tu -ally passed on to [2715] [2716] [2717] [2718] Underfull \hbox (badness 3333) in paragraph at lines 7808--7810 []\T1/ptm/m/n/10 default colours are ob-tained from []\T1/zi4/m/sl/10 plot.symb ol []\T1/ptm/m/n/10 and []\T1/zi4/m/sl/10 plot.line []\T1/ptm/m/n/10 us-ing Underfull \hbox (badness 2318) in paragraph at lines 7836--7844 []\T1/zi4/m/sl/10 "spline" []\T1/ptm/m/n/10 adds a cu-bic smooth-ing spline fit (same as [][][]\T1/zi4/m/sl/10 panel.spline[][][][]\T1/ptm/m/n/10 ). [2719] [2720] [2721] Underfull \vbox (badness 10000) has occurred while \output is active [2722] [2723] [2724] [2725] Underfull \hbox (badness 1436) in paragraph at lines 8309--8315 []\T1/ptm/m/n/10 A log-i-cal flag de-ter-min-ing whether the de-fault graph-i-c al pa-ram-e-ters for [2726] [2727] [2728] [2729] [2730] [2731] [2732] [2733] Underfull \hbox (badness 10000) in paragraph at lines 8878--8881 []\T1/ptm/m/n/10 Extra ar-gu-ments. Passed down to []\T1/zi4/m/sl/10 panel.supe rpose []\T1/ptm/m/n/10 from [2734] Underfull \hbox (badness 1092) in paragraph at lines 8924--8926 []\T1/ptm/m/n/10 Deepayan Sarkar \T1/zi4/m/sl/10 \T1/ptm/m/n/10 ([]\T1/zi4/m/sl/10 panel.superpose.2 []\T1/ptm/m/n/10 orig-i-n ally con- [2735] [2736] [2737] Underfull \hbox (badness 3895) in paragraph at lines 9085--9088 []\T1/ptm/m/n/10 details of his-togram cal-cu-la-tions. []\T1/zi4/m/sl/10 type []\T1/ptm/m/n/10 has a dif-fer-ent mean-ing in Underfull \hbox (badness 6625) in paragraph at lines 9095--9095 []\T1/zi4/m/sl/10 perspective[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 distance[]\T1 /ptm/m/n/10 , []\T1/zi4/m/sl/10 xlim[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 ylim[] \T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 zlim[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 scr een[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 R.mat[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/ 10 aspect[]\T1/ptm/m/n/10 , [2738] Underfull \hbox (badness 1515) in paragraph at lines 9160--9164 []\T1/ptm/m/n/10 numeric vec-tor of length two, rep-re-sent-ing prob-a-bil-i-ti es. If used with [2739] [2740] Underfull \hbox (badness 6316) in paragraph at lines 9266--9271 []\T1/ptm/m/n/10 which packet (counted ac-cord-ing to the packet or-der, de-scr ibed in Underfull \hbox (badness 5908) in paragraph at lines 9283--9286 []\T1/ptm/m/n/10 list, sim-i-lar to those pro-duced by []\T1/zi4/m/sl/10 xscale .components.default []\T1/ptm/m/n/10 and [2741] [2742] Underfull \vbox (badness 10000) has occurred while \output is active [2743] [2744] [2745] Underfull \hbox (badness 2418) in paragraph at lines 9574--9578 []\T1/ptm/m/n/10 returns a list with sev-eral com-po-nents, in-clud-ing []\T1/z i4/m/sl/10 left, right, left.name, right.name, [2746] [2747] [2748] [2749] [2750] [2751] Underfull \hbox (badness 2310) in paragraph at lines 10018--10022 []\T1/ptm/m/n/10 Factor with lev-els []\T1/zi4/m/sl/10 "Svansota"[]\T1/ptm/m/n/ 10 , []\T1/zi4/m/sl/10 "No. 462"[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 "Manchuria "[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 "No. 475"[]\T1/ptm/m/n/10 , []\T1/zi4/m/s l/10 "Velvet"[]\T1/ptm/m/n/10 , Underfull \hbox (badness 3701) in paragraph at lines 10023--10026 []\T1/ptm/m/n/10 Factor with 6 lev-els: []\T1/zi4/m/sl/10 "Grand Rapids"[]\T1/p tm/m/n/10 , []\T1/zi4/m/sl/10 "Duluth"[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 "Uni versity Farm"[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 "Morris"[]\T1/ptm/m/n/10 , [2752] [2753] [2754] [2755] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.melanoma} ) has been already used, duplicate ignored \relax l.10249 \aliasA{melanoma}{H\_melanoma}{melanoma} [2756] [2757] [2758] [2759] Underfull \hbox (badness 4144) in paragraph at lines 10473--10476 []\T1/ptm/m/n/10 Rural Health Re-form Pol-icy Re-search Cen-ter. _Ex-plor-ing R u-ral and Ur-ban Mor-tal- Underfull \hbox (badness 1509) in paragraph at lines 10473--10476 \T1/ptm/m/n/10 ity Dif-fer-ences_, Au-gust 2015 Bethesda, MD. [][]$\T1/zi4/m/sl /10 https : / / ruralhealth . und . edu / projects / [2760]) (./MASS-pkg.tex Chapter 22. [2761] [2762] [2763] [2764] [2765] [2766] [2767] [2768] [2769] [2770] [2771] [2772] [2773] [2774] [2775] [2776] [2777] [2778] [2779] [2780] [2781] [2782] [2783] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.confint.g lm}) has been already used, duplicate ignored \relax l.1477 ...{confint.glm}{confint-MASS}{confint.glm} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.confint.n ls}) has been already used, duplicate ignored \relax l.1478 ...{confint.nls}{confint-MASS}{confint.nls} [2784] [2785] [2786] [2787] [2788] [2789] [2790] [2791] [2792] [2793] [2794] [2795] [2796] [2797] [2798] [2799] [2800] [2801] [2802] Underfull \hbox (badness 10000) in paragraph at lines 2785--2790 []\T1/zi4/m/sl/10 "geometric"[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 "log-normal"[ ]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 "lognormal"[]\T1/ptm/m/n/10 , []\T1/zi4/m/s l/10 "logistic"[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 "negative [2803] [2804] [2805] Underfull \hbox (badness 4686) in paragraph at lines 2957--2959 []\T1/ptm/m/n/10 An early ter-mi-na-tion cri-te-rion. If any par-tial de-nom-i- na-tor ex-ceeds [2806] [2807] [2808] [2809] [2810] [2811] [2812] [2813] [2814] [2815] [2816] [2817] [2818] [2819] [2820] [2821] [2822] [2823] [2824] [2825] [2826] [2827] [2828] [2829] [2830] [2831] [2832] Underfull \hbox (badness 1117) in paragraph at lines 4732--4735 []\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo rm []\T1/zi4/m/sl/10 response ~ [2833] Underfull \hbox (badness 1117) in paragraph at lines 4811--4814 []\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo rm []\T1/zi4/m/sl/10 response ~ [2834] [2835] [2836] [2837] [2838] [2839] [2840] [2841] [2842] [2843] [2844] [2845] [2846] [2847] [2848] [2849] [2850] [2851] [2852] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.npk}) has been already used, duplicate ignored \relax l.6080 ...sical N, P, K Factorial Experiment}{npk} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.npk.1}) h as been already used, duplicate ignored \relax l.6080 ...sical N, P, K Factorial Experiment}{npk} [2853] [2854] [2855] [2856] [2857] [2858] Underfull \vbox (badness 10000) has occurred while \output is active [2859] [2860] [2861] [2862] [2863] [2864] [2865] [2866] Underfull \hbox (badness 1117) in paragraph at lines 6981--6988 []\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo rm []\T1/zi4/m/sl/10 response ~ [2867] Underfull \hbox (badness 3138) in paragraph at lines 7052--7058 []\T1/ptm/m/n/10 The log-log and com-ple-men-tary log-log links are the in-crea s-ing func-tions $\OML/cmm/m/it/10 F[]\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 p\OT1/c mr/m/n/10 ) = [2868] [2869] [2870] Underfull \hbox (badness 1910) in paragraph at lines 7231--7234 []\T1/ptm/m/n/10 the di-men-sion of the space to be used. If this is less than []\T1/zi4/m/sl/10 min(p, [2871] [2872] [2873] [2874] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.profile.g lm}) has been already used, duplicate ignored \relax l.7508 ... for Profiling glm Objects}{profile.glm} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.profile.g lm.1}) has been already used, duplicate ignored \relax l.7508 ... for Profiling glm Objects}{profile.glm} [2875] [2876] [2877] [2878] Underfull \hbox (badness 4686) in paragraph at lines 7803--7805 []\T1/ptm/m/n/10 An early ter-mi-na-tion cri-te-rion. If any par-tial de-nom-i- na-tor ex-ceeds [2879] [2880] [2881] [2882] [2883] [2884] [2885] [2886] [2887] [2888] [2889] [2890] [2891] [2892] [2893] [2894] [2895] [2896] [2897] [2898] [2899] [2900] [2901] [2902] [2903] [2904] [2905] [2906] [2907] [2908] [2909] [2910] [2911] [2912] [2913] [2914] [2915] [2916] [2917] [2918]) (./Matrix-pkg.tex Chapter 23. Underfull \hbox (badness 10000) in paragraph at lines 35--38 []\T1/ptm/m/n/10 Note that the cur-rent im-ple-men-ta-tion de-tails are sub-jec t to change, and if you Underfull \hbox (badness 10000) in paragraph at lines 35--38 \T1/ptm/m/n/10 con-sider work-ing with these classes, please con-tact the pack- age main-tain-ers [2919] Underfull \hbox (badness 1769) in paragraph at lines 89--92 []\T1/ptm/m/n/10 This is cur-rently ex-per-i-men-tal and not yet used for our o wn code. Please con-tact us [2920] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.all.equal }) has been already used, duplicate ignored \relax l.182 ...{all.equal}{all.equal-methods}{all.equal} [2921] Underfull \hbox (badness 3098) in paragraph at lines 264--266 []\T1/ptm/m/n/10 optional ar-gu-ments passed to the de-fault method for generic func-tion [2922] [2923] [2924] [2925] Underfull \hbox (badness 5119) in paragraph at lines 492--496 []\T1/ptm/m/n/10 logical; if true the re-sult will be sym-met-ric (in-her-it-in g from class [2926] Underfull \hbox (badness 2035) in paragraph at lines 590--593 []\T1/ptm/m/n/10 The value of []\T1/zi4/m/sl/10 bdiag() []\T1/ptm/m/n/10 in-her -its from class [][][]\T1/zi4/m/sl/10 CsparseMatrix[][][][]\T1/ptm/m/n/10 , whe reas []\T1/zi4/m/sl/10 .bdiag() []\T1/ptm/m/n/10 re-turns a [2927] [2928] [2929] [2930] Underfull \hbox (badness 5817) in paragraph at lines 913--916 []\T1/ptm/m/n/10 Class [][][]\T1/zi4/m/sl/10 BunchKaufmanFactorization[][][][]\ T1/ptm/m/n/10 , di-rectly. Class [][][]\T1/zi4/m/sl/10 MatrixFactorization[][][ ][]\T1/ptm/m/n/10 , by class Underfull \hbox (badness 6758) in paragraph at lines 919--924 []\T1/ptm/m/n/10 Objects can be gen-er-ated di-rectly by calls of the form []\T 1/zi4/m/sl/10 new("BunchKaufman", ...) Underfull \hbox (badness 2961) in paragraph at lines 919--924 []\T1/ptm/m/n/10 or []\T1/zi4/m/sl/10 new("pBunchKaufman", ...)[]\T1/ptm/m/n/10 , but they are more typ-i-cally ob-tained as the value of [2931] [2932] Underfull \hbox (badness 10000) in paragraph at lines 1081--1086 []\T1/ptm/m/n/10 An ob-ject rep-re-sent-ing the fac-tor-iza-tion, in-her-it-ing from vir-tual class [2933] [2934] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.cbind2.Rd ash.methods}) has been already used, duplicate ignored \relax l.1185 ... on cbind2/rbind2}{cbind2.Rdash.methods} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.cbind2}) has been already used, duplicate ignored \relax l.1186 \aliasA{cbind2}{cbind2-methods}{cbind2} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.rbind2}) has been already used, duplicate ignored \relax l.1195 \aliasA{rbind2}{cbind2-methods}{rbind2} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.rbind2.Rd ash.methods}) has been already used, duplicate ignored \relax l.1204 ...s}{cbind2-methods}{rbind2.Rdash.methods} [2935] Underfull \hbox (badness 10000) in paragraph at lines 1322--1329 []\T1/ptm/m/n/10 The im-ple-men-ta-tion of class []\T1/zi4/m/sl/10 CHMfactor [] \T1/ptm/m/n/10 is based on CHOLMOD's C-level [2936] [2937] [2938] [2939] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.chol}) ha s been already used, duplicate ignored \relax l.1625 \aliasA{chol}{chol-methods}{chol} [2940] Underfull \hbox (badness 6220) in paragraph at lines 1656--1658 []\T1/ptm/m/n/10 Methods for [][][]\T1/zi4/m/sl/10 sparseMatrix[][][] []\T1/ptm /m/n/10 are built on CHOLMOD rou-tines []\T1/zi4/m/sl/10 cholmod_analyze []\T1/ ptm/m/n/10 and [2941] Underfull \hbox (badness 2334) in paragraph at lines 1730--1734 []\T1/ptm/m/n/10 The LA-PACK source code, in-clud-ing doc-u-men-ta-tion; see [] []$\T1/zi4/m/sl/10 https : / / netlib . org / lapack / Underfull \hbox (badness 1616) in paragraph at lines 1730--1734 \T1/zi4/m/sl/10 double / dpstrf . f$[][]\T1/ptm/m/n/10 , [][]$\T1/zi4/m/sl/10 h ttps : / / netlib . org / lapack / double / dpotrf . f$[][]\T1/ptm/m/n/10 , and [][]$\T1/zi4/m/sl/10 https : / / netlib . [2942] Underfull \vbox (badness 10000) has occurred while \output is active [2943] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.chol2inv} ) has been already used, duplicate ignored \relax l.1854 ...sA{chol2inv}{chol2inv-methods}{chol2inv} [2944] [2945] Underfull \hbox (badness 10000) in paragraph at lines 2005--2008 []\T1/ptm/m/n/10 Class [][][]\T1/zi4/m/sl/10 CholeskyFactorization[][][][]\T1/p tm/m/n/10 , di-rectly. Class [][][]\T1/zi4/m/sl/10 MatrixFactorization[][][][]\ T1/ptm/m/n/10 , by class Underfull \hbox (badness 7722) in paragraph at lines 2011--2019 []\T1/ptm/m/n/10 Objects can be gen-er-ated di-rectly by calls of the form []\T 1/zi4/m/sl/10 new("Cholesky", ...) []\T1/ptm/m/n/10 or Underfull \hbox (badness 1990) in paragraph at lines 2051--2060 []\T1/ptm/m/n/10 In \T1/ptm/b/n/10 Ma-trix []\T1/zi4/m/sl/10 < 1.6-0[]\T1/ptm/m /n/10 , class []\T1/zi4/m/sl/10 Cholesky []\T1/ptm/m/n/10 ex-tended [][][]\T1/z i4/m/sl/10 dtrMatrix[][][] []\T1/ptm/m/n/10 and class []\T1/zi4/m/sl/10 pCholes ky []\T1/ptm/m/n/10 ex-tended Underfull \hbox (badness 2334) in paragraph at lines 2066--2070 []\T1/ptm/m/n/10 The LA-PACK source code, in-clud-ing doc-u-men-ta-tion; see [] []$\T1/zi4/m/sl/10 https : / / netlib . org / lapack / Underfull \hbox (badness 1616) in paragraph at lines 2066--2070 \T1/zi4/m/sl/10 double / dpstrf . f$[][]\T1/ptm/m/n/10 , [][]$\T1/zi4/m/sl/10 h ttps : / / netlib . org / lapack / double / dpotrf . f$[][]\T1/ptm/m/n/10 , and [][]$\T1/zi4/m/sl/10 https : / / netlib . [2946] [2947] Underfull \hbox (badness 6220) in paragraph at lines 2185--2187 []\T1/ptm/m/n/10 Methods for [][][]\T1/zi4/m/sl/10 sparseMatrix[][][] []\T1/ptm /m/n/10 are built on CHOLMOD rou-tines []\T1/zi4/m/sl/10 cholmod_analyze []\T1/ ptm/m/n/10 and [2948] [2949] Underfull \hbox (badness 2334) in paragraph at lines 2315--2319 []\T1/ptm/m/n/10 The LA-PACK source code, in-clud-ing doc-u-men-ta-tion; see [] []$\T1/zi4/m/sl/10 https : / / netlib . org / lapack / Underfull \hbox (badness 1616) in paragraph at lines 2315--2319 \T1/zi4/m/sl/10 double / dpstrf . f$[][]\T1/ptm/m/n/10 , [][]$\T1/zi4/m/sl/10 h ttps : / / netlib . org / lapack / double / dpotrf . f$[][]\T1/ptm/m/n/10 , and [][]$\T1/zi4/m/sl/10 https : / / netlib . [2950] Underfull \vbox (badness 10000) has occurred while \output is active [2951] Underfull \vbox (badness 10000) has occurred while \output is active [2952] Underfull \vbox (badness 10000) has occurred while \output is active [2953] [2954] [2955] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.colMeans} ) has been already used, duplicate ignored \relax l.2696 ...asA{colMeans}{colSums-methods}{colMeans} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.colSums}) has been already used, duplicate ignored \relax l.2704 \aliasA{colSums}{colSums-methods}{colSums} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.rowMeans} ) has been already used, duplicate ignored \relax l.2711 ...asA{rowMeans}{colSums-methods}{rowMeans} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.rowSums}) has been already used, duplicate ignored \relax l.2719 \aliasA{rowSums}{colSums-methods}{rowSums} [2956] [2957] Underfull \hbox (badness 3547) in paragraph at lines 2888--2891 []\T1/ptm/m/n/10 a num-ber $\OML/cmm/m/it/10 > \OT1/cmr/m/n/10 0$\T1/ptm/m/n/10 , the es-ti-mated (1-norm) con-di-tion num-ber $[]$; when [2958] [2959] [2960] [2961] [2962] [2963] [2964] Underfull \hbox (badness 1983) in paragraph at lines 3390--3398 []\T1/ptm/m/n/10 and [][][]\T1/zi4/m/sl/10 unpackedMatrix[][][][]\T1/ptm/m/n/10 . Al-ter-na-tively into the (cur-rently) three sub-classes [][][]\T1/zi4/m/sl/ 10 ddenseMatrix[][][][]\T1/ptm/m/n/10 , [2965] [2966] [2967] [2968] Underfull \hbox (badness 2717) in paragraph at lines 3712--3716 []\T1/ptm/m/n/10 However this means that a ma-trix typ-i-cally can be stored in more than one pos-si-ble [2969] [2970] Underfull \hbox (badness 3417) in paragraph at lines 3828--3830 []\T1/zi4/m/sl/10 .sparseDiagonal() []\T1/ptm/m/n/10 ex-ists pri-mar-ily to lev er-age ef-fi-cient C-level meth-ods avail-able for [2971] Underfull \hbox (badness 8019) in paragraph at lines 3933--3935 []\T1/zi4/m/sl/10 signature(x = "nMatrix")[]\T1/ptm/m/n/10 , se-man-ti-cally eq uiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion [][][]\T1/zi4/m/sl/1 0 which[][][](x, Underfull \hbox (badness 10000) in paragraph at lines 3936--3940 []\T1/zi4/m/sl/10 signature(x = "diagonalMatrix")[]\T1/ptm/m/n/10 : all these g roup meth-ods re-turn a [2972] [2973] [2974] [2975] [2976] Underfull \hbox (badness 1902) in paragraph at lines 4263--4265 [][][]\T1/zi4/m/sl/10 drop0[][][](x, tol=1e-10) []\T1/ptm/m/n/10 is some-times prefer-able to (and more ef-fi-cient than) []\T1/zi4/m/sl/10 zapsmall(x, Underfull \hbox (badness 2020) in paragraph at lines 4300--4303 []\T1/ptm/m/n/10 a typ-i-cally sparse ma-trix; in-ter-nally co-erced to ei-ther []\T1/zi4/m/sl/10 "[][]dgCMatrix[][][]" []\T1/ptm/m/n/10 or [2977] [2978] [2979] Underfull \hbox (badness 4378) in paragraph at lines 4503--4512 []\T1/ptm/m/n/10 or [][][]\T1/zi4/m/sl/10 chol[][][]() []\T1/ptm/m/n/10 is typ- i-cally used, e.g., see []\T1/zi4/m/sl/10 selectMethod("coerce", c(from="dsyMat rix", [2980] [2981] [2982] [2983] [2984] Underfull \hbox (badness 10000) in paragraph at lines 4834--4837 []\T1/ptm/m/n/10 Class []\T1/zi4/m/sl/10 "dMatrix"[]\T1/ptm/m/n/10 , by class [ ]\T1/zi4/m/sl/10 "dsparseMatrix"[]\T1/ptm/m/n/10 ; class []\T1/zi4/m/sl/10 "spa rseMatrix"[]\T1/ptm/m/n/10 , by classes [2985] Underfull \hbox (badness 4518) in paragraph at lines 4929--4932 []\T1/zi4/m/sl/10 signature(x = "dspMatrix", type = "character")[]\T1/ptm/m/n/1 0 , or []\T1/zi4/m/sl/10 x = "dsyMatrix" []\T1/ptm/m/n/10 or []\T1/zi4/m/sl/10 type = Underfull \hbox (badness 3690) in paragraph at lines 4932--4935 []\T1/zi4/m/sl/10 signature(x = "dspMatrix", type = "character")[]\T1/ptm/m/n/1 0 , or []\T1/zi4/m/sl/10 x = "dsyMatrix" []\T1/ptm/m/n/10 or []\T1/zi4/m/sl/10 type = [2986] [2987] Underfull \hbox (badness 2318) in paragraph at lines 5035--5039 []\T1/ptm/m/n/10 Class []\T1/zi4/m/sl/10 "dgCMatrix"[]\T1/ptm/m/n/10 , di-rectl y. Class []\T1/zi4/m/sl/10 "triangularMatrix"[]\T1/ptm/m/n/10 , di-rectly. Clas s []\T1/zi4/m/sl/10 "dMatrix"[]\T1/ptm/m/n/10 , [2988] [2989] Underfull \hbox (badness 3240) in paragraph at lines 5151--5155 []\T1/zi4/m/sl/10 signature(x = "dtpMatrix", logarithm = "logical")[]\T1/ptm/m/ n/10 : the [][][]\T1/zi4/m/sl/10 determinant[][][](x) [2990] [2991] [2992] Underfull \hbox (badness 10000) in paragraph at lines 5399--5401 []\T1/ptm/m/n/10 a ma-trix fac-tor-iza-tion, typ-i-cally in-her-it-ing from vir -tual class [2993] [2994] Underfull \hbox (badness 10000) in paragraph at lines 5522--5529 []\T1/zi4/m/sl/10 signature(x = "CHMfactor")[]\T1/ptm/m/n/10 : as []\T1/zi4/m/s l/10 expand2[]\T1/ptm/m/n/10 , but re-turn-ing []\T1/zi4/m/sl/10 list(P, L)[]\T 1/ptm/m/n/10 . Underfull \hbox (badness 1776) in paragraph at lines 5522--5529 []\T1/zi4/m/sl/10 expand(x)[["P"]] []\T1/ptm/m/n/10 and []\T1/zi4/m/sl/10 expan d2(x)[["P1"]] []\T1/ptm/m/n/10 rep-re-sent the same per-mu-ta-tion ma-trix Underfull \hbox (badness 10000) in paragraph at lines 5529--5544 []\T1/zi4/m/sl/10 signature(x = "sparseLU")[]\T1/ptm/m/n/10 : as []\T1/zi4/m/sl /10 expand2[]\T1/ptm/m/n/10 , but re-turn-ing []\T1/zi4/m/sl/10 list(P, L, U, Q )[]\T1/ptm/m/n/10 . Underfull \hbox (badness 10000) in paragraph at lines 5544--5549 []\T1/zi4/m/sl/10 signature(x = "denseLU")[]\T1/ptm/m/n/10 : as []\T1/zi4/m/sl/ 10 expand2[]\T1/ptm/m/n/10 , but re-turn-ing []\T1/zi4/m/sl/10 list(L, U, P)[]\ T1/ptm/m/n/10 . Underfull \hbox (badness 1142) in paragraph at lines 5544--5549 []\T1/zi4/m/sl/10 expand(x)[["P"]] []\T1/ptm/m/n/10 and []\T1/zi4/m/sl/10 expan d2(x)[["P1."]] []\T1/ptm/m/n/10 are iden-ti-cal mod-ulo []\T1/zi4/m/sl/10 Dimna mes[]\T1/ptm/m/n/10 . The [2995] [2996] [2997] [2998] [2999] [3000] [3001] Underfull \hbox (badness 1087) in paragraph at lines 5987--5993 []\T1/ptm/m/n/10 a string whose first three char-ac-ters spec-ify the class of the re-sult. It Underfull \hbox (badness 10000) in paragraph at lines 6000--6002 []\T1/ptm/m/n/10 a string in []\T1/zi4/m/sl/10 c("trace", "sumLog", "prod", "mi n", "max", "range", [3002] [3003] [3004] [3005] Underfull \hbox (badness 1931) in paragraph at lines 6262--6264 []\T1/ptm/m/n/10 a string spec-i-fy-ing how the []\T1/zi4/m/sl/10 zero.print [] \T1/ptm/m/n/10 codes should be aligned, see [3006] [3007] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.image}) h as been already used, duplicate ignored \relax l.6399 \aliasA{image}{image-methods}{image} [3008] Underfull \hbox (badness 1005) in paragraph at lines 6476--6481 []\T1/ptm/m/n/10 color for the bor-der of each rect-an-gle. []\T1/zi4/m/sl/10 N A []\T1/ptm/m/n/10 means no bor-der is drawn. Underfull \hbox (badness 1189) in paragraph at lines 6476--6481 \T1/ptm/m/n/10 When []\T1/zi4/m/sl/10 NULL []\T1/ptm/m/n/10 as by de-fault, []\ T1/zi4/m/sl/10 border.col <- if(lwd < .01) NA else NULL []\T1/ptm/m/n/10 is Underfull \hbox (badness 5862) in paragraph at lines 6495--6498 []\T1/ptm/m/n/10 All meth-ods cur-rently end up call-ing the method for the [][ ][]\T1/zi4/m/sl/10 dgTMatrix[][][] []\T1/ptm/m/n/10 class. Use [3009] Overfull \hbox (42.75635pt too wide) in paragraph at lines 6545--6545 []\T1/zi4/m/n/9 image(USCounties, c(1,100), c(1,100), useAbs=FALSE, lwd=3, bor der.col = adjustcolor("skyblue", 1/2))[] [3010] [3011] [3012] [3013] Underfull \hbox (badness 1509) in paragraph at lines 6810--6812 []\T1/ptm/m/n/10 an in-te-ger off-set, in-di-cat-ing that the re-sult should be a per-mu-ta-tion of [3014] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.anyNA}) h as been already used, duplicate ignored \relax l.6888 \aliasA{anyNA}{is.na-methods}{anyNA} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.is.finite }) has been already used, duplicate ignored \relax l.6895 ...asA{is.finite}{is.na-methods}{is.finite} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.is.infini te}) has been already used, duplicate ignored \relax l.6903 ...is.infinite}{is.na-methods}{is.infinite} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.is.na}) h as been already used, duplicate ignored \relax l.6911 \aliasA{is.na}{is.na-methods}{is.na} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.is.nan}) has been already used, duplicate ignored \relax l.6918 \aliasA{is.nan}{is.na-methods}{is.nan} [3015] [3016] [3017] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.isSymmetr ic}) has been already used, duplicate ignored \relax l.7077 ...etric}{isSymmetric-methods}{isSymmetric} Overfull \hbox (26.39984pt too wide) in paragraph at lines 7124--7124 []\T1/zi4/m/sl/10 isSymmetric(object, checkDN = TRUE, tol = 100 * .Machine$dou ble.eps, tol1 = 8 * tol, ...)[] [3018] [3019] [3020] [3021] [3022] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.kronecker }) has been already used, duplicate ignored \relax l.7453 ...kronecker}{kronecker-methods}{kronecker} [3023] [3024] [3025 pdfTeX warning (ext4): destination with the same identifier (name{Rfn.*,ndiMatr ix,Matrix.Rdash.method}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.7718 \end{Description} ] Underfull \hbox (badness 2478) in paragraph at lines 7736--7741 []\T1/ptm/m/n/10 Class []\T1/zi4/m/sl/10 "ldenseMatrix"[]\T1/ptm/m/n/10 , di-re ctly. Class []\T1/zi4/m/sl/10 "lMatrix"[]\T1/ptm/m/n/10 , by class []\T1/zi4/m/ sl/10 "ldenseMatrix"[]\T1/ptm/m/n/10 . Class Underfull \hbox (badness 10000) in paragraph at lines 7744--7747 []\T1/ptm/m/n/10 Currently, mainly [][][]\T1/zi4/m/sl/10 t[][][]() []\T1/ptm/m/ n/10 and co-er-cion meth-ods (for [][][]\T1/zi4/m/sl/10 as[][][](.)[]\T1/ptm/m/ n/10 ); use, e.g., [3026] [3027] [3028] Underfull \hbox (badness 10000) in paragraph at lines 7968--7971 []\T1/ptm/m/n/10 Currently, mainly [][][]\T1/zi4/m/sl/10 t[][][]() []\T1/ptm/m/ n/10 and co-er-cion meth-ods (for [][][]\T1/zi4/m/sl/10 as[][][](.)[]\T1/ptm/m/ n/10 ; use, e.g., [3029] Underfull \hbox (badness 10000) in paragraph at lines 8029--8032 []\T1/ptm/m/n/10 Currently, mainly [][][]\T1/zi4/m/sl/10 t[][][]() []\T1/ptm/m/ n/10 and co-er-cion meth-ods (for [][][]\T1/zi4/m/sl/10 as[][][](.)[]\T1/ptm/m/ n/10 ; use, e.g., [3030] [3031] [3032] [3033] pdfTeX warning (ext4): destination with the same identifier (name{Rfn..Rpcent.* .Rpcent.}) has been already used, duplicate ignored \relax l.8310 ...*\%}{matmult-methods}{.Rpcent.*.Rpcent.} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.crossprod }) has been already used, duplicate ignored \relax l.8384 ...A{crossprod}{matmult-methods}{crossprod} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.tcrosspro d}) has been already used, duplicate ignored \relax l.8460 ...tcrossprod}{matmult-methods}{tcrossprod} [3034] Underfull \hbox (badness 10000) in paragraph at lines 8618--8623 []\T1/zi4/m/sl/10 signature(x = "dtrMatrix", y = "matrix") []\T1/ptm/m/n/10 and other sig-na-tures (use Underfull \hbox (badness 5359) in paragraph at lines 8618--8623 []\T1/zi4/m/sl/10 showMethods("%*%", class="dtrMatrix")[]\T1/ptm/m/n/10 ): ma-t rix mul-ti-pli-ca-tion. Mul-ti-pli-ca-tion Underfull \hbox (badness 10000) in paragraph at lines 8627--8629 []\T1/zi4/m/sl/10 signature(x = "CsparseMatrix", y = "missing") []\T1/ptm/m/n/1 0 re-turns []\T1/zi4/m/sl/10 t(x) %*% x []\T1/ptm/m/n/10 as an Underfull \hbox (badness 10000) in paragraph at lines 8629--8631 []\T1/zi4/m/sl/10 signature(x = "TsparseMatrix", y = "missing") []\T1/ptm/m/n/1 0 re-turns []\T1/zi4/m/sl/10 t(x) %*% x []\T1/ptm/m/n/10 as an [3035] [3036] [3037] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.det}) has been already used, duplicate ignored \relax l.8856 \aliasA{det}{Matrix-class}{det} [3038] Underfull \hbox (badness 1527) in paragraph at lines 8933--8935 []\T1/zi4/m/sl/10 signature(x = "Matrix")[]\T1/ptm/m/n/10 : sim-ply de-fined as []\T1/zi4/m/sl/10 prod(dim(x)) []\T1/ptm/m/n/10 (and hence of mode Underfull \hbox (badness 4846) in paragraph at lines 8941--8944 []\T1/zi4/m/sl/10 signature(object = "Matrix")[]\T1/ptm/m/n/10 : draws an [][][ ]\T1/zi4/m/sl/10 image[][][] []\T1/ptm/m/n/10 of the ma-trix en-tries, us-ing Underfull \hbox (badness 10000) in paragraph at lines 8946--8949 [3039] [3040] [3041] Underfull \hbox (badness 10000) in paragraph at lines 9148--9150 []\T1/zi4/m/sl/10 signature(x = "MatrixFactorization", logarithm = "missing")[] \T1/ptm/m/n/10 : sets Underfull \hbox (badness 10000) in paragraph at lines 9154--9156 []\T1/zi4/m/sl/10 signature(x = "MatrixFactorization", value = "NULL")[]\T1/ptm /m/n/10 : re-turns []\T1/zi4/m/sl/10 x []\T1/ptm/m/n/10 with Underfull \hbox (badness 10000) in paragraph at lines 9156--9158 []\T1/zi4/m/sl/10 signature(x = "MatrixFactorization", value = "list")[]\T1/ptm /m/n/10 : re-turns []\T1/zi4/m/sl/10 x []\T1/ptm/m/n/10 with [3042] Underfull \hbox (badness 10000) in paragraph at lines 9193--9196 []\T1/ptm/m/n/10 Generic func-tions [][][]\T1/zi4/m/sl/10 expand1[][][] []\T1/p tm/m/n/10 and [][][]\T1/zi4/m/sl/10 expand2[][][] []\T1/ptm/m/n/10 for con-stru ct-ing ma-trix fac-tors from [3043] Underfull \hbox (badness 10000) in paragraph at lines 9311--9313 []\T1/ptm/m/n/10 logical in-di-cat-ing if []\T1/zi4/m/sl/10 X <- (X + t(X))/2 [ ]\T1/ptm/m/n/10 should be done, af-ter []\T1/zi4/m/sl/10 X <- [3044] [3045] [3046] Underfull \hbox (badness 2478) in paragraph at lines 9507--9512 []\T1/ptm/m/n/10 Class []\T1/zi4/m/sl/10 "ndenseMatrix"[]\T1/ptm/m/n/10 , di-re ctly. Class []\T1/zi4/m/sl/10 "lMatrix"[]\T1/ptm/m/n/10 , by class []\T1/zi4/m/ sl/10 "ndenseMatrix"[]\T1/ptm/m/n/10 . Class [3047] Underfull \hbox (badness 10000) in paragraph at lines 9515--9518 []\T1/ptm/m/n/10 Currently, mainly [][][]\T1/zi4/m/sl/10 t[][][]() []\T1/ptm/m/ n/10 and co-er-cion meth-ods (for [][][]\T1/zi4/m/sl/10 as[][][](.)[]\T1/ptm/m/ n/10 ); use, e.g., [3048] [3049] Underfull \hbox (badness 5924) in paragraph at lines 9696--9698 []\T1/ptm/m/n/10 fast sim-ple meth-ods pdfTeX warning (ext4): destination with the same identifier (name{Rfn.norm}) ha s been already used, duplicate ignored \relax l.9738 \aliasA{norm}{norm-methods}{norm} [3050] [3051] [3052] [3053] Underfull \hbox (badness 10000) in paragraph at lines 10031--10034 []\T1/ptm/m/n/10 Currently, mainly [][][]\T1/zi4/m/sl/10 t[][][]() []\T1/ptm/m/ n/10 and co-er-cion meth-ods (for [][][]\T1/zi4/m/sl/10 as[][][](.)[]\T1/ptm/m/ n/10 ; use, e.g., [3054] Underfull \hbox (badness 10000) in paragraph at lines 10095--10098 []\T1/ptm/m/n/10 Currently, mainly [][][]\T1/zi4/m/sl/10 t[][][]() []\T1/ptm/m/ n/10 and co-er-cion meth-ods (for [][][]\T1/zi4/m/sl/10 as[][][](.)[]\T1/ptm/m/ n/10 ; use, e.g., [3055] [3056] [3057] Underfull \hbox (badness 4242) in paragraph at lines 10295--10298 [][][]\T1/zi4/m/sl/10 pack[][][] []\T1/ptm/m/n/10 and [][][]\T1/zi4/m/sl/10 unp ack[][][][]\T1/ptm/m/n/10 ; its vir-tual "com-ple-ment" []\T1/zi4/m/sl/10 "[][] unpackedMatrix[][][]"[]\T1/ptm/m/n/10 ; its proper sub-classes [3058] Underfull \hbox (badness 3547) in paragraph at lines 10383--10386 []\T1/zi4/m/sl/10 signature(x = "pMatrix", y = "Matrix") []\T1/ptm/m/n/10 and o th-ers listed by []\T1/zi4/m/sl/10 showMethods("%*%", [3059] [3060] [3061] [3062] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.qr}) has been already used, duplicate ignored \relax l.10601 \aliasA{qr}{qr-methods}{qr} [3063] [3064] Underfull \vbox (badness 10000) has occurred while \output is active [3065] [3066] Underfull \hbox (badness 7186) in paragraph at lines 10845--10851 []\T1/ptm/m/n/10 for a dense ma-trix, this is the rank of [][][]\T1/zi4/m/sl/10 qr[][][](x, tol, [3067] [3068] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.rcond}) h as been already used, duplicate ignored \relax l.11002 \aliasA{rcond}{rcond-methods}{rcond} [3069] [3070] [3071] [3072] Underfull \hbox (badness 2351) in paragraph at lines 11284--11292 []\T1/ptm/m/n/10 The al-go-rithm first sam-ples ``en-coded'' $\OT1/cmr/m/n/10 ( \OML/cmm/m/it/10 i; j\OT1/cmr/m/n/10 )$\T1/ptm/m/n/10 s with-out re-place-ment, via one di-men-sional Underfull \hbox (badness 1509) in paragraph at lines 11284--11292 \T1/ptm/m/n/10 in-dices, if not []\T1/zi4/m/sl/10 symmetric [][]sample.int[][][ ](nrow*ncol, nnz)[]\T1/ptm/m/n/10 , then---if []\T1/zi4/m/sl/10 rand.x []\T1/pt m/m/n/10 is not []\T1/zi4/m/sl/10 NULL[]\T1/ptm/m/n/10 --- [3073] [3074] Underfull \hbox (badness 10000) in paragraph at lines 11441--11444 []\T1/ptm/m/n/10 Class [][][]\T1/zi4/m/sl/10 SchurFactorization[][][][]\T1/ptm/ m/n/10 , di-rectly. Class [][][]\T1/zi4/m/sl/10 MatrixFactorization[][][][]\T1/ ptm/m/n/10 , by class [3075] [3076] [3077] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.solve}) h as been already used, duplicate ignored \relax l.11630 \aliasA{solve}{solve-methods}{solve} [3078] [3079] Underfull \hbox (badness 5316) in paragraph at lines 11816--11821 []\T1/ptm/m/n/10 Methods for dense []\T1/zi4/m/sl/10 a []\T1/ptm/m/n/10 are bui lt on 14 LA-PACK rou-tines: class []\T1/zi4/m/sl/10 d..Matrix[]\T1/ptm/m/n/10 , where [3080] Underfull \hbox (badness 10000) in paragraph at lines 11916--11919 []\T1/ptm/m/n/10 Construct a sparse model or ``de-sign'' ma-trix, from a for-mu la and data frame [3081] Underfull \hbox (badness 10000) in paragraph at lines 11952--11955 []\T1/ptm/m/n/10 character string or []\T1/zi4/m/sl/10 NULL []\T1/ptm/m/n/10 or (co-er-ca-ble to) Underfull \hbox (badness 10000) in paragraph at lines 11963--11967 []\T1/ptm/m/n/10 should fac-tors have un-used lev-els dropped? The de-fault for [3082] [3083] [3084] [3085] [3086] [3087] [3088] [3089] Underfull \hbox (badness 10000) in paragraph at lines 12500--12508 []\T1/zi4/m/sl/10 (object = "sparseMatrix", uniqT=FALSE)[]\T1/ptm/m/n/10 : Re-t urns an ob-ject of S3 class Underfull \hbox (badness 1796) in paragraph at lines 12500--12508 []\T1/zi4/m/sl/10 "sparseSummary" []\T1/ptm/m/n/10 which is ba-si-cally a [][][ ]\T1/zi4/m/sl/10 data.frame[][][] []\T1/ptm/m/n/10 with columns []\T1/zi4/m/sl/ 10 (i,j,x) []\T1/ptm/m/n/10 (or just Underfull \hbox (badness 10000) in paragraph at lines 12525--12533 []\T1/zi4/m/sl/10 signature(from = "factor", to = "sparseMatrix")[]\T1/ptm/m/n/ 10 : Co-er-cion of a fac-tor to Underfull \hbox (badness 1112) in paragraph at lines 12525--12533 []\T1/zi4/m/sl/10 "sparseMatrix" []\T1/ptm/m/n/10 pro-duces the ma-trix of in-d i-ca-tor \T1/ptm/b/n/10 rows \T1/ptm/m/n/10 stored as an ob-ject of class [3090] [3091] [3092] [3093] [3094] Underfull \hbox (badness 5036) in paragraph at lines 12918--12920 []\T1/ptm/m/n/10 vector of the non zero en-tries; may be miss-ing in which case a [3095] [3096] Underfull \hbox (badness 2828) in paragraph at lines 13084--13087 []\T1/zi4/m/sl/10 signature(x = "sparseVector", mode = "character") []\T1/ptm/m /n/10 co-erces sparse vec-tors to Underfull \hbox (badness 2486) in paragraph at lines 13106--13109 []\T1/zi4/m/sl/10 signature(x = "sparseVector") []\T1/ptm/m/n/10 re-peat []\T1/ zi4/m/sl/10 x[]\T1/ptm/m/n/10 , with the same ar-gu-ment list []\T1/zi4/m/sl/10 (x, times, [3097] [3098] [3099] [3100] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.[<.Rdash. }) has been already used, duplicate ignored \relax l.13311 ...\Rdash{}}{subassign-methods}{[<.Rdash.} Underfull \hbox (badness 6910) in paragraph at lines 13398--13400 []\T1/ptm/m/n/10 is cur-rently a sim-ple fall-back [3101] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.[}) has b een already used, duplicate ignored \relax l.13445 \aliasA{[}{subscript-methods}{[} [3102] [3103] Underfull \hbox (badness 2057) in paragraph at lines 13656--13658 []\T1/ptm/m/n/10 These are generic func-tions with sev-eral meth-ods for dif-fe r-ent ma-trix classes, use e.g., Underfull \hbox (badness 10000) in paragraph at lines 13670--13675 []\T1/zi4/m/sl/10 skewpart(x) []\T1/ptm/m/n/10 re-turns a skew-symmetric ma-tri x, in-her-it-ing from [][][]\T1/zi4/m/sl/10 generalMatrix[][][][]\T1/ptm/m/n/10 , [3104] [3105] [3106] Underfull \hbox (badness 10000) in paragraph at lines 13826--13831 []\T1/ptm/m/n/10 Note that all []\T1/zi4/m/sl/10 new(.)[]\T1/ptm/m/n/10 , [][][ ]\T1/zi4/m/sl/10 spMatrix[][][] []\T1/ptm/m/n/10 and [][][]\T1/zi4/m/sl/10 spar seMatrix[][][](*, repr="T") []\T1/ptm/m/n/10 con-struc-tors for Underfull \hbox (badness 1831) in paragraph at lines 13832--13838 []\T1/ptm/m/n/10 For con-ve-nience, meth-ods for some op-er-a-tions such as []\ T1/zi4/m/sl/10 %*% []\T1/ptm/m/n/10 and []\T1/zi4/m/sl/10 crossprod []\T1/ptm/m /n/10 are de-fined [3107] [3108] [3109] Overfull \hbox (21.75807pt too wide) in paragraph at lines 14021--14027 []\T1/ptm/m/n/10 GAL lat-tice file `\T1/zi4/m/sl/10 usc_q.GAL\T1/ptm/m/n/10 ' ( re-trieved in 2008 from `\T1/zi4/m/sl/10 http://sal.uiuc.edu/weights/zips/usc.z ip\T1/ptm/m/n/10 ' [3110] [3111] [3112]) (./mgcv-pkg.tex Chapter 24. [3113] [3114] [3115] Underfull \hbox (badness 1142) in paragraph at lines 185--189 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from Underfull \hbox (badness 1043) in paragraph at lines 210--215 \T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known scale. [3116] [3117] [3118] [3119] [3120] Underfull \hbox (badness 10000) in paragraph at lines 379--386 [][][]\T1/zi4/m/sl/10 mgcv.parallel[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/ 10 mgcv-package[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 gamObject[][][][] \T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 gam.models[][][][]\T1/ptm/m/n/10 , [][][ ]\T1/zi4/m/sl/10 smooth.terms[][][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 7168) in paragraph at lines 379--386 [][][]\T1/zi4/m/sl/10 linear.functional.terms[][][][]\T1/ptm/m/n/10 , [][][]\T1 /zi4/m/sl/10 s[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 te[][][] [][]predi ct.gam[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 plot.gam[][][][]\T1/ptm/m/ n/10 , [][][]\T1/zi4/m/sl/10 summary.gam[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/ m/sl/10 gam.side[][][][]\T1/ptm/m/n/10 , [3121] [3122] [3123] [3124] [3125] [3126] Underfull \hbox (badness 1406) in paragraph at lines 704--705 []\T1/ptm/m/n/10 The MKL BLAS is mut-lithreaded by de-fault. Un-der linux set-t ing en-vi-ron-ment vari-able [3127] [3128] Underfull \hbox (badness 1158) in paragraph at lines 814--816 []\T1/ptm/m/n/10 Choosing the ba-sis di-men-sion, and check-ing the choice, whe n us-ing pe-nal-ized re-gres-sion [3129] Underfull \hbox (badness 1259) in paragraph at lines 877--878 []\T1/ptm/m/n/10 Wood, S.N. (2017) Gen-er-al-ized Ad-di-tive Mod-els: An In-tro -duc-tion with R (2nd edi-tion). [3130] Underfull \vbox (badness 10000) has occurred while \output is active [3131] [3132] [3133] [3134] [3135] [3136] [3137] Underfull \hbox (badness 1281) in paragraph at lines 1272--1273 []\T1/zi4/m/sl/10 deviance[]\T1/ptm/m/n/10 ,[]\T1/zi4/m/sl/10 martingale[]\T1/p tm/m/n/10 ,[]\T1/zi4/m/sl/10 score[]\T1/ptm/m/n/10 , or []\T1/zi4/m/sl/10 schoe nfeld []\T1/ptm/m/n/10 resid-u-als can be ex-tracted. See Klein amd [3138] [3139] Underfull \vbox (badness 10000) has occurred while \output is active [3140] [3141] [3142] Underfull \vbox (badness 10000) has occurred while \output is active [3143] [3144] [3145] [3146] [3147] [3148] [3149] [3150] [3151] [3152] [3153] [3154] [3155] [3156] [3157] Underfull \vbox (badness 2302) has occurred while \output is active [3158] [3159] [3160] [3161] [3162] Underfull \hbox (badness 1142) in paragraph at lines 2604--2608 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from Underfull \hbox (badness 1043) in paragraph at lines 2630--2636 \T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known scale. [3163] [3164] [3165] [3166] [3167] [3168] [3169] Underfull \vbox (badness 10000) has occurred while \output is active [3170] Underfull \vbox (badness 10000) has occurred while \output is active [3171] [3172] [3173] [3174] [3175] [3176] [3177] [3178] [3179] [3180] [3181] [3182] [3183] [3184] [3185] [3186] [3187] [3188] Underfull \hbox (badness 10000) in paragraph at lines 4071--4075 []\T1/ptm/m/n/10 Random ef-fects can be added to []\T1/zi4/m/sl/10 gam []\T1/pt m/m/n/10 mod-els us-ing []\T1/zi4/m/sl/10 s(...,bs="re") []\T1/ptm/m/n/10 terms (see [3189] [3190] Underfull \vbox (badness 10000) has occurred while \output is active [3191] Underfull \vbox (badness 10000) has occurred while \output is active [3192] [3193] Underfull \hbox (badness 1184) in paragraph at lines 4358--4362 []\T1/ptm/m/n/10 list of the square root penal-ties: last en-try is root of fix ed penalty, if [3194] [3195] [3196] [3197] [3198] [3199] [3200] [3201] [3202] [3203] [3204] [3205] [3206] Underfull \hbox (badness 1142) in paragraph at lines 5081--5085 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from [3207] [3208] Underfull \hbox (badness 1231) in paragraph at lines 5185--5187 []\T1/zi4/m/sl/10 gamm []\T1/ptm/m/n/10 per-forms poorly with bi-nary data, sin ce it uses PQL. It is bet-ter to use []\T1/zi4/m/sl/10 gam []\T1/ptm/m/n/10 wit h [3209] [3210] Underfull \vbox (badness 10000) has occurred while \output is active [3211] Underfull \vbox (badness 10000) has occurred while \output is active [3212] [3213] [3214] [3215] Underfull \hbox (badness 2181) in paragraph at lines 5626--5627 []\T1/ptm/m/n/10 one sided for-mula con-tain-ing vari-ables needed for pre-dic- tion, used by [3216] [3217] [3218] [3219] [3220] [3221] [3222] [3223] [3224] Underfull \vbox (badness 3803) has occurred while \output is active [3225] Underfull \hbox (badness 10000) in paragraph at lines 6130--6131 []\T1/ptm/m/n/10 A pre-fit gam ob-ject, as pro-duced by []\T1/zi4/m/sl/10 gam(. ..,fit=FALSE) []\T1/ptm/m/n/10 or [3226] [3227] [3228] [3229] [3230] [3231] [3232] [3233] [3234] [3235] [3236] Underfull \hbox (badness 1142) in paragraph at lines 6715--6719 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from [3237] [3238] [3239] [3240] Underfull \vbox (badness 3803) has occurred while \output is active [3241] [3242] [3243] [3244] Underfull \hbox (badness 1087) in paragraph at lines 7087--7088 []\T1/ptm/m/n/10 If []\T1/zi4/m/sl/10 rho []\T1/ptm/m/n/10 and []\T1/zi4/m/sl/1 0 theta []\T1/ptm/m/n/10 were sup-plied then deriva-tives are w.r.t. these. In this case, and if [3245] [3246] [3247] Underfull \vbox (badness 10000) has occurred while \output is active [3248] Underfull \vbox (badness 10000) has occurred while \output is active [3249] [3250] [3251] [3252] [3253] [3254] [3255] [3256] [3257] [3258] [3259] Underfull \vbox (badness 4805) has occurred while \output is active [3260] [3261] [3262] Underfull \hbox (badness 1242) in paragraph at lines 8046--8047 []\T1/ptm/m/n/10 Development of mgcv ver-sion 1.8 was part funded by EP-SRC gra nts EP/K005251/1 and Underfull \hbox (badness 1122) in paragraph at lines 8072--8073 []\T1/ptm/m/n/10 When us-ing [][][]\T1/zi4/m/sl/10 NCV[][][] []\T1/ptm/m/n/10 w ith [][][]\T1/zi4/m/sl/10 gam[][][] []\T1/ptm/m/n/10 worth-while per-for-mance im-prove-ments are avail-able by set-ting [3263] [3264] [3265] [3266] [3267] [3268] [3269] [3270] [3271] [3272] [3273] [3274] [3275] [3276] [3277] Underfull \hbox (badness 6001) in paragraph at lines 8785--8787 []\T1/ptm/m/n/10 Simon N. Wood \T1/zi4/m/sl/10 \T1/p tm/m/n/10 mod-i-fied from Ven-ables and Rip-ley's [3278] [3279] [3280] [3281] [3282] [3283] [3284] [3285] [3286] [3287] [3288] Underfull \vbox (badness 10000) has occurred while \output is active [3289] [3290] Underfull \hbox (badness 1038) in paragraph at lines 9533--9536 []\T1/ptm/m/n/10 The fol-low-ing func-tions are pro-vided: []\T1/zi4/m/sl/10 Di m.pdIndot[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 coef.pdIdnot[]\T1/ptm/m/n/10 , [] \T1/zi4/m/sl/10 corMatrix.pdIdnot[]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 9533--9536 []\T1/zi4/m/sl/10 logDet.pdIdnot[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 pdConstruc t.pdIdnot[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 pdFactor.pdIdnot[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 pdMatrix.pdIdnot[]\T1/ptm/m/n/10 , [3291] Underfull \hbox (badness 10000) in paragraph at lines 9589--9592 []\T1/ptm/m/n/10 These func-tions ([]\T1/zi4/m/sl/10 pdTens[]\T1/ptm/m/n/10 , [ ]\T1/zi4/m/sl/10 pdConstruct.pdTens[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 pdFacto r.pdTens[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 pdMatrix.pdTens[]\T1/ptm/m/n/10 , [3292] [3293] [3294] [3295] [3296] [3297] [3298] [3299] [3300] [3301] [3302] [3303] Underfull \hbox (badness 1852) in paragraph at lines 10261--10264 []\T1/ptm/m/n/10 To fa-cil-i-tate plot-ting with [][][]\T1/zi4/m/sl/10 termplot [][][][]\T1/ptm/m/n/10 , if []\T1/zi4/m/sl/10 object []\T1/ptm/m/n/10 pos-sesse s an at-tribute []\T1/zi4/m/sl/10 "para.only" []\T1/ptm/m/n/10 and [3304] [3305] [3306] Underfull \hbox (badness 1852) in paragraph at lines 10430--10433 []\T1/ptm/m/n/10 To fa-cil-i-tate plot-ting with [][][]\T1/zi4/m/sl/10 termplot [][][][]\T1/ptm/m/n/10 , if []\T1/zi4/m/sl/10 object []\T1/ptm/m/n/10 pos-sesse s an at-tribute []\T1/zi4/m/sl/10 "para.only" []\T1/ptm/m/n/10 and [3307] [3308] Underfull \vbox (badness 10000) has occurred while \output is active [3309] Underfull \vbox (badness 10000) has occurred while \output is active [3310] Underfull \hbox (badness 1205) in paragraph at lines 10670--10671 []\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a tes at which Underfull \hbox (badness 2689) in paragraph at lines 10670--10671 \T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are as for Underfull \hbox (badness 1975) in paragraph at lines 10676--10681 []\T1/ptm/m/n/10 Smooth terms in a GAM for-mula are turned into smooth spec-i-f i-ca-tion ob-jects of class [3311] [3312] Underfull \hbox (badness 1205) in paragraph at lines 10760--10761 []\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a tes at which Underfull \hbox (badness 2689) in paragraph at lines 10760--10761 \T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are as for [3313] [3314] Underfull \vbox (badness 3803) has occurred while \output is active [3315] Underfull \hbox (badness 1253) in paragraph at lines 10959--10961 []\T1/ptm/m/n/10 Note that the op-ti-mized smooth-ing pa-ram-e-ter se-lec-tion cri-te-rion re-ported is one of GCV, [3316] [3317] [3318] [3319] [3320] [3321] Underfull \hbox (badness 4792) in paragraph at lines 11220--11223 []\T1/ptm/m/n/10 Alternatively, but less straight-for-wardly, the []\T1/zi4/m/s l/10 paraPen []\T1/ptm/m/n/10 ar-gu-ment to [][][]\T1/zi4/m/sl/10 gam[][][] []\ T1/ptm/m/n/10 can be used: Underfull \hbox (badness 10000) in paragraph at lines 11220--11223 \T1/ptm/m/n/10 see [][][]\T1/zi4/m/sl/10 gam.models[][][][]\T1/ptm/m/n/10 . If smooth-ing pa-ram-e-ter es-ti-ma-tion is by ML or REML (e.g. [3322] [3323] Underfull \hbox (badness 10000) in paragraph at lines 11327--11330 []\T1/ptm/m/n/10 the type of resid-u-als wanted. Usu-ally one of []\T1/zi4/m/sl /10 "deviance"[]\T1/ptm/m/n/10 , [3324] [3325] [3326] [3327] [3328] [3329] [3330] [3331] [3332] [3333] [3334] [3335] Underfull \vbox (badness 10000) has occurred while \output is active [3336] [3337] Underfull \hbox (badness 3861) in paragraph at lines 12118--12121 []\T1/ptm/m/n/10 INTERNAL rou-tine to ap-ply ini-tial Sl re-parameterization to model ma-trix X, or, if [3338] [3339] [3340] Underfull \hbox (badness 1320) in paragraph at lines 12233--12238 \T1/ptm/m/n/10 and []\T1/zi4/m/sl/10 b.orig = D*b.repara []\T1/ptm/m/n/10 (wher e []\T1/zi4/m/sl/10 b.orig []\T1/ptm/m/n/10 is the orig-i-nal pa-ram-e-ter vec- tor). If ma- [3341] [3342] Underfull \hbox (badness 1975) in paragraph at lines 12339--12344 []\T1/ptm/m/n/10 Smooth terms in a GAM for-mula are turned into smooth spec-i-f i-ca-tion ob-jects of class [3343] Underfull \hbox (badness 1762) in paragraph at lines 12428--12440 \T1/ptm/m/n/10 plate re-gres-sion splines: see [][][]\T1/zi4/m/sl/10 tprs[][][] []\T1/ptm/m/n/10 ); []\T1/zi4/m/sl/10 ts.smooth.spec []\T1/ptm/m/n/10 (thin pla te re-gres-sion splines with [3344] [3345] [3346] Underfull \vbox (badness 3803) has occurred while \output is active [3347] Underfull \hbox (badness 7667) in paragraph at lines 12640--12646 [][][]\T1/zi4/m/sl/10 gam[][][] []\T1/ptm/m/n/10 can use adap-tive smooths of o ne or two vari-ables, spec-i-fied via terms like [3348] Underfull \hbox (badness 10000) in paragraph at lines 12681--12682 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3349] [3350] [3351] [3352] Underfull \vbox (badness 3803) has occurred while \output is active [3353] Underfull \hbox (badness 10000) in paragraph at lines 12958--12960 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3354] [3355] [3356] Underfull \hbox (badness 10000) in paragraph at lines 13088--13089 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3357] [3358] Underfull \hbox (badness 1436) in paragraph at lines 13224--13231 \T1/ptm/m/n/10 nest-ing of the smooth within the fac-tor. Note how-ever that: i ) []\T1/zi4/m/sl/10 gamm []\T1/ptm/m/n/10 only al-lows one [3359] [3360] Underfull \hbox (badness 10000) in paragraph at lines 13323--13324 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3361] [3362] [3363] [3364] [3365] [3366] [3367] [3368] Underfull \vbox (badness 10000) has occurred while \output is active [3369] [3370] [3371] [3372] Underfull \hbox (badness 10000) in paragraph at lines 13924--13930 []\T1/ptm/m/n/10 A smooth spec-i-fi-ca-tion ob-ject as pro-duced by a Underfull \hbox (badness 1292) in paragraph at lines 13924--13930 []\T1/zi4/m/sl/10 s(...,bs="so",xt=list(bnd=bnd,...)) []\T1/ptm/m/n/10 term in a []\T1/zi4/m/sl/10 gam []\T1/ptm/m/n/10 for-mula. Note [3373] [3374] [3375] Underfull \vbox (badness 10000) has occurred while \output is active [3376] Underfull \vbox (badness 10000) has occurred while \output is active [3377] [3378] Underfull \hbox (badness 10000) in paragraph at lines 14268--14269 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3379] [3380] [3381] [3382] Overfull \hbox (35.26862pt too wide) in paragraph at lines 14480--14480 []\T1/zi4/m/n/9 b <- gam(y ~ s(x)+s(f1,x,bs="sz")+s(f2,x,bs="sz")+s(f1,f2,x,bs ="sz",id=1),data=dat,method="REML")[] [3383] [3384] Underfull \hbox (badness 3895) in paragraph at lines 14626--14629 [][][]\T1/zi4/m/sl/10 gam[][][] []\T1/ptm/m/n/10 can use isotropic smooths of a ny num-ber of vari-ables, spec-i-fied via terms like [3385] Underfull \hbox (badness 10000) in paragraph at lines 14671--14673 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3386] [3387] [3388] [3389] [3390] [3391] Underfull \hbox (badness 1371) in paragraph at lines 14951--14957 []\T1/zi4/m/sl/10 bs="ad" []\T1/ptm/m/n/10 Uni-vari-ate and bi-vari-ate adap-ti ve smooths are avail-able (see Underfull \hbox (badness 10000) in paragraph at lines 14962--14964 []\T1/zi4/m/sl/10 bs="fs" []\T1/ptm/m/n/10 A spe-cial smoother class (see Underfull \hbox (badness 1132) in paragraph at lines 14962--14964 [][][]\T1/zi4/m/sl/10 smooth.construct.fs.smooth.spec[][][][]\T1/ptm/m/n/10 ) i s avail-able for the case in which a smooth is [3392] Underfull \hbox (badness 6461) in paragraph at lines 14996--15000 [][][]\T1/zi4/m/sl/10 s[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 te[][][][ ]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 t2[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi 4/m/sl/10 tprs[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 Duchon.spline[][][ ][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 cubic.regression.spline[][][][]\T1/pt m/m/n/10 , [][][]\T1/zi4/m/sl/10 p.spline[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4 /m/sl/10 d.spline[][][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 14996--15000 [][][]\T1/zi4/m/sl/10 mrf[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 soap[][ ][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 Spherical.Spline[][][][]\T1/ptm/m/n /10 , [][][]\T1/zi4/m/sl/10 adaptive.smooth[][][][]\T1/ptm/m/n/10 , [][][]\T1/z i4/m/sl/10 user.defined.smooth[][][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 14996--15000 [][][]\T1/zi4/m/sl/10 smooth.construct.re.smooth.spec[][][][]\T1/ptm/m/n/10 , [ ][][]\T1/zi4/m/sl/10 smooth.construct.gp.smooth.spec[][][][]\T1/ptm/m/n/10 , [3393] [3394] [3395] [3396] Underfull \hbox (badness 2326) in paragraph at lines 15200--15207 []\T1/ptm/m/n/10 These wrap-per func-tions ex-ist to al-low smooths spec-i-fied us-ing [][][]\T1/zi4/m/sl/10 smooth.construct[][][] []\T1/ptm/m/n/10 and [3397] Underfull \hbox (badness 2158) in paragraph at lines 15285--15285 []\T1/ptm/m/it/10 Extract smooth-ing pa-ram-e-ter es-ti-ma-tor co-vari-ance ma- trix from [3398] [3399] [3400] [3401] [3402] [3403] [3404] [3405] [3406] [3407] [3408] [3409] [3410] [3411] [3412] [3413] [3414] [3415] [3416] [3417] [3418] [3419] [3420] [3421] [3422] [3423] [3424] Overfull \hbox (21.42029pt too wide) in paragraph at lines 16847--16847 []\T1/zi4/m/sl/10 vcov(object, sandwich=FALSE, freq = FALSE, dispersion = NULL ,unconditional=FALSE, ...)[] [3425] [3426] [3427] Underfull \hbox (badness 1796) in paragraph at lines 16960--16963 []\T1/ptm/m/n/10 other op-tions to pass on to [][][]\T1/zi4/m/sl/10 persp[][][] []\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 image[][][] []\T1/ptm/m/n/10 or [][][] \T1/zi4/m/sl/10 contour[][][][]\T1/ptm/m/n/10 . In par-tic-u-lar [3428] [3429] [3430] [3431] [3432] [3433] Underfull \vbox (badness 3803) has occurred while \output is active [3434] [3435] [3436]) (./nlme-pkg.tex Chapter 25. [3437] [3438] [3439] [3440] [3441] [3442] [3443] [3444] [3445] [3446] [3447] [3448] [3449] [3450] [3451] [3452] [3453] [3454] [3455] [3456] [3457] [3458] [3459] [3460] [3461] [3462] [3463] [3464] [3465] [3466] [3467] [3468] [3469] [3470] [3471] [3472] [3473] Underfull \hbox (badness 10000) in paragraph at lines 2238--2244 [][][]\T1/zi4/m/sl/10 ACF.lme[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 cor ARMA[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 corClasses[][][][]\T1/ptm/m/ n/10 , [][][]\T1/zi4/m/sl/10 Dim.corSpatial[][][][]\T1/ptm/m/n/10 , [][][]\T1/z i4/m/sl/10 Initialize.corStruct[][][][]\T1/ptm/m/n/10 , [3474] [3475] [3476] [3477] [3478] [3479] [3480] [3481] [3482] [3483] [3484] [3485] [3486] [3487] [3488] [3489] [3490] [3491] [3492] [3493] [3494] [3495] [3496] [3497] [3498] [3499] [3500] [3501] [3502] [3503] [3504] [3505] [3506] [3507] [3508] [3509] Underfull \hbox (badness 1067) in paragraph at lines 4372--4377 \T1/ptm/m/n/10 ma-trix), []\T1/zi4/m/sl/10 fitted []\T1/ptm/m/n/10 (fit-ted val -ues), and []\T1/zi4/m/sl/10 residuals []\T1/ptm/m/n/10 (resid-u-als). De-fault s to [3510] [3511] [3512] [3513] [3514] [3515] [3516] [3517] [3518] [3519] [3520] [3521] [3522] Underfull \hbox (badness 10000) in paragraph at lines 5116--5120 [][][]\T1/zi4/m/sl/10 getCovariate.corStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/ zi4/m/sl/10 getCovariate.data.frame[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/ 10 getCovariate.varFunc[][][][]\T1/ptm/m/n/10 , [3523] [3524] [3525] [3526] [3527] [3528] [3529] [3530] Underfull \hbox (badness 10000) in paragraph at lines 5540--5543 [][][]\T1/zi4/m/sl/10 getGroups.corStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4 /m/sl/10 getGroups.data.frame[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 get Groups.gls[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 getGroups.lmList[][][] []\T1/ptm/m/n/10 , [3531] [3532] [3533] [3534] [3535] [3536] [3537] Underfull \hbox (badness 10000) in paragraph at lines 5915--5920 [][][]\T1/zi4/m/sl/10 getGroupsFormula.gls[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi 4/m/sl/10 getGroupsFormula.lmList[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 getGroupsFormula.lme[][][][]\T1/ptm/m/n/10 , [3538] [3539] [3540] [3541] [3542] Underfull \hbox (badness 1490) in paragraph at lines 6194--6205 [][][]\T1/zi4/m/sl/10 corClasses[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 glsControl[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 glsObject[][][][]\T1/p tm/m/n/10 , [][][]\T1/zi4/m/sl/10 glsStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/z i4/m/sl/10 plot.gls[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 predict.gls[] [][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 qqnorm.gls[][][][]\T1/ptm/m/n/10 , [3543] Underfull \hbox (badness 10000) in paragraph at lines 6258--6260 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is [3544] [3545] [3546] [3547] [3548] [3549] [3550] Underfull \hbox (badness 10000) in paragraph at lines 6667--6669 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is [3551] [3552] [3553] [3554] Underfull \hbox (badness 10000) in paragraph at lines 6936--6943 [][][]\T1/zi4/m/sl/10 formula[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 gap ply[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 gsummary[][][][]\T1/ptm/m/n/1 0 , [][][]\T1/zi4/m/sl/10 lme[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 plo t.nffGroupedData[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 plot.nfnGroupedD ata[][][][]\T1/ptm/m/n/10 , [3555] [3556] [3557] [3558] Underfull \hbox (badness 10000) in paragraph at lines 7196--7202 [][][]\T1/zi4/m/sl/10 Initialize.corStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi 4/m/sl/10 Initialize.glsStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 In itialize.lmeStruct[][][][]\T1/ptm/m/n/10 , [3559] [3560] [3561] [3562] [3563] [3564] [3565] [3566] [3567] [3568] [3569] [3570] [3571] [3572] [3573] [3574] [3575] [3576] [3577] [3578] [3579] Underfull \hbox (badness 10000) in paragraph at lines 8466--8468 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is [3580] [3581] [3582] [3583] [3584] Underfull \hbox (badness 10000) in paragraph at lines 8751--8758 [][][]\T1/zi4/m/sl/10 lm[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 lme.lmLi st[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 plot.lmList[][][][]\T1/ptm/m/n /10 , [][][]\T1/zi4/m/sl/10 pooledSD[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl /10 predict.lmList[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 residuals.lmLi st[][][][]\T1/ptm/m/n/10 , [3585] [3586] [3587] [3588] [3589] [3590] [3591] [3592] [3593] Underfull \hbox (badness 10000) in paragraph at lines 9266--9273 [][][]\T1/zi4/m/sl/10 lme[][][][]\T1/ptm/m/n/10 ,[][][]\T1/zi4/m/sl/10 gls[][][ ][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 logLik.corStruct[][][][]\T1/ptm/m/n/1 0 , [][][]\T1/zi4/m/sl/10 logLik.glsStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi 4/m/sl/10 logLik.lmeStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 logLik .lmList[][][][]\T1/ptm/m/n/10 , [3594] [3595] [3596] [3597] [3598] [3599] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Matrix}) has been already used, duplicate ignored \relax l.9628 ...rA{Matrix}{Assign Matrix Values}{Matrix} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Matrix.1} ) has been already used, duplicate ignored \relax l.9628 ...rA{Matrix}{Assign Matrix Values}{Matrix} [3600] [3601] [3602] [3603] [3604] [3605] [3606] [3607] [3608] [3609] [3610] [3611] [3612] Underfull \hbox (badness 1596) in paragraph at lines 10395--10421 []\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a two-sided for-mula o f the form [3613] [3614] Underfull \hbox (badness 1490) in paragraph at lines 10511--10517 [][][]\T1/zi4/m/sl/10 nlmeControl[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 nlme.nlsList[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 nlmeObject[][][][]\ T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 nlsList[][][][]\T1/ptm/m/n/10 , [][][]\T1 /zi4/m/sl/10 nlmeStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 pdClasses [][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 reStruct[][][][]\T1/ptm/m/n/10 , [3615] [3616] [3617] [3618] Underfull \hbox (badness 10000) in paragraph at lines 10752--10754 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is [3619] [3620] [3621] [3622] [3623] [3624] [3625] [3626] [3627] [3628] [3629] [3630] [3631] [3632] [3633] [3634] [3635] [3636] [3637] [3638] [3639] [3640] [3641] [3642] [3643] [3644] [3645] [3646] [3647] [3648] [3649] [3650] [3651] [3652] [3653] [3654] [3655] [3656] [3657] [3658] [3659] [3660] [3661] [3662] [3663] [3664] [3665] Underfull \hbox (badness 1286) in paragraph at lines 13655--13662 []\T1/ptm/m/n/10 an op-tional log-i-cal func-tion or func-tion. If []\T1/zi4/m/ sl/10 TRUE []\T1/ptm/m/n/10 and ei-ther []\T1/zi4/m/sl/10 inner []\T1/ptm/m/n/1 0 or [3666] [3667] [3668] [3669] [3670] [3671] [3672] [3673] [3674] [3675] [3676] [3677] [3678] [3679] [3680] [3681] [3682] [3683] [3684] [3685] [3686] [3687] [3688] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.random.ef fects}) has been already used, duplicate ignored \relax l.15098 ...Extract Random Effects}{random.effects} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.random.ef fects.1}) has been already used, duplicate ignored \relax l.15098 ...Extract Random Effects}{random.effects} [3689] [3690] [3691] [3692] [3693] [3694] [3695] [3696] [3697] [3698] [3699] [3700] [3701] Underfull \hbox (badness 1067) in paragraph at lines 15840--15845 \T1/ptm/m/n/10 ma-trix), []\T1/zi4/m/sl/10 fitted []\T1/ptm/m/n/10 (fit-ted val -ues), and []\T1/zi4/m/sl/10 residuals []\T1/ptm/m/n/10 (resid-u-als). De-fault s to [3702] [3703] [3704] [3705] Underfull \hbox (badness 1448) in paragraph at lines 16083--16092 \T1/ptm/m/n/10 Op-tions in-clude []\T1/zi4/m/sl/10 "response" []\T1/ptm/m/n/10 for the "raw" resid-u-als (ob-served - fit-ted), [3706] [3707] [3708] [3709] [3710] [3711] [3712] [3713] [3714] [3715] [3716] Underfull \hbox (badness 1728) in paragraph at lines 16786--16789 []\T1/ptm/m/n/10 an op-tional log-i-cal value used to con-trol the amount of ou t-put in the [3717] [3718] [3719] [3720] [3721] Underfull \hbox (badness 8056) in paragraph at lines 17120--17129 \T1/zi4/m/sl/10 Symmetry" []\T1/ptm/m/n/10 for []\T1/zi4/m/sl/10 pdCompSymm[]\T 1/ptm/m/n/10 , []\T1/zi4/m/sl/10 "Diagonal" []\T1/ptm/m/n/10 for []\T1/zi4/m/sl /10 pdDiag[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 "Multiple of Underfull \hbox (badness 10000) in paragraph at lines 17120--17129 \T1/zi4/m/sl/10 an Identity" []\T1/ptm/m/n/10 for []\T1/zi4/m/sl/10 pdIdent[]\T 1/ptm/m/n/10 , []\T1/zi4/m/sl/10 "General Positive-Definite, Natural Underfull \hbox (badness 5756) in paragraph at lines 17120--17129 \T1/zi4/m/sl/10 Parametrization" []\T1/ptm/m/n/10 for []\T1/zi4/m/sl/10 pdNatur al[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 "General Positive-Definite" []\T1/ptm/m/ n/10 for [3722] [3723] [3724] [3725] [3726] Underfull \hbox (badness 10000) in paragraph at lines 17441--17449 [][][]\T1/zi4/m/sl/10 varComb[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 var ConstPower[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 varConstProp[][][][]\T 1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 varExp[][][][]\T1/ptm/m/n/10 , [][][]\T1/z i4/m/sl/10 varFixed[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 varIdent[][][ ][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 varPower[][][][]\T1/ptm/m/n/10 , [3727] [3728] [3729] [3730] [3731] [3732] [3733] [3734] [3735] [3736] [3737] [3738] Underfull \hbox (badness 10000) in paragraph at lines 18153--18163 [][][]\T1/zi4/m/sl/10 Variogram.corExp[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/ sl/10 Variogram.corGaus[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 Variogram .corLin[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 Variogram.corRatio[][][][ ]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 18153--18163 [][][]\T1/zi4/m/sl/10 Variogram.corSpatial[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi 4/m/sl/10 Variogram.corSpher[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 Vari ogram.default[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 Variogram.gls[][][] []\T1/ptm/m/n/10 , [3739] [3740] [3741] [3742] [3743] [3744] Underfull \hbox (badness 5036) in paragraph at lines 18471--18480 [][][]\T1/zi4/m/sl/10 corSpatial[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 Variogram[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 Variogram.default[][][] []\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 Variogram.corExp[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 Variogram.corGaus[][][][]\T1/ptm/m/n/10 , [3745] [3746] [3747] [3748] [3749] [3750] [3751] [3752] [3753] [3754] [3755] [3756] [3757] [3758]) (./nnet-pkg.tex Chapter 26. [3759] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.multinom} ) has been already used, duplicate ignored \relax l.47 ...t Multinomial Log-linear Models}{multinom} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.multinom. 1}) has been already used, duplicate ignored \relax l.47 ...t Multinomial Log-linear Models}{multinom} Underfull \hbox (badness 1117) in paragraph at lines 79--88 []\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo rm []\T1/zi4/m/sl/10 response ~ [3760] [3761] [3762] [3763] [3764] [3765] [3766] [3767]) (./rpart-pkg.tex [3768] Chapter 27. [3769] [3770] [3771] [3772] [3773] [3774] [3775] [3776] [3777] [3778] [3779] Underfull \hbox (badness 10000) in paragraph at lines 771--775 []\T1/ptm/m/n/10 Logical. If []\T1/zi4/m/sl/10 TRUE []\T1/ptm/m/n/10 (de-fault) , adds to the la-bel Underfull \hbox (badness 1348) in paragraph at lines 771--775 \T1/zi4/m/sl/10 #events level1/ #events level2/ \T1/ptm/m/n/10 etc. for method []\T1/zi4/m/sl/10 class[]\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 n \T1/ptm/m/n/10 for [3780] [3781] [3782] [3783] [3784] [3785] [3786] [3787] [3788] [3789] [3790] [3791] [3792] [3793] [3794] [3795] [3796] [3797] [3798] [3799]) (./spatial-pkg.tex [3800] Chapter 28. [3801] [3802] [3803] [3804] [3805] [3806] Underfull \hbox (badness 10000) in paragraph at lines 423--427 [3807] [3808] [3809] [3810] [3811] [3812] [3813] [3814] [3815] [3816] [3817] [3818] [3819] [3820] [3821]) (./survival-pkg.tex [3822] Chapter 29. [3823] [3824] [3825] [3826] Underfull \hbox (badness 6412) in paragraph at lines 284--286 []\T1/ptm/m/n/10 an op-tional list or vec-tor of group-ing el-e-ments, each as long as [3827] [3828] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.aml}) has been already used, duplicate ignored \relax l.384 ... Myelogenous Leukemia survival data}{aml} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.aml.1}) h as been already used, duplicate ignored \relax l.384 ... Myelogenous Leukemia survival data}{aml} [3829] [3830] [3831] [3832] [3833] [3834] [3835] [3836] [3837] [3838] [3839] [3840] [3841] Underfull \hbox (badness 1097) in paragraph at lines 1205--1207 []\T1/ptm/m/n/10 F.J. Anscombe (1949). Trans-for-ma-tions of Pois-son, bi-no-mi al and negative-binomial data. [3842] [3843] [3844] [3845] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.colon}) h as been already used, duplicate ignored \relax l.1407 ...erapy for Stage B/C colon cancer}{colon} [3846] Underfull \hbox (badness 3679) in paragraph at lines 1455--1459 []\T1/ptm/m/n/10 Peter Hig-gins has pointed out a data in-con-sis-tency, re-vea led by []\T1/zi4/m/sl/10 table(colon$nodes, [3847] [3848] [3849] [3850] [3851] [3852] [3853] [3854] [3855] Underfull \hbox (badness 3250) in paragraph at lines 2145--2150 \T1/ptm/m/n/10 ing guides and prepend []\T1/zi4/m/sl/10 survival:: []\T1/ptm/m/ n/10 onto ev-er-thing, in-clud-ing the spe-cial terms, e.g., Underfull \hbox (badness 10000) in paragraph at lines 2145--2150 []\T1/zi4/m/sl/10 survival::coxph(survival:Surv(time, status) ~ age + survival: :strata(inst), [3856] [3857] [3858] [3859] [3860] [3861] [3862] [3863] [3864] [3865] [3866] [3867] [3868] [3869] [3870] [3871] [3872] [3873] [3874] [3875] [3876] [3877] [3878] [3879] Underfull \hbox (badness 1389) in paragraph at lines 3683--3685 []\T1/ptm/m/n/10 Often used to add the ex-pected sur-vival curve(s) to a Kaplan -Meier plot gen-er-ated with [3880] [3881] [3882] [3883] [3884] Overfull \hbox (467.89665pt too wide) in alignment at lines 3976--3976 [] [] [3885] [3886] [3887] [3888] [3889] [3890] [3891] [3892] [3893] [3894] [3895] [3896] [3897] [3898] [3899] [3900] [3901] [3902] [3903] [3904] [3905] [3906] [3907] [3908] [3909] [3910] [3911] [3912] [3913] Underfull \hbox (badness 5274) in paragraph at lines 5766--5768 []\T1/ptm/m/n/10 an ob-ject of class []\T1/zi4/m/sl/10 "summary.survfit"[]\T1/p tm/m/n/10 , which is the re-sult of the [3914] [3915] [3916] [3917] [3918] [3919] [3920] [3921] [3922] [3923] [3924] [3925] [3926] [3927] [3928] [3929] [3930] [3931] [3932] [3933] [3934] Underfull \hbox (badness 1281) in paragraph at lines 7046--7049 []\T1/ptm/m/n/10 type of resid-u-als, with choices of []\T1/zi4/m/sl/10 "respon se"[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 "deviance"[]\T1/ptm/m/n/10 , []\T1/zi4/ m/sl/10 "dfbeta"[]\T1/ptm/m/n/10 , [3935] [3936] [3937] [3938] [3939] [3940] [3941] [3942] [3943] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.solder}) has been already used, duplicate ignored \relax l.7635 ...ata from a soldering experiment}{solder} [3944] [3945] [3946] [3947] [3948] [3949] [3950] [3951] [3952] [3953] [3954] [3955] [3956] [3957] [3958] [3959] [3960] [3961] [3962] [3963] [3964] [3965] [3966] [3967] [3968] Underfull \hbox (badness 1038) in paragraph at lines 9294--9300 []\T1/ptm/m/n/10 op-tion does not cre-ate a curve, rather it re-trieves the pre -dicted sur-vival [3969] [3970] [3971] [3972] [3973] Underfull \hbox (badness 10000) in paragraph at lines 9652--9657 [][][]\T1/zi4/m/sl/10 survfit.formula[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/s l/10 survfit.coxph[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 survfit.object [][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 print.survfit[][][][]\T1/ptm/m/n /10 , [][][]\T1/zi4/m/sl/10 plot.survfit[][][][]\T1/ptm/m/n/10 , [3974] [3975] [3976] [3977] [3978] Underfull \hbox (badness 4441) in paragraph at lines 10042--10052 []\T1/ptm/m/n/10 by de-fault, the surv-fit rou-tines only re-turn in-for-ma-tio n at the [3979] [3980] [3981] Underfull \hbox (badness 1490) in paragraph at lines 10217--10226 [][][]\T1/zi4/m/sl/10 survfit.coxph[][][] []\T1/ptm/m/n/10 for sur-vival curves from Cox mod-els, [][][]\T1/zi4/m/sl/10 survfit.object[][][] []\T1/ptm/m/n/10 for a de-scrip-tion Underfull \hbox (badness 2213) in paragraph at lines 10217--10226 \T1/ptm/m/n/10 of the com-po-nents of a surv-fit ob-ject, [][][]\T1/zi4/m/sl/10 print.survfit[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 plot.survfit[][][] []\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 lines.survfit[][][][]\T1/ptm/m/n/10 , [3982] [3983] [3984] [3985] [3986] [3987] [3988] Underfull \hbox (badness 1354) in paragraph at lines 10715--10719 []\T1/ptm/m/n/10 survival times, for time de-pen-dent pre-dic-tion. It gives th e time range [3989] [3990] [3991] [3992] [3993] [3994] [3995] [3996] [3997] [3998] [3999] [4000] [4001] [4002] [4003] [4004] [4005] [4006] [4007] [4008] [4009] [4010] [4011] [4012] [4013] [4014]) No file fullrefman.ind. (./fullrefman.aux) LaTeX Font Warning: Some font shapes were not available, defaults substituted. Package rerunfilecheck Warning: File `fullrefman.out' has changed. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. ) (see the transcript file for additional information) pdfTeX warning (dest): name{Rfn.tree} has been referenced but does not exist, r eplaced by a fixed one pdfTeX warning (dest): name{Rfn.memory.limit} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.nearcor} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Rfn.posdefify} has been referenced but does not exi st, replaced by a fixed one pdfTeX warning (dest): name{Rfn.summary\\unhbox\040\\voidb@x\040\\kern\040\\z@\ 040\\char\040`\\protect\040\\protect\040\\leavevmode@ifvmode\040\\kern\040+.166 7em\\relax\040sparseMatrix.Rdash.method} has been referenced but does not exist , replaced by a fixed one pdfTeX warning (dest): name{Rfn.showClass} has been referenced but does not exi st, replaced by a fixed one pdfTeX warning (dest): name{Rfn.matrix.csr} has been 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Transcript written on fullrefman.log. This is makeindex, version 2.17 [TeX Live 2024] (kpathsea + Thai support). Scanning input file fullrefman.idx.............................done (25738 entries accepted, 111 rejected). Sorting entries...................................................................................................................................................................................................................................................................................................done (430988 comparisons). Generating output file fullrefman.ind...........................done (26373 lines written, 111 warnings). Output written in fullrefman.ind. Transcript written in fullrefman.ilg. 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[3] [4] Underfull \hbox (badness 6252) in paragraph at lines 149--157 []\T1/ptm/m/n/10 a small pos-i-tive floating-point num-ber []\T1/zi4/m/n/10 x [ ]\T1/ptm/m/n/10 such that []\T1/zi4/m/n/10 1 - x != 1[]\T1/ptm/m/n/10 . It Underfull \hbox (badness 10000) in paragraph at lines 149--157 \T1/ptm/m/n/10 equals []\T1/zi4/m/n/10 double.base ^ double.neg.ulp.digits []\T 1/ptm/m/n/10 if []\T1/zi4/m/n/10 double.base Underfull \hbox (badness 10000) in paragraph at lines 149--157 []\T1/ptm/m/n/10 is 2 or []\T1/zi4/m/n/10 double.rounding []\T1/ptm/m/n/10 is 0 ; oth-er-wise, it is []\T1/zi4/m/n/10 (double.base Underfull \hbox (badness 10000) in paragraph at lines 149--157 \T1/zi4/m/n/10 ^ double.neg.ulp.digits) / 2[]\T1/ptm/m/n/10 . Nor-mally []\T1/z i4/m/n/10 1.110223e-16[]\T1/ptm/m/n/10 . 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This reads the [122] Underfull \hbox (badness 2261) in paragraph at lines 7741--7746 \T1/zi4/m/n/10 / / github . com / astrand / xclip$[][]\T1/ptm/m/n/10 ) or []\T1 /zi4/m/n/10 xsel []\T1/ptm/m/n/10 ([][]$\T1/zi4/m/n/10 https : / / www . vergen et . net / ~conrad / software / [123] [124] Underfull \vbox (badness 10000) has occurred while \output is active [125] [126] [127] [128] [129] [130] [131] [132] [133] Underfull \hbox (badness 2096) in paragraph at lines 8474--8478 \T1/zi4/m/n/10 status _ codes$[][] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / List _ of _ FTP _ server _ return _ codes$ [][]\T1/ptm/m/n/10 . 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First, the leap sec-onds a re ig-nored, and real times Underfull \hbox (badness 2875) in paragraph at lines 9334--9346 []\T1/zi4/m/n/10 NA[]\T1/ptm/m/n/10 , and hence []\T1/zi4/m/n/10 as.POSIXct("19 69-12-31 23:59:59", tz = "UTC") []\T1/ptm/m/n/10 will give []\T1/zi4/m/n/10 "19 69-12-31 [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157] [158] [159] Underfull \hbox (badness 1178) in paragraph at lines 10200--10204 []\T1/ptm/m/n/10 If true, [][][]\T1/zi4/m/n/10 list[][][][]\T1/ptm/m/n/10 s and atomic vec-tors with non-[][][]\T1/zi4/m/n/10 NA[][][] []\T1/ptm/m/n/10 names (see [][][]\T1/zi4/m/n/10 names[][][][]\T1/ptm/m/n/10 ) are de- [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] [183] [184] [185] [186] [187] [188] [189] [190] [191] [192] [193] [194] [195] Underfull \hbox (badness 2744) in paragraph at lines 12540--12542 []\T1/ptm/m/n/10 Changing the cur-rent en-cod-ing from a run-ning R ses-sion ma y lead to con-fu-sion (see [196] [197] [198] [199] [200] [201] [202] [203] Underfull \vbox (badness 10000) has occurred while \output is active [204] [205] [206] [207] [208] [209] [210] [211] [212] [213] [214] [215] [216] [217] [218] [219] [220] [221] [222] [223] [224] [225] [226] [227] [228] Underfull \hbox (badness 2253) in paragraph at lines 14746--14748 []\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is done: see Underfull \hbox (badness 1490) in paragraph at lines 14781--14784 []\T1/ptm/m/n/10 Junction points and sym-bolic links are fol-lowed, so in-for-m a-tion is given about the [229] Underfull \hbox (badness 1565) in paragraph at lines 14863--14867 [][][]\T1/zi4/m/n/10 Sys.readlink[][][] []\T1/ptm/m/n/10 to find out about sym- bolic links, [][][]\T1/zi4/m/n/10 files[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m /n/10 file.access[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 list.files[][][] []\T1/ptm/m/n/10 , and [230] Underfull \hbox (badness 4927) in paragraph at lines 14914--14916 []\T1/ptm/m/n/10 It can also be used for en-vi-ron-ment paths such as []\T1/zi4 /m/n/10 PATH []\T1/ptm/m/n/10 and []\T1/zi4/m/n/10 R_LIBS []\T1/ptm/m/n/10 with []\T1/zi4/m/n/10 fsep = [231] [232] [233] Underfull \hbox (badness 1466) in paragraph at lines 15065--15068 []\T1/ptm/m/n/10 character vec-tors, con-tain-ing file names or paths. For []\T 1/zi4/m/n/10 file.copy []\T1/ptm/m/n/10 and [234] Underfull \hbox (badness 10000) in paragraph at lines 15196--15200 [][][]\T1/zi4/m/n/10 file.info[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 fil e.access[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 file.path[][][][]\T1/ptm/ m/n/10 , [][][]\T1/zi4/m/n/10 file.show[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m /n/10 list.files[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 unlink[][][][]\T1 /ptm/m/n/10 , [][][]\T1/zi4/m/n/10 basename[][][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 15207--15210 [][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][ ] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wik i / [235] [236] [237] [238] [239] Underfull \hbox (badness 3965) in paragraph at lines 15504--15508 []\T1/ptm/m/n/10 This is the same com-pu-ta-tion as for the em-pir-i-cal dis-tr i-bu-tion func-tion, and in-deed, [240] [241] [242] [243] [244] [245] [246] [247] Underfull \hbox (badness 5260) in paragraph at lines 16006--16006 []\T1/zi4/m/n/10 big.mark[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 big.interval[]\T1/ ptm/m/n/10 , []\T1/zi4/m/n/10 small.mark[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 sma ll.interval[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 decimal.mark[]\T1/ptm/m/n/10 , [248] [249] [250] [251] Underfull \hbox (badness 4429) in paragraph at lines 16296--16299 []\T1/ptm/m/n/10 an atomic nu-mer-i-cal or char-ac-ter ob-ject, pos-si-bly [][] []\T1/zi4/m/n/10 complex[][][] []\T1/ptm/m/n/10 only for [252] [253] Underfull \hbox (badness 10000) in paragraph at lines 16403--16405 []\T1/ptm/m/n/10 This works via []\T1/zi4/m/n/10 prettyNum()[]\T1/ptm/m/n/10 , which calls []\T1/zi4/m/n/10 .format.zeros(*, [254] Underfull \hbox (badness 2035) in paragraph at lines 16476--16480 []\T1/ptm/m/n/10 The de-fault for []\T1/zi4/m/n/10 decimal.mark []\T1/ptm/m/n/1 0 in []\T1/zi4/m/n/10 formatC() []\T1/ptm/m/n/10 was changed in \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.2.0: for use within [255] Underfull \vbox (badness 10000) has occurred while \output is active [256] [257] [258] [259] [260] [261] [262] [263] [264] Underfull \hbox (badness 2452) in paragraph at lines 17099--17103 []\T1/zi4/m/n/10 gctorture2 []\T1/ptm/m/n/10 can also be in-voked via en-vi-ron -ment vari-ables at the start of the \T1/phv/m/n/10 R \T1/ptm/m/n/10 ses- Underfull \hbox (badness 1147) in paragraph at lines 17099--17103 \T1/ptm/m/n/10 sion. []\T1/zi4/m/n/10 R_GCTORTURE []\T1/ptm/m/n/10 cor-re-spond s to the []\T1/zi4/m/n/10 step []\T1/ptm/m/n/10 ar-gu-ment, []\T1/zi4/m/n/10 R_ GCTORTURE_WAIT []\T1/ptm/m/n/10 to []\T1/zi4/m/n/10 wait[]\T1/ptm/m/n/10 , and [265] [266] [267] Underfull \hbox (badness 1092) in paragraph at lines 17273--17278 [][][]\T1/zi4/m/n/10 library.dynam[][][][]\T1/ptm/m/n/10 , or can be found af-t er the DLL has been loaded us-ing [268] [269] [270] Underfull \hbox (badness 6741) in paragraph at lines 17526--17530 \T1/ptm/m/n/10 Additionally, the list will have an ad-di-tional class, be-ing [ ]\T1/zi4/m/n/10 CRoutine[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 CallRoutine[]\T1/pt m/m/n/10 , [271] [272] [273] [274] [275] [276] [277] [278] [279] [280] [281] Underfull \vbox (badness 3803) has occurred while \output is active [282] Underfull \vbox (badness 10000) has occurred while \output is active [283] [284] [285] [286] [287] [288] [289] [290] [291] [292] Underfull \hbox (badness 1769) in paragraph at lines 18999--19002 []\T1/ptm/m/n/10 a char-ac-ter vec-tor, or an ob-ject to be con-verted to a cha r-ac-ter vec-tor [293] [294] [295] [296] [297] Underfull \hbox (badness 10000) in paragraph at lines 19308--19310 []\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/zi4/m/n/10 https : / / ww w . unicode . org / reports / tr35 / Underfull \hbox (badness 2088) in paragraph at lines 19314--19323 []\T1/ptm/m/n/10 For the spec-i-fi-ca-tions of `real' ICU lo-cales, see [][]$\T 1/zi4/m/n/10 https : / / unicode-[]org . github . io / icu / [298] [299] [300] [301] [302] [303] [304] [305] [306] [307] Underfull \hbox (badness 1442) in paragraph at lines 19922--19924 []\T1/ptm/m/n/10 the choice of de-fault graph-ics de-vice launched when needed and by [][][]\T1/zi4/m/n/10 dev.new[][][][]\T1/ptm/m/n/10 : see [308] Underfull \hbox (badness 2452) in paragraph at lines 20018--20044 [][][]\T1/zi4/m/n/10 as.character[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 as.complex[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 as.double[][][][]\T1/pt m/m/n/10 , [][][]\T1/zi4/m/n/10 as.integer[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi 4/m/n/10 as.logical[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 as.raw[][][][] \T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 as.vector[][][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 5726) in paragraph at lines 20018--20044 [][][]\T1/zi4/m/n/10 as.call[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 as.en vironment[][][] [][]is.array[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 is.ma trix[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 is.na[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 anyNA[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 is.nan [][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 is.finite[][][] [309] [310] [311] [312] [313] [314] Underfull \hbox (badness 1248) in paragraph at lines 20416--20419 []\T1/zi4/m/n/10 is.atomic []\T1/ptm/m/n/10 is true for the [][]atomic[][][] ty pes ([]\T1/zi4/m/n/10 "logical"[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 "integer"[]\ T1/ptm/m/n/10 , []\T1/zi4/m/n/10 "numeric"[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 " complex"[]\T1/ptm/m/n/10 , [315] [316] [317] [318] [319] Underfull \hbox (badness 4739) in paragraph at lines 20683--20685 []\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere d, see [320] [321] [322] [323] [324] Underfull \vbox (badness 10000) has occurred while \output is active [325] [326] [327] [328] [329] [330] [331] [332] [333] [334] [335] [336] [337] [338] Underfull \hbox (badness 2469) in paragraph at lines 21851--21856 []\T1/ptm/m/n/10 In late 2017 a []\T1/zi4/m/n/10 libcurl []\T1/ptm/m/n/10 in-st al-la-tion was seen di-vided into two li-braries, []\T1/zi4/m/n/10 libcurl []\T 1/ptm/m/n/10 and [339] Underfull \hbox (badness 1675) in paragraph at lines 21938--21947 []\T1/ptm/m/n/10 At startup, the li-brary search path is ini-tial-ized from the en-vi-ron-ment vari-ables []\T1/zi4/m/n/10 R_LIBS[]\T1/ptm/m/n/10 , Underfull \hbox (badness 3189) in paragraph at lines 21948--21961 []\T1/ptm/m/n/10 First, []\T1/zi4/m/n/10 .Library.site []\T1/ptm/m/n/10 is ini- tial-ized from []\T1/zi4/m/n/10 R_LIBS_SITE[]\T1/ptm/m/n/10 . If this is un-set or empty, the [340] Underfull \hbox (badness 10000) in paragraph at lines 21996--21999 []\T1/zi4/m/n/10 LOCALAPPDATA []\T1/ptm/m/n/10 (usu-ally []\T1/zi4/m/n/10 C:\Us ers\username\AppData\Local[]\T1/ptm/m/n/10 ) on Win-dows is a hid- Underfull \hbox (badness 4752) in paragraph at lines 21996--21999 \T1/ptm/m/n/10 den di-rec-tory and may not be viewed by some soft-ware. It may be opened by [341] [342] Underfull \hbox (badness 1014) in paragraph at lines 22130--22135 []\T1/ptm/m/n/10 Normally []\T1/zi4/m/n/10 library []\T1/ptm/m/n/10 re-turns (i n-vis-i-bly) the list of at-tached pack-ages, but []\T1/zi4/m/n/10 TRUE []\T1/p tm/m/n/10 or []\T1/zi4/m/n/10 FALSE []\T1/ptm/m/n/10 if [343] [344] [345] [346] [347] [348] [349] [350] [351] [352] [353] [354] [355] Underfull \hbox (badness 1264) in paragraph at lines 22977--22985 []\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways be sup-ported: Underfull \hbox (badness 4441) in paragraph at lines 23012--23015 []\T1/ptm/m/n/10 Note that set-ting cat-e-gory []\T1/zi4/m/n/10 "LC_ALL" []\T1/ ptm/m/n/10 sets only cat-e-gories []\T1/zi4/m/n/10 "LC_COLLATE"[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 "LC_CTYPE"[]\T1/ptm/m/n/10 , [356] [357] [358] [359] [360] [361] [362] [363] [364] [365] [366] [367] [368] Underfull \hbox (badness 5231) in paragraph at lines 23830--23832 []\T1/ptm/m/n/10 The al-go-rithm used by []\T1/zi4/m/n/10 make.unique []\T1/ptm /m/n/10 has the prop-erty that []\T1/zi4/m/n/10 make.unique(c(A, B)) == [369] [370] [371] [372] [373] [374] [375] [376] [377] [378] [379] [380] [381] [382] [383] [384] [385] Underfull \hbox (badness 6380) in paragraph at lines 24940--24946 [][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Data _ compress ion$[][] \T1/ptm/m/n/10 for back-ground on data com-pres- Underfull \hbox (badness 1472) in paragraph at lines 24940--24946 [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Bzip2$[][]\T1/ptm /m/n/10 , and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / XZ _ Utils$[][] [386] [387] [388] [389] [390] [391] [392] [393] [394] Underfull \hbox (badness 2790) in paragraph at lines 25453--25456 []\T1/zi4/m/n/10 packageStartupMessage []\T1/ptm/m/n/10 is a vari-ant whose mes -sages can be sup-pressed sep-a-rately by Underfull \hbox (badness 1571) in paragraph at lines 25453--25456 []\T1/zi4/m/n/10 suppressPackageStartupMessages[]\T1/ptm/m/n/10 . (They are sti ll mes-sages, so can be sup-pressed by [395] [396] [397] [398] [399] Underfull \hbox (badness 1194) in paragraph at lines 25781--25784 []\T1/ptm/m/n/10 The de-fault method for []\T1/zi4/m/n/10 anyNA []\T1/ptm/m/n/1 0 han-dles atomic vec-tors with-out a class and []\T1/zi4/m/n/10 NULL[]\T1/ptm/ m/n/10 . It calls [400] [401] [402] Underfull \hbox (badness 2368) in paragraph at lines 25988--25994 []\T1/ptm/m/n/10 For an [][][]\T1/zi4/m/n/10 environment[][][] env[]\T1/ptm/m/n /10 , []\T1/zi4/m/n/10 names(env) []\T1/ptm/m/n/10 gives the names of the cor-r e-spond-ing list, i.e., [403] [404] [405] [406] [407] [408] Underfull \hbox (badness 10000) in paragraph at lines 26378--26381 []\T1/ptm/m/n/10 optional [][][]\T1/zi4/m/n/10 logical[][][] []\T1/ptm/m/n/10 e ven-tu-ally to be passed to []\T1/zi4/m/n/10 print()[]\T1/ptm/m/n/10 , used by [409] [410] [411] [412] [413] [414] [415] [416] [417] [418] Underfull \hbox (badness 10000) in paragraph at lines 27006--27008 []\T1/zi4/m/n/10 isNamespaceLoaded(pkg) []\T1/ptm/m/n/10 is equiv-a-lent to but more ef-fi-cient than []\T1/zi4/m/n/10 pkg %in% [419] [420] [421] [422] [423] [424] [425] Underfull \hbox (badness 2443) in paragraph at lines 27497--27505 \T1/ptm/m/n/10 suit-able char-ac-ter vec-tors as above, or nu-meric ver-sion ob -jects. For [426] [427] [428] [429] [430] [431] [432] Underfull \hbox (badness 1881) in paragraph at lines 27927--27930 []\T1/ptm/m/n/10 integer value con-trol-ling the print-ing of lan-guage con-str ucts which are Underfull \hbox (badness 6220) in paragraph at lines 27952--27954 []\T1/ptm/m/n/10 Extra command-line ar-gu-ment(s) for non-default meth-ods: see [433] [434] Underfull \hbox (badness 2142) in paragraph at lines 28093--28097 []\T1/ptm/m/n/10 the de-fault pa-per for-mat used by [][][]\T1/zi4/m/n/10 posts cript[][][][]\T1/ptm/m/n/10 ; set by en-vi-ron-ment vari-able Underfull \hbox (badness 1968) in paragraph at lines 28150--28155 []\T1/ptm/m/n/10 the com-mand used by [][][]\T1/zi4/m/n/10 postscript[][][] []\ T1/ptm/m/n/10 for print-ing; set by en-vi-ron-ment vari-able [435] [436] [437] [438] Underfull \hbox (badness 10000) in paragraph at lines 28446--28452 []\T1/ptm/m/n/10 The URL of a Bio-con-duc-tor mir-ror for use by [][][]\T1/zi4/ m/n/10 setRepositories[][][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 28446--28452 \T1/ptm/m/n/10 e.g. the de-fault `[]\T1/zi4/m/n/10 "https://bioconductor.org"[] \T1/ptm/m/n/10 ' or the Eu-ro-pean mir-ror Underfull \hbox (badness 10000) in paragraph at lines 28446--28452 \T1/ptm/m/n/10 `[]\T1/zi4/m/n/10 "https://bioconductor.statistik.tu-dortmund.de "[]\T1/ptm/m/n/10 '. Can be set by Underfull \hbox (badness 5878) in paragraph at lines 28459--28462 []\T1/ptm/m/n/10 default Cc: ad-dress used by [][][]\T1/zi4/m/n/10 create.post[ ][][] []\T1/ptm/m/n/10 (and hence [][][]\T1/zi4/m/n/10 bug.report[][][] []\T1/p tm/m/n/10 and Underfull \hbox (badness 2689) in paragraph at lines 28485--28487 []\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na l HTTP server, see Underfull \hbox (badness 10000) in paragraph at lines 28531--28536 []\T1/ptm/m/n/10 Used by [][][]\T1/zi4/m/n/10 install.packages[][][] []\T1/ptm/ m/n/10 (and in-di-rectly [439] Underfull \hbox (badness 2529) in paragraph at lines 28537--28548 \T1/ptm/m/n/10 in-di-rectly [][][]\T1/zi4/m/n/10 update.packages[][][][]\T1/ptm /m/n/10 ) on plat-forms which sup-port bi-nary pack-ages. Pos-si- Underfull \hbox (badness 2512) in paragraph at lines 28537--28548 \T1/ptm/m/n/10 ble val-ues are []\T1/zi4/m/n/10 "never"[]\T1/ptm/m/n/10 , []\T1 /zi4/m/n/10 "interactive" []\T1/ptm/m/n/10 (which means ask in in-ter-ac-tive u se and Underfull \hbox (badness 7203) in paragraph at lines 28549--28552 []\T1/ptm/m/n/10 default email-ing method used by [][][]\T1/zi4/m/n/10 create.p ost[][][] []\T1/ptm/m/n/10 and hence [][][]\T1/zi4/m/n/10 bug.report[][][] []\T 1/ptm/m/n/10 and [440] [441] [442] [443] [444] Underfull \vbox (badness 10000) has occurred while \output is active [445] Underfull \hbox (badness 10000) in paragraph at lines 28967--28971 \T1/ptm/m/n/10 el-e-ment []\T1/zi4/m/n/10 A[c(arrayindex.x, arrayindex.y)] = FU N(X[arrayindex.x], Y[arrayindex.y], [446] [447] Underfull \hbox (badness 10000) in paragraph at lines 29114--29117 []\T1/zi4/m/n/10 str2expression(s) []\T1/ptm/m/n/10 and []\T1/zi4/m/n/10 str2la ng(s) []\T1/ptm/m/n/10 re-turn spe-cial ver-sions of []\T1/zi4/m/n/10 parse(tex t=s, [448] Underfull \hbox (badness 7925) in paragraph at lines 29195--29199 []\T1/ptm/m/n/10 for a [][][]\T1/zi4/m/n/10 character[][][] []\T1/ptm/m/n/10 ve c-tor []\T1/zi4/m/n/10 s[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 str2expression(s) [ ]\T1/ptm/m/n/10 cor-re-sponds to Underfull \hbox (badness 1253) in paragraph at lines 29195--29199 [][][]\T1/zi4/m/n/10 parse[][][](text = s, keep.source=FALSE)[]\T1/ptm/m/n/10 , which is al-ways of type ([][][]\T1/zi4/m/n/10 typeof[][][][]\T1/ptm/m/n/10 ) and [][][]\T1/zi4/m/n/10 class[][][] Underfull \hbox (badness 2521) in paragraph at lines 29200--29209 []\T1/ptm/m/n/10 for a [][][]\T1/zi4/m/n/10 character[][][] []\T1/ptm/m/n/10 st ring []\T1/zi4/m/n/10 s[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 str2lang(s) []\T1/pt m/m/n/10 cor-re-sponds to [][][]\T1/zi4/m/n/10 parse[][][](text = s, [449] [450] [451] [452] [453] [454] [455] [456] [457] [458] [459] [460] [461] [462] [463] [464] Underfull \hbox (badness 2726) in paragraph at lines 30214--30217 []\T1/ptm/m/n/10 character string (or []\T1/zi4/m/n/10 NULL[]\T1/ptm/m/n/10 ) i n-di-cat-ing [][][]\T1/zi4/m/n/10 NA[][][] []\T1/ptm/m/n/10 val-ues in printed out-put, see [465] [466] [467] [468] [469] [470] [471] [472] [473] [474] [475] [476] [477] [478] [479] [480] [481] [482] [483] Underfull \vbox (badness 3803) has occurred while \output is active [484] [485] [486] [487] [488] [489] [490] [491] [492] Underfull \hbox (badness 1533) in paragraph at lines 32024--32027 []\T1/ptm/m/n/10 As with all com-piled code, mis-specifying these func-tions ca n crash \T1/phv/m/n/10 R\T1/ptm/m/n/10 . Do in-clude the [493] [494] [495] Underfull \hbox (badness 1163) in paragraph at lines 32195--32206 []\T1/ptm/m/n/10 If all com-po-nents are dif-fer-ent (and no []\T1/zi4/m/n/10 N A[]\T1/ptm/m/n/10 s), the ranks are well de-fined, with val-ues in [496] [497] [498] [499] [500] [501] [502] Underfull \vbox (badness 3803) has occurred while \output is active [503] [504] Underfull \hbox (badness 6300) in paragraph at lines 32741--32743 []\T1/ptm/m/n/10 The sec-tion `Pro-cess-ing doc-u-men-ta-tion files' in the `Wr it-ing R Ex-ten-sions' man-ual: [505] [506] [507] [508] [509] [510] [511] [512] [513] [514] [515] [516] [517] [518] [519] [520] [521] Underfull \hbox (badness 10000) in paragraph at lines 33864--33868 []\T1/zi4/m/n/10 regexpr []\T1/ptm/m/n/10 and []\T1/zi4/m/n/10 gregexpr []\T1/p tm/m/n/10 sup-port `named cap-ture'. If groups are named, e.g., Underfull \hbox (badness 1221) in paragraph at lines 33864--33868 []\T1/zi4/m/n/10 "(?[A-Z][a-z]+)" []\T1/ptm/m/n/10 then the po-si-tions of the matches are also re-turned by name. Underfull \hbox (badness 3557) in paragraph at lines 33885--33887 []\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/zi4/m/n/10 https : / / pubs . opengroup . org / onlinepubs / 9699919799 / Underfull \hbox (badness 1122) in paragraph at lines 33888--33892 []\T1/ptm/m/n/10 The []\T1/zi4/m/n/10 pcre2pattern []\T1/ptm/m/n/10 or []\T1/zi 4/m/n/10 pcrepattern man []\T1/ptm/m/n/10 page (found as part of [][]$\T1/zi4/m /n/10 https : / / www . pcre . org / [522] [523] Underfull \vbox (badness 10000) has occurred while \output is active [524] [525] [526] [527] [528] [529] [530] [531] Underfull \hbox (badness 1655) in paragraph at lines 34490--34492 []\T1/ptm/m/n/10 a vec-tor (atomic, not a list) for []\T1/zi4/m/n/10 rle()[]\T1 /ptm/m/n/10 ; an ob-ject of class []\T1/zi4/m/n/10 "rle" []\T1/ptm/m/n/10 for [532] [533] [534] [535] [536] [537] [538] [539] [540] [541] [542] [543] [544] [545] [546] [547] [548] [549] [550] Underfull \hbox (badness 2261) in paragraph at lines 35693--35698 []\T1/ptm/m/n/10 If []\T1/zi4/m/n/10 strip.white []\T1/ptm/m/n/10 is of length 1, it ap-plies to all fields; oth-er-wise, if [551] [552] [553] [554] [555] [556] [557] [558] [559] [560] [561] [562] [563] [564] [565] [566] Underfull \hbox (badness 3668) in paragraph at lines 36728--36732 []\T1/zi4/m/n/10 getAllConnections []\T1/ptm/m/n/10 re-turns a se-quence of in- te-ger con-nec-tion de-scrip-tors for use with [567] Underfull \hbox (badness 10000) in paragraph at lines 36819--36830 \T1/zi4/m/n/10 / / learn . microsoft . com / en-[]us / cpp / c-[]language / par sing-[]c-[]command-[]line-[]arguments ? [568] [569] [570] [571] [572] [573] [574] [575] [576] [577] [578] [579] [580] [581] [582] [583] [584] [585] [586] [587] [588] [589] [590] [591] [592] Underfull \hbox (badness 10000) in paragraph at lines 38451--38453 [][][]$\T1/zi4/m/n/10 https : / / pubs . opengroup . org / onlinepubs / 9699919 799 / functions / snprintf . html$[][] \T1/ptm/m/n/10 for [593] [594] [595] [596] [597] [598] [599] Underfull \hbox (badness 2913) in paragraph at lines 38869--38873 \T1/ptm/m/n/10 ber of nested \T1/phv/m/n/10 R \T1/ptm/m/n/10 ex-pres-sions cur- rently un-der eval-u-a-tion, ex-ceeds the limit set by [600] [601] [602] Underfull \hbox (badness 1072) in paragraph at lines 39115--39119 []\T1/ptm/m/n/10 On front-ends which sup-port it, the com-mands his-tory is rea d from the file spec-i-fied by [603] Underfull \hbox (badness 10000) in paragraph at lines 39120--39124 []\T1/ptm/m/n/10 The command-line op-tion `[]\T1/zi4/m/n/10 --vanilla[]\T1/ptm/ m/n/10 ' im-plies `[]\T1/zi4/m/n/10 --no-site-file[]\T1/ptm/m/n/10 ', `[]\T1/zi 4/m/n/10 --no-init-file[]\T1/ptm/m/n/10 ', Underfull \hbox (badness 10000) in paragraph at lines 39160--39166 []\T1/ptm/m/n/10 On sys-tems with sub-architectures (mainly Win-dows), the file s `\T1/zi4/m/n/10 Renviron.site\T1/ptm/m/n/10 ' Underfull \hbox (badness 10000) in paragraph at lines 39160--39166 \T1/ptm/m/n/10 and `\T1/zi4/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' are looked for first in architecture-specific di-rec-to-ries, Underfull \hbox (badness 1320) in paragraph at lines 39160--39166 \T1/ptm/m/n/10 e.g. `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/zi4/m/n/10 /etc/i386/R environ.site\T1/ptm/m/n/10 '. And e.g. `\T1/zi4/m/n/10 .Renviron.i386\T1/ptm/m/ n/10 ' will be used in Underfull \hbox (badness 3009) in paragraph at lines 39175--39182 []\T1/ptm/m/n/10 On Unix ver-sions of \T1/phv/m/n/10 R \T1/ptm/m/n/10 there is also a file `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/zi4/m/n/10 /etc/Renviron\T1/pt m/m/n/10 ' which is read Underfull \hbox (badness 1038) in paragraph at lines 39175--39182 \T1/ptm/m/n/10 very early in the start-up pro-cess-ing. It con-tains en-vi-ron- ment vari-ables set by \T1/phv/m/n/10 R \T1/ptm/m/n/10 in the Underfull \hbox (badness 2573) in paragraph at lines 39175--39182 \T1/ptm/m/n/10 con-fig-ure pro-cess. Val-ues in that file can be over-rid-den i n site or user en-vi-ron-ment Underfull \hbox (badness 1917) in paragraph at lines 39175--39182 \T1/ptm/m/n/10 files: do not change `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/zi4/m/ n/10 /etc/Renviron\T1/ptm/m/n/10 ' it-self. Note that this is dis-tinct from [604] [605] [606] [607] Underfull \hbox (badness 2644) in paragraph at lines 39410--39414 []\T1/ptm/m/n/10 alternative to []\T1/zi4/m/n/10 exprs []\T1/ptm/m/n/10 or []\T 1/zi4/m/n/10 ...[]\T1/ptm/m/n/10 : an `expression-like' ob-ject, typ-i-cally an [608] [609] [610] Underfull \hbox (badness 1389) in paragraph at lines 39573--39580 []\T1/ptm/m/n/10 a char-ac-ter string. The de-fault for the []\T1/zi4/m/n/10 fo rmat []\T1/ptm/m/n/10 meth-ods is []\T1/zi4/m/n/10 "%Y-%m-%d [611] [612] [613] [614] [615] [616] [617] [618] [619] [620] [621] [622] [623] [624] [625] [626] [627] [628] [629] [630] [631] Underfull \hbox (badness 1158) in paragraph at lines 40939--40941 []\T1/ptm/m/n/10 integer code used in []\T1/zi4/m/n/10 quantile(*, type=quantil e.type) []\T1/ptm/m/n/10 for the de-fault [632] [633] [634] [635] [636] [637] [638] [639] [640] [641] Underfull \hbox (badness 1137) in paragraph at lines 41539--41545 []\T1/ptm/m/n/10 This ex-pands tilde (see [][]tilde ex-pan-sion[][][]) and wild -cards in file paths. For pre-cise de-tails Underfull \hbox (badness 4967) in paragraph at lines 41557--41562 []\T1/ptm/m/n/10 If a file-name starts with []\T1/zi4/m/n/10 . []\T1/ptm/m/n/10 this may need to be matched ex-plic-itly: for ex-am-ple [642] [643] Underfull \hbox (badness 1616) in paragraph at lines 41677--41682 []\T1/zi4/m/n/10 system("id") []\T1/ptm/m/n/10 is much more portable on Unix-al ikes, pro-vided only the POSIX op-tions [644] [645] [646] [647] Underfull \vbox (badness 3803) has occurred while \output is active [648] [649] [650] [651] [652] Underfull \hbox (badness 1472) in paragraph at lines 42224--42227 []\T1/ptm/m/n/10 logical. If []\T1/zi4/m/n/10 TRUE[]\T1/ptm/m/n/10 , func-tions keep their source in-clud-ing com-ments, see [653] [654] [655] LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/n' instead on input line 42436. [656] [657] [658] [659] [660] [661] [662] [663] [664] [665] [666] [667] Underfull \hbox (badness 10000) in paragraph at lines 43175--43179 []\T1/ptm/m/n/10 On 64-bit plat-forms []\T1/zi4/m/sl/10 bin []\T1/ptm/m/n/10 ca n have $\OT1/cmr/m/n/10 2[]$ \T1/ptm/m/n/10 or more el-e-ments (i.e., []\T1/zi4 /m/sl/10 length(bin) > [668] [669] [670] [671] [672] Underfull \hbox (badness 10000) in paragraph at lines 43534--43537 [][][]\T1/zi4/m/sl/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [][]$https : / / developer . r-[]project . org / [673] [674] [675] Underfull \hbox (badness 10000) in paragraph at lines 43718--43722 [][][]\T1/zi4/m/sl/10 addTaskCallback[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/s l/10 removeTaskCallback[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 taskCallb ackManager[][][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/sl/10 https : / / developer . [676] [677] [678] [679] [680] [681] [682] [683] [684] [685] Underfull \hbox (badness 10000) in paragraph at lines 44366--44369 [][][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / wiki / Time _ zone$[] [] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/sl/10 https : / / data . iana . org / time -[]zones / [686] [687] [688] [689] [690] [691] Underfull \vbox (badness 10000) has occurred while \output is active [692] [693] [694] [695] [696] [697] [698] [699] Underfull \hbox (badness 1990) in paragraph at lines 45282--45290 []\T1/zi4/m/sl/10 try []\T1/ptm/m/n/10 eval-u-ates an ex-pres-sion and traps an y er-rors that oc-cur dur-ing the eval-u-a-tion. If Underfull \hbox (badness 4846) in paragraph at lines 45282--45290 \T1/ptm/m/n/10 an er-ror oc-curs then the er-ror mes-sage is printed to the [][ ][]\T1/zi4/m/sl/10 stderr[][][] []\T1/ptm/m/n/10 con-nec-tion un-less [700] [701] [702] [703] [704] [705] [706] [707] [708] [709] [710] [711] [712] [713] [714] [715] [716] [717] [718] [719] [720] [721] Underfull \hbox (badness 1014) in paragraph at lines 46719--46722 []\T1/ptm/m/n/10 logical, in-di-cat-ing if the warn-ing should be out-put im-me -di-ately, even if [722] [723] Underfull \hbox (badness 2401) in paragraph at lines 46852--46856 []\T1/ptm/m/n/10 See the de-scrip-tion of [][][]\T1/zi4/m/sl/10 options[][][](" warn") []\T1/ptm/m/n/10 for the cir-cum-stances un-der which there is a [724] [725] Underfull \hbox (badness 3492) in paragraph at lines 46978--46980 []\T1/zi4/m/sl/10 weekdays []\T1/ptm/m/n/10 and []\T1/zi4/m/sl/10 months []\T1/ ptm/m/n/10 re-turn a char-ac-ter vec-tor of names in the lo-cale in use, i.e., [726] [727] Underfull \hbox (badness 2111) in paragraph at lines 47064--47069 \T1/ptm/m/n/10 If [][][]\T1/zi4/m/sl/10 names[][][](.dimnames) []\T1/ptm/m/n/10 is not empty, these are used as col-umn names. [728] [729] [730] Underfull \hbox (badness 4001) in paragraph at lines 47312--47314 []\T1/ptm/m/n/10 Thomas Lum-ley (2003) \T1/ptm/m/it/10 Stan-dard non-stan-dard eval-u-a-tion rules\T1/ptm/m/n/10 . [][]$\T1/zi4/m/sl/10 https : / / developer . [731] [732] [733] [734] [735] [736] [737] Underfull \hbox (badness 5417) in paragraph at lines 47713--47717 []\T1/zi4/m/sl/10 .packages() []\T1/ptm/m/n/10 re-turns the names of the cur-re ntly at-tached pack-ages \T1/ptm/m/it/10 in-vis-i-bly \T1/ptm/m/n/10 whereas [738] Underfull \hbox (badness 10000) in paragraph at lines 47774--47778 []\T1/zi4/m/sl/10 .standard_regexps []\T1/ptm/m/n/10 re-turns a list of `stan-d ard' reg-exps, in-clud-ing el-e-ments named [739]) (./compiler-pkg.tex [740] Chapter 2. [741] [742] [743] [744]) (./datasets-pkg.tex Chapter 3. [745] [746] [747] [748] [749] [750] [751] [752] [753] [754] [755] [756] [757] [758] [759] [760] [761] Underfull \hbox (badness 1097) in paragraph at lines 1034--1038 []\T1/ptm/m/n/10 MacDonell, W.R. (1902). On crim-i-nal an-thro-pom-e-try and th e iden-ti-fi-ca-tion of crim-i-nals. [762] [763] [764] [765] [766] [767] [768] [769] [770] [771] [772] [773] [774] [775] [776] [777] [778] [779] [780] [781] [782] [783] [784] [785] [786] [787] [788] [789] [790] [791] [792] [793] [794] [795] [796] [797] [798] [799] [800] [801] [802] [803] Overfull \hbox (2.27475pt too wide) in paragraph at lines 3524--3524 []\T1/zi4/m/n/9 ## From https://pubs.usgs.gov/gip/Elevations-Distances/elvadis t.html#Geographic%20Centers[] [804] [805] [806] [807] [808] [809] [810] [811] [812] [813] [814] [815] [816] [817] [818] [819] [820] [821] [822] [823] [824] [825] [826] [827]) (./graphics-pkg.tex [828] Chapter 4. [829] [830] [831] [832] [833] [834] [835] [836] [837] [838] [839] Underfull \vbox (badness 3803) has occurred while \output is active [840] [841] [842] [843] [844] [845] Overfull \hbox (12.71341pt too wide) in paragraph at lines 1037--1037 [] \T1/zi4/m/n/9 main = "barplot(Freq ~ Class + Survived, *)", ylab = " # {passengers}", legend.text = TRUE)[] [846] [847] [848] [849] [850] [851] Underfull \hbox (badness 4634) in paragraph at lines 1410--1413 [][][]\T1/zi4/m/sl/10 boxplot.default[][][] []\T1/ptm/m/n/10 which al-ready wor ks nowa-days with data.frames; [][][]\T1/zi4/m/sl/10 boxplot.formula[][][][]\T1 /ptm/m/n/10 , [852] [853] [854] [855] [856] [857] [858] [859] [860] [861] [862] [863] [864] [865] [866] [867] [868] Underfull \hbox (badness 1728) in paragraph at lines 2388--2390 []\T1/ptm/m/n/10 a string in-di-cat-ing the x-axis style; use []\T1/zi4/m/sl/10 "n" []\T1/ptm/m/n/10 to sup-press and see also [869] Underfull \hbox (badness 1009) in paragraph at lines 2481--2488 \T1/ptm/m/n/10 be in as-cend-ing or-der. (The rest of this de-scrip-tion does n ot ap-ply to [870] [871] [872] [873] [874] [875] [876] [877] [878] [879] [880] [881] [882] [883] [884] [885] [886] [887] [888] [889] [890] [891] [892] Underfull \vbox (badness 10000) has occurred while \output is active [893] Underfull \vbox (badness 10000) has occurred while \output is active [894] [895] [896] [897] [898] [899] Underfull \vbox (badness 3803) has occurred while \output is active [900] [901] [902] [903] [904] [905] [906] Underfull \hbox (badness 3229) in paragraph at lines 4733--4738 []\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing if log-a-rith-mic axes are to be used, see [907] [908] [909] [910] [911] Underfull \hbox (badness 1107) in paragraph at lines 5233--5239 []\T1/ptm/m/n/10 is []\T1/zi4/m/sl/10 par("cin")/par("pin") []\T1/ptm/m/n/10 sc aled to user co-or-di-nates. Note that []\T1/zi4/m/sl/10 c([][]strwidth[][][](c h), [912] [913] Underfull \hbox (badness 10000) in paragraph at lines 5362--5365 [914 ] Underfull \hbox (badness 10000) in paragraph at lines 5423--5425 [915 ] [916] [917] [918] [919] [920] [921] [922] [923] [924] [925] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.plot}) ha s been already used, duplicate ignored \relax l.6097 \aliasA{plot}{plot.default}{plot} [926] [927] [928] [929] [930] [931] [932] [933] [934] [935] [936] [937] [938] [939] Overfull \hbox (31.57222pt too wide) in paragraph at lines 6997--6998 [][] [940 ] [941] Underfull \vbox (badness 3803) has occurred while \output is active [942] [943] [944] [945] [946] [947] [948] [949] [950] [951] [952] [953] [954] [955] [956] [957] [958] [959] [960] [961] [962] [963] [964] [965] [966] [967] [968] [969] [970] [971] [972] [973] [974] Underfull \hbox (badness 4954) in paragraph at lines 9109--9111 []\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color []\T1/zi4/m /sl/10 par(c("font.sub", Underfull \hbox (badness 1019) in paragraph at lines 9111--9113 []\T1/ptm/m/n/10 X axis la-bel us-ing font, size and color []\T1/zi4/m/sl/10 pa r(c("font.lab", "cex.lab", [975] [976] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.units}) h as been already used, duplicate ignored \relax l.9191 \HeaderA{units}{Graphical Units}{units} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.units.1}) has been already used, duplicate ignored \relax l.9191 \HeaderA{units}{Graphical Units}{units} [977] [978] [979] [980]) (./grDevices-pkg.tex Chapter 5. [981] [982] [983] [984] [985] Underfull \hbox (badness 2221) in paragraph at lines 282--286 []\T1/ptm/m/n/10 numeric vec-tor of length 3, []\T1/zi4/m/sl/10 c(mi, ma, n.)[] \T1/ptm/m/n/10 , with iden-ti-cal mean-ing to Underfull \hbox (badness 10000) in paragraph at lines 297--302 []\T1/ptm/m/n/10 Apart from that, [][][]\T1/zi4/m/sl/10 axisTicks[][][]() []\T1 /ptm/m/n/10 just calls the C func-tion []\T1/zi4/m/sl/10 CreateAtVector() []\T1 /ptm/m/n/10 in [986] [987] [988] [989] [990] [991] [992] [993] [994] Underfull \hbox (badness 1424) in paragraph at lines 901--903 [][][]\T1/zi4/m/sl/10 NA[][][] []\T1/ptm/m/n/10 (as in-te-ger or char-ac-ter) a nd []\T1/zi4/m/sl/10 "NA" []\T1/ptm/m/n/10 mean trans-par-ent, which can also b e spec-i-fied as [995] [996] [997] [998] [999] [1000] Underfull \hbox (badness 5175) in paragraph at lines 1229--1231 []\T1/ptm/m/n/10 There is cur-rently no doc-u-men-ta-tion about the al-go-rithm . The source code is in [1001] [1002] Underfull \hbox (badness 2512) in paragraph at lines 1348--1350 []\T1/ptm/m/n/10 For the white points [][]$\T1/zi4/m/sl/10 https : / / web . ar chive . org / web / 20190613001950 / http : / / efg2 . com / [1003] [1004] [1005] [1006] [1007] Underfull \hbox (badness 1490) in paragraph at lines 1648--1653 \T1/ptm/m/n/10 by [][][]\T1/zi4/m/sl/10 rasterImage[][][] []\T1/ptm/m/n/10 and [][][]\T1/zi4/m/sl/10 grid.raster[][][][]\T1/ptm/m/n/10 ? Pos-si-ble val-ues [] \T1/zi4/m/sl/10 "no"[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 "yes" []\T1/ptm/m/n/10 and Underfull \hbox (badness 3302) in paragraph at lines 1661--1665 []\T1/ptm/m/n/10 character: Does the de-vice sup-port pat-tern fills? One or mo re of [1008] [1009] [1010] [1011] [1012] [1013] Underfull \hbox (badness 1325) in paragraph at lines 2076--2086 []\T1/zi4/m/sl/10 "png48"[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 "pngmono"[]\T1/pt m/m/n/10 , []\T1/zi4/m/sl/10 "pnggray"[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 "png alpha"[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 "bmp16"[]\T1/ptm/m/n/10 , []\T1/zi4/ m/sl/10 "bmp16m" "bmp256"[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 "bmp32b"[]\T1/ptm /m/n/10 , [1014] [1015] Underfull \hbox (badness 10000) in paragraph at lines 2188--2190 []\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the set-ting of [1016] [1017] [1018] Underfull \hbox (badness 6758) in paragraph at lines 2376--2379 []\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript doc-u-men-ta-tion) are [1019] [1020] [1021] [1022] [1023] [1024] [1025] [1026] [1027] [1028] [1029] [1030] Underfull \hbox (badness 10000) in paragraph at lines 3132--3133 [1031] [1032] [1033] [1034] [1035] [1036] [1037] [1038] [1039] [1040] [1041] [1042] Underfull \vbox (badness 3803) has occurred while \output is active [1043] [1044] [1045] [1046] Underfull \vbox (badness 10000) has occurred while \output is active [1047] [1048] [1049] [1050] Underfull \hbox (badness 1418) in paragraph at lines 4410--4417 \T1/ptm/m/n/10 it is one of []\T1/zi4/m/sl/10 "AvantGarde"[]\T1/ptm/m/n/10 , [] \T1/zi4/m/sl/10 "Bookman"[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 "Courier"[]\T1/pt m/m/n/10 , []\T1/zi4/m/sl/10 "Helvetica"[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 "H elvetica-Narrow"[]\T1/ptm/m/n/10 , [1051] [1052] [1053] [1054] [1055] [1056] [1057] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.symbol}) has been already used, duplicate ignored \relax l.4875 \aliasA{symbol}{plotmath}{symbol} [1058] [1059] [1060] [1061] Underfull \vbox (badness 3803) has occurred while \output is active [1062] [1063] Underfull \hbox (badness 1584) in paragraph at lines 5268--5270 []\T1/ptm/m/n/10 For type []\T1/zi4/m/sl/10 "cairo"[]\T1/ptm/m/n/10 , the []\T1 /zi4/m/sl/10 symbolfamily []\T1/ptm/m/n/10 ar-gu-ment can be sup-plied. See Underfull \hbox (badness 1067) in paragraph at lines 5272--5279 \T1/ptm/m/n/10 The lat-ter will only be avail-able if the sys-tem was com-piled with sup- [1064] [1065] [1066] [1067] Underfull \hbox (badness 1377) in paragraph at lines 5574--5579 []\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the color model: cur-rently al-lowed val-ues [1068] [1069] Underfull \hbox (badness 1377) in paragraph at lines 5678--5683 []\T1/ptm/m/n/10 Color mod-els pro-vided for back-wards com-pat-i-bil-ity are [ ]\T1/zi4/m/sl/10 "rgb" []\T1/ptm/m/n/10 (which is RGB+gray) and [1070] Underfull \hbox (badness 7344) in paragraph at lines 5747--5749 []\T1/ptm/m/n/10 Support for Com-puter Mod-ern fonts is based on a con-tri-bu-t ion by Brian D'Urso [1071] [1072] Underfull \hbox (badness 2035) in paragraph at lines 5886--5895 []\T1/ptm/m/n/10 Mappings for a num-ber of stan-dard Adobe fonts (and URW equiv -a-lents) are also pro- Underfull \hbox (badness 10000) in paragraph at lines 5886--5895 \T1/ptm/m/n/10 vided: []\T1/zi4/m/sl/10 "AvantGarde"[]\T1/ptm/m/n/10 , []\T1/zi 4/m/sl/10 "Bookman"[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 "Courier"[]\T1/ptm/m/n/ 10 , []\T1/zi4/m/sl/10 "Helvetica"[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 "Helveti ca-Narrow"[]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 5886--5895 []\T1/zi4/m/sl/10 "NewCenturySchoolbook"[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 "P alatino" []\T1/ptm/m/n/10 and []\T1/zi4/m/sl/10 "Times"[]\T1/ptm/m/n/10 ; []\T1 /zi4/m/sl/10 "URWGothic"[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 "URWBookman"[]\T1/ ptm/m/n/10 , [1073] Underfull \hbox (badness 10000) in paragraph at lines 5953--5958 []\T1/zi4/m/sl/10 BousungEG-Light-GB []\T1/ptm/m/n/10 can be found at [][]$\T1/ zi4/m/sl/10 https : / / ftp . gnu . org / pub / non-[]gnu / [1074] [1075] [1076] Underfull \hbox (badness 1546) in paragraph at lines 6093--6101 []\T1/ptm/m/n/10 arguments []\T1/zi4/m/sl/10 onefile[]\T1/ptm/m/n/10 , []\T1/zi 4/m/sl/10 family[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 title[]\T1/ptm/m/n/10 , [] \T1/zi4/m/sl/10 fonts[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 encoding[]\T1/ptm/m/n /10 , []\T1/zi4/m/sl/10 bg[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 fg[]\T1/ptm/m/n/ 10 , []\T1/zi4/m/sl/10 width[]\T1/ptm/m/n/10 , [1077] [1078] [1079] [1080] [1081] [1082] Underfull \hbox (badness 6625) in paragraph at lines 6537--6540 []\T1/ptm/m/n/10 Murrell, P., Ooms, J., Al-laire, J.J. (2015), "Record-ing and Re-play-ing the Graph- [1083] [1084] Underfull \hbox (badness 10000) in paragraph at lines 6641--6644 []\T1/zi4/m/sl/10 rgb2hsv []\T1/ptm/m/n/10 trans-forms col-ors from RGB space ( red/green/blue) into HSV space [1085] [1086] [1087] [1088] Overfull \hbox (9.73488pt too wide) in paragraph at lines 6878--6878 []\T1/zi4/m/n/9 ## but now, x in [-0.5, 20] -- "too far" ==> "wrap around" pro blem (without \TS1/zi4/m/n/9 '\T1/zi4/m/n/9 continuous=TRUE\TS1/zi4/m/n/9 '\T1/ zi4/m/n/9 ):[] [1089] [1090] [1091] [1092] [1093] [1094] [1095] [1096] [1097] [1098] Underfull \hbox (badness 1189) in paragraph at lines 7507--7509 []\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used . One of [1099] Underfull \hbox (badness 10000) in paragraph at lines 7612--7614 []\T1/zi4/m/sl/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" []\T1/ptm/m/n/10 for C JK lan-guages and [1100] [1101] [1102] [1103] [1104] Underfull \hbox (badness 3780) in paragraph at lines 7927--7933 []\T1/ptm/m/n/10 the font fam-ily to be used. This must be one of []\T1/zi4/m/s l/10 "AvantGarde"[]\T1/ptm/m/n/10 , [1105] [1106] [1107] [1108] [1109] [1110]) (./grid-pkg.tex Chapter 6. [1111] [1112] [1113] [1114] [1115] [1116] [1117] [1118] [1119] Underfull \hbox (badness 2680) in paragraph at lines 551--554 []\T1/ptm/m/n/10 Note that []\T1/zi4/m/sl/10 preDrawDetails []\T1/ptm/m/n/10 an d []\T1/zi4/m/sl/10 postDrawDetails []\T1/ptm/m/n/10 are also called in the cal -cu-la-tion of [1120] [1121] [1122] [1123] [1124] [1125] [1126] [1127] [1128] [1129] [1130] Underfull \hbox (badness 4279) in paragraph at lines 1188--1197 [][][]\T1/ptm/m/n/10 Grid[][][], [][][]\T1/zi4/m/sl/10 pushViewport[][][][]\T1/ ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 popViewport[][][][]\T1/ptm/m/n/10 , [][][]\T 1/zi4/m/sl/10 downViewport[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 seekVi ewport[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 upViewport[][][][]\T1/ptm/ m/n/10 , [][][]\T1/zi4/m/sl/10 unit[][][][]\T1/ptm/m/n/10 , [1131] [1132] [1133] [1134] [1135] [1136] [1137] [1138] [1139] [1140] [1141] [1142] [1143] [1144] [1145] [1146] [1147] [1148] [1149] [1150] [1151] [1152] [1153] [1154] [1155] [1156] [1157] [1158] [1159] [1160] [1161] [1162] Underfull \hbox (badness 10000) in paragraph at lines 3103--3105 []\T1/ptm/m/n/10 A func-tion that re-turns an affine trans-for-ma-tion ma-trix; see [1163] [1164] [1165] [1166] [1167] [1168] [1169] [1170] [1171] [1172] [1173] [1174] [1175] [1176] [1177] [1178] Underfull \vbox (badness 10000) has occurred while \output is active [1179] [1180] [1181] [1182] [1183] [1184] [1185] [1186] [1187] [1188] [1189] [1190] [1191] [1192] Underfull \hbox (badness 1067) in paragraph at lines 4842--4845 []\T1/ptm/m/n/10 Both func-tions cre-ate a seg-ments grob (a graph-i-cal ob-jec t de-scrib-ing seg-ments), but only [1193] [1194] [1195] [1196] [1197] [1198] Underfull \hbox (badness 7256) in paragraph at lines 5193--5195 []\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject s are co-erced by [1199] [1200] [1201] [1202] [1203] [1204] [1205] Underfull \hbox (badness 2142) in paragraph at lines 5647--5651 []\T1/ptm/m/n/10 ob-jects. For []\T1/zi4/m/sl/10 gridGTreeCoords []\T1/ptm/m/n/ 10 a list of ei-ther []\T1/zi4/m/sl/10 "GridGrobCoords" []\T1/ptm/m/n/10 or [1206] [1207] Underfull \hbox (badness 4699) in paragraph at lines 5729--5734 []\T1/ptm/m/n/10 Either a []\T1/zi4/m/sl/10 "GridGrobCoords" []\T1/ptm/m/n/10 o b-ject (a list of lists with com-po-nents []\T1/zi4/m/sl/10 x []\T1/ptm/m/n/10 and []\T1/zi4/m/sl/10 y[]\T1/ptm/m/n/10 ) or a [1208] [1209] [1210] [1211] [1212] [1213] [1214] [1215] [1216] [1217] [1218] [1219] [1220] [1221] [1222] [1223] [1224] [1225] [1226] [1227] [1228] [1229] [1230] [1231] [1232] [1233] [1234] [1235] [1236] [1237] [1238] [1239]) (./methods-pkg.tex [1240] Chapter 7. [1241] [1242] [1243] [1244] [1245] [1246] [1247] [1248] Underfull \vbox (badness 10000) has occurred while \output is active [1249] Underfull \vbox (badness 10000) has occurred while \output is active [1250] [1251] [1252] [1253] [1254] [1255] [1256] [1257] [1258] [1259] Underfull \hbox (badness 2237) in paragraph at lines 1384--1386 []\T1/ptm/m/n/10 The class []\T1/zi4/m/sl/10 "className" []\T1/ptm/m/n/10 ex-te nds []\T1/zi4/m/sl/10 "character" []\T1/ptm/m/n/10 and has a slot []\T1/zi4/m/s l/10 "package"[]\T1/ptm/m/n/10 , also of class [1260] [1261] [1262] [1263] [1264] [1265] [1266] [1267] [1268] Underfull \hbox (badness 10000) in paragraph at lines 1980--1985 []\T1/ptm/m/n/10 The ar-gu-ment to []\T1/zi4/m/sl/10 insertSource []\T1/ptm/m/n /10 can be an ob-ject of class Underfull \hbox (badness 1038) in paragraph at lines 1980--1985 \T1/ptm/m/n/10 file name is passed to []\T1/zi4/m/sl/10 insertSource []\T1/ptm/ m/n/10 it calls []\T1/zi4/m/sl/10 evalSource []\T1/ptm/m/n/10 to ob-tain the [1269] [1270] [1271] Underfull \hbox (badness 2213) in paragraph at lines 2212--2217 []\T1/ptm/m/n/10 To re-strict the search to classes in a par-tic-u-lar pack-age , use []\T1/zi4/m/sl/10 where = [1272] [1273] [1274] [1275] [1276] Underfull \hbox (badness 10000) in paragraph at lines 2572--2575 []\T1/ptm/m/n/10 As you might ex-pect [][][]\T1/zi4/m/sl/10 setGeneric[][][] [] \T1/ptm/m/n/10 and [][][]\T1/zi4/m/sl/10 setGroupGeneric[][][] []\T1/ptm/m/n/10 cre-ate ob-jects of class [1277] [1278] Underfull \hbox (badness 1132) in paragraph at lines 2712--2716 []\T1/ptm/m/n/10 In []\T1/zi4/m/sl/10 getGenerics[]\T1/ptm/m/n/10 , if []\T1/zi 4/m/sl/10 TRUE[]\T1/ptm/m/n/10 , the []\T1/zi4/m/sl/10 package []\T1/ptm/m/n/10 slot of the re-turned re-sult is in [1279] Underfull \hbox (badness 1033) in paragraph at lines 2748--2753 \T1/ptm/m/n/10 In ad-di-tion, []\T1/zi4/m/sl/10 removeGeneric []\T1/ptm/m/n/10 re-moves the func-tion it-self; []\T1/zi4/m/sl/10 removeMethods []\T1/ptm/m/n/1 0 re-stores the [1280] [1281] [1282] [1283] [1284] [1285] [1286] Underfull \hbox (badness 1102) in paragraph at lines 3305--3307 []\T1/zi4/m/sl/10 getPackageName []\T1/ptm/m/n/10 re-turns the character-string name of the pack-age (with-out the ex-tra-ne-ous [1287] [1288] [1289] [1290] [1291] Underfull \hbox (badness 10000) in paragraph at lines 3642--3651 []\T1/ptm/m/n/10 The [1292] [1293] Underfull \hbox (badness 10000) in paragraph at lines 3762--3763 [] \T1/zi4/m/sl/10 Pos <- setClass("Pos", slots = c(latitude = "numeric", longi tude = "numeric", [1294] Underfull \hbox (badness 10000) in paragraph at lines 3846--3847 []\T1/zi4/m/sl/10 Currency <- setClass("Currency", slots = c(unit = "character" ), contains = [1295] [1296] [1297] [1298] [1299] [1300] [1301] [1302] [1303] [1304] Underfull \hbox (badness 1769) in paragraph at lines 4477--4483 []\T1/ptm/m/n/10 class [][][]\T1/zi4/m/sl/10 MethodsList[][][] []\T1/ptm/m/n/10 for the ob-jects defin-ing sets of meth-ods as-so-ci-ated with a par-tic-u-lar Underfull \hbox (badness 1939) in paragraph at lines 4477--4483 []\T1/zi4/m/sl/10 MethodDefinition[]\T1/ptm/m/n/10 , or an ex-ten-sion. Class [ ][][]\T1/zi4/m/sl/10 MethodWithNext[][][] []\T1/ptm/m/n/10 for an ex-ten-sion u sed by [1305] [1306] [1307] [1308] [1309] [1310] [1311] [1312] [1313] [1314] Underfull \vbox (badness 10000) has occurred while \output is active [1315] [1316] [1317] Underfull \hbox (badness 4036) in paragraph at lines 5442--5445 []\T1/ptm/m/n/10 Object of class []\T1/zi4/m/sl/10 "PossibleMethod" []\T1/ptm/m /n/10 the method to use in re-sponse to a [1318] [1319] Underfull \hbox (badness 3803) in paragraph at lines 5517--5519 []\T1/ptm/m/n/10 arguments to spec-ify prop-er-ties of the new ob-ject, to be p assed to [1320] [1321] [1322] Underfull \hbox (badness 1087) in paragraph at lines 5748--5753 []\T1/ptm/m/n/10 In ad-di-tion, the cur-rently avail-able gener-ics with meth-o ds for this class are found (us-ing [1323] [1324] [1325] [1326] [1327] [1328] [1329] [1330] [1331] Underfull \hbox (badness 1675) in paragraph at lines 6455--6461 []\T1/ptm/m/n/10 can be con-verted ex-plic-itly as []\T1/zi4/m/sl/10 externalRe fMethod(f)[]\T1/ptm/m/n/10 , which re-turns an ob-ject of class [1332] [1333] [1334] [1335] Underfull \vbox (badness 10000) has occurred while \output is active [1336] [1337] [1338] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.S4}) has been already used, duplicate ignored \relax l.6976 \aliasA{S4}{S3Part}{S4} [1339] [1340] [1341] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Complex}) has been already used, duplicate ignored \relax l.7232 \aliasA{Complex}{S4groupGeneric}{Complex} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Logic}) h as been already used, duplicate ignored \relax l.7234 \aliasA{Logic}{S4groupGeneric}{Logic} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Math}) ha s been already used, duplicate ignored \relax l.7235 \aliasA{Math}{S4groupGeneric}{Math} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Ops}) has been already used, duplicate ignored \relax l.7237 \aliasA{Ops}{S4groupGeneric}{Ops} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Summary}) has been already used, duplicate ignored \relax l.7238 \aliasA{Summary}{S4groupGeneric}{Summary} [1342] Underfull \hbox (badness 2050) in paragraph at lines 7299--7303 []\T1/ptm/m/n/10 The mem-bers of the group de-fined by a par-tic-u-lar generic can be ob-tained by call-ing [1343] [1344] [1345] Underfull \hbox (badness 1286) in paragraph at lines 7487--7489 []\T1/ptm/m/n/10 for []\T1/zi4/m/sl/10 .selectSuperClasses() []\T1/ptm/m/n/10 o nly, a [][][]\T1/zi4/m/sl/10 list[][][] []\T1/ptm/m/n/10 of class ex-ten-sions, typ-i-cally [1346] [1347] [1348] [1349] [1350] [1351] [1352] [1353] [1354] [1355] [1356] [1357] [1358] [1359] [1360] [1361] [1362] [1363] [1364] [1365] [1366] [1367] [1368] [1369] [1370] [1371] [1372] Underfull \vbox (badness 10000) has occurred while \output is active [1373] [1374] [1375] [1376] [1377] [1378] [1379] [1380] [1381] [1382] [1383] [1384] [1385] [1386] Underfull \hbox (badness 1158) in paragraph at lines 10494--10497 []\T1/ptm/m/n/10 Chambers, John M. (2009) \T1/ptm/m/it/10 Class In-her-i-tance in R [][]$\T1/zi4/m/sl/10 https : / / johnmchambers . su . domains / [1387] Underfull \hbox (badness 1852) in paragraph at lines 10572--10576 []\T1/ptm/m/n/10 Each of the classes ex-tends the cor-re-spond-ing un-traced cl ass, from the data part; e.g., [1388] [1389] [1390] [1391]) (./parallel-pkg.tex [1392] Chapter 8. Underfull \hbox (badness 5490) in paragraph at lines 14--16 []\T1/ptm/m/n/10 There is sup-port for mul-ti-ple RNG streams with the `[]\T1/z i4/m/sl/10 "L\TS1/zi4/m/n/10 '\T1/zi4/m/sl/10 Ecuyer-CMRG"[]\T1/ptm/m/n/10 ' [] []RNG[][][]: see [1393] [1394] [1395] [1396] [1397] Underfull \hbox (badness 1320) in paragraph at lines 300--303 []\T1/ptm/m/n/10 It has meth-ods to do so for Linux, ma-cOS, FreeBSD, OpenBSD, So-laris and Win-dows. [1398] [1399] [1400] [1401] [1402] [1403] [1404] [1405] [1406] [1407] [1408] [1409] [1410] [1411] [1412] [1413] [1414] Underfull \hbox (badness 3386) in paragraph at lines 1400--1403 []\T1/ptm/m/n/10 An in-te-ger vec-tor of length 7 as given by []\T1/zi4/m/sl/10 .Random.seed []\T1/ptm/m/n/10 when the [1415] [1416]) (./splines-pkg.tex Chapter 9. Underfull \hbox (badness 10000) in paragraph at lines 22--24 []\T1/ptm/m/n/10 Douglas M. Bates \T1/zi4/m/sl/10 \T1/ptm /m/n/10 and William N. Ven-ables [1417] [1418] [1419] [1420] [1421] [1422] [1423] [1424] [1425] [1426] [1427] [1428] [1429] [1430] [1431] [1432]) (./stats-pkg.tex Chapter 10. [1433] [1434] [1435] [1436] [1437] [1438] [1439] [1440] [1441] [1442] [1443] [1444] [1445] [1446] Underfull \hbox (badness 1412) in paragraph at lines 901--903 []\T1/ptm/m/n/10 A fit-ted model ob-ject, for ex-am-ple from []\T1/zi4/m/sl/10 lm []\T1/ptm/m/n/10 or []\T1/zi4/m/sl/10 aov[]\T1/ptm/m/n/10 , or a for-mula fo r [1447] [1448] [1449] [1450] [1451] [1452] [1453] [1454] Underfull \hbox (badness 2503) in paragraph at lines 1389--1392 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of []\T1/zi4/m/sl/10 "two.sided"[]\T1/ptm/m/n/10 , [1455] [1456] [1457] [1458] [1459] [1460] [1461] [1462] [1463] [1464] [1465] [1466] [1467] [1468] [1469] [1470] [1471] [1472] [1473] [1474] [1475] [1476] [1477] [1478] [1479] [1480] [1481] [1482] [1483] [1484] [1485] [1486] [1487] [1488] Underfull \hbox (badness 2503) in paragraph at lines 3561--3564 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of []\T1/zi4/m/sl/10 "two.sided"[]\T1/ptm/m/n/10 , [1489] [1490] Package amsmath Warning: Foreign command \atopwithdelims; (amsmath) \frac or \genfrac should be used instead (amsmath) on input line 3674. [1491] [1492] [1493] [1494] [1495] [1496] [1497] [1498] [1499] [1500] [1501] [1502] [1503] [1504] [1505] [1506] [1507] [1508] Underfull \hbox (badness 3989) in paragraph at lines 4820--4827 []\T1/ptm/m/n/10 a nu-meric vec-tor of length 2, equal to say $\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 g[]; g[]\OT1/cmr/m/n/10 )$\T1/ptm/m/n/10 , where $\OML/cmm/m/ it/10 g[] \OT1/cmr/m/n/10 = [1509] [1510] [1511] [1512] [1513] [1514] [1515] [1516] [1517] [1518] Underfull \hbox (badness 2556) in paragraph at lines 5474--5477 []\T1/ptm/m/n/10 character; par-tially matched to []\T1/zi4/m/sl/10 "circular"[ ]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 "open"[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 "filter"[]\T1/ptm/m/n/10 . For [1519] [1520] [1521] [1522] [1523] [1524] [1525] Underfull \hbox (badness 2503) in paragraph at lines 5886--5890 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of []\T1/zi4/m/sl/10 "two.sided"[]\T1/ptm/m/n/10 , [1526] [1527] [1528] [1529] [1530] [1531] [1532] [1533] [1534] [1535] [1536] [1537] [1538] Underfull \hbox (badness 7081) in paragraph at lines 6678--6681 []\T1/ptm/m/n/10 Objects of class []\T1/zi4/m/sl/10 "hclust" []\T1/ptm/m/n/10 c an be con-verted to class []\T1/zi4/m/sl/10 "dendrogram" []\T1/ptm/m/n/10 us-in g method Underfull \hbox (badness 10000) in paragraph at lines 6682--6684 []\T1/zi4/m/sl/10 rev.dendrogram []\T1/ptm/m/n/10 sim-ply re-turns the den-dro- gram []\T1/zi4/m/sl/10 x []\T1/ptm/m/n/10 with re-versed nodes, see also [1539] [1540] [1541] [1542] [1543] [1544] Underfull \vbox (badness 10000) has occurred while \output is active [1545] [1546] [1547] Underfull \vbox (badness 10000) has occurred while \output is active [1548] [1549] [1550] [1551] [1552] Underfull \hbox (badness 10000) in paragraph at lines 7578--7581 []\T1/ptm/m/n/10 optionally, the dis-tance method used; re-sult-ing from [][][] \T1/zi4/m/sl/10 dist[][][]()[]\T1/ptm/m/n/10 , the [1553] [1554] [1555] [1556] [1557] [1558] Underfull \vbox (badness 3803) has occurred while \output is active [1559] [1560] [1561] [1562] [1563] [1564] [1565] [1566] [1567] [1568] [1569] [1570] [1571] [1572] [1573] [1574] Underfull \vbox (badness 3803) has occurred while \output is active [1575] [1576] [1577] [1578] [1579] [1580] Underfull \hbox (badness 2626) in paragraph at lines 9275--9278 []\T1/ptm/m/n/10 Either []\T1/zi4/m/sl/10 "convolution" []\T1/ptm/m/n/10 or []\ T1/zi4/m/sl/10 "recursive" []\T1/ptm/m/n/10 (and can be ab-bre-vi-ated). If [1581] Underfull \hbox (badness 2503) in paragraph at lines 9382--9386 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of []\T1/zi4/m/sl/10 "two.sided"[]\T1/ptm/m/n/10 , [1582] [1583] [1584] [1585] [1586] [1587] [1588] [1589] [1590] [1591] [1592] [1593] [1594] [1595] [1596] [1597] [1598] [1599] [1600] [1601] [1602] Underfull \hbox (badness 4518) in paragraph at lines 10730--10735 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1603] [1604] [1605] [1606] [1607] Underfull \hbox (badness 2142) in paragraph at lines 11092--11095 []\T1/ptm/m/n/10 positive con-ver-gence tol-er-ance $\OML/cmm/m/it/10 ^^O$\T1/p tm/m/n/10 ; the it-er-a-tions con-verge when $\OMS/cmsy/m/n/10 j\OML/cmm/m/it/1 0 dev \OMS/cmsy/m/n/10 ^^@ Underfull \hbox (badness 1253) in paragraph at lines 11111--11114 []\T1/ptm/m/n/10 When []\T1/zi4/m/sl/10 trace []\T1/ptm/m/n/10 is true, calls t o [][][]\T1/zi4/m/sl/10 cat[][][] []\T1/ptm/m/n/10 pro-duce the out-put for eac h IWLS it-er-a-tion. Hence, [1608] Underfull \hbox (badness 1708) in paragraph at lines 11173--11177 []\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter- na-tives are: [1609] [1610] [1611] [1612] [1613] [1614] Underfull \hbox (badness 1694) in paragraph at lines 11569--11572 []\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these de-fault to [1615] [1616] [1617] [1618] [1619] [1620] [1621] [1622] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.hat}) has been already used, duplicate ignored \relax l.12050 \aliasA{hat}{influence.measures}{hat} [1623] [1624] Underfull \hbox (badness 1484) in paragraph at lines 12195--12197 []\T1/ptm/m/n/10 The func-tion []\T1/zi4/m/sl/10 hat() []\T1/ptm/m/n/10 ex-ists mainly for S (ver-sion 2) com-pat-i-bil-ity; we rec-om-mend us-ing [1625] [1626] [1627] [1628] [1629] [1630] [1631] [1632] [1633] [1634] Underfull \hbox (badness 10000) in paragraph at lines 12782--12784 []\T1/ptm/m/n/10 tolerance even-tu-ally passed to [][][]\T1/zi4/m/sl/10 solve.d efault[][][] []\T1/ptm/m/n/10 when []\T1/zi4/m/sl/10 SSinit = [1635] [1636] [1637] [1638] [1639] Underfull \hbox (badness 2894) in paragraph at lines 13124--13128 []\T1/ptm/m/n/10 logical or in-te-ger num-ber, cur-rently only used in the de-f ault method [1640] [1641] [1642] [1643] [1644] [1645] [1646] Underfull \hbox (badness 1496) in paragraph at lines 13552--13558 []\T1/ptm/m/n/10 Gunar Schröer and Di-et-rich Tren-kler (1995). Ex-act and Ran- dom-iza-tion Dis-tri-bu-tions of [1647] [1648] [1649] [1650] [1651] [1652] Underfull \hbox (badness 4518) in paragraph at lines 13955--13960 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1653] [1654] [1655] [1656] [1657] [1658] [1659] [1660] [1661] [1662] Underfull \hbox (badness 4518) in paragraph at lines 14617--14622 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1663] [1664] [1665] Underfull \hbox (badness 6412) in paragraph at lines 14757--14761 []\T1/ptm/m/n/10 Only for the (de-fault) case []\T1/zi4/m/sl/10 (surface = "int erpolate", statistics = Underfull \hbox (badness 1199) in paragraph at lines 14764--14766 []\T1/ptm/m/n/10 the num-ber of it-er-a-tions used in ro-bust fit-ting, i.e. on ly if []\T1/zi4/m/sl/10 family []\T1/ptm/m/n/10 is [1666] [1667] [1668] [1669] [1670] [1671] [1672] [1673] [1674] [1675] [1676] [1677] [1678] [1679] [1680] [1681] [1682] [1683] Underfull \hbox (badness 2503) in paragraph at lines 15841--15845 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of []\T1/zi4/m/sl/10 "two.sided"[]\T1/ptm/m/n/10 , [1684] [1685] [1686] [1687] [1688] [1689] [1690] [1691] Underfull \hbox (badness 10000) in paragraph at lines 16354--16360 []\T1/zi4/m/sl/10 model.extract(m, "offset") []\T1/ptm/m/n/10 and []\T1/zi4/m/s l/10 model.extract(m, "response") []\T1/ptm/m/n/10 are equiv-a-lent to Underfull \hbox (badness 1867) in paragraph at lines 16354--16360 []\T1/zi4/m/sl/10 model.offset(m) []\T1/ptm/m/n/10 and []\T1/zi4/m/sl/10 model. response(m) []\T1/ptm/m/n/10 re-spec-tively. []\T1/zi4/m/sl/10 model.offset []\ T1/ptm/m/n/10 sums any terms [1692] [1693] [1694] [1695] [1696] [1697] [1698] [1699] [1700] [1701] [1702] [1703] [1704] [1705] [1706] [1707] [1708] [1709] [1710] [1711] [1712] [1713] [1714] [1715] [1716] [1717] [1718] Underfull \hbox (badness 1158) in paragraph at lines 18012--18015 []\T1/ptm/m/n/10 the ex-pres-sion that was passed to []\T1/zi4/m/sl/10 nls []\T 1/ptm/m/n/10 as the data ar-gu-ment. The ac- [1719] [1720] Underfull \vbox (badness 10000) has occurred while \output is active [1721] Underfull \vbox (badness 10000) has occurred while \output is active [1722] [1723] [1724] [1725] [1726] [1727] [1728] [1729] [1730] [1731] [1732] [1733] [1734] [1735] Underfull \hbox (badness 1377) in paragraph at lines 19055--19060 []\T1/ptm/m/n/10 A vec-tor of scal-ing val-ues for the pa-ram-e-ters. Op-ti-miz a-tion is per-formed on Underfull \hbox (badness 1735) in paragraph at lines 19060--19063 []\T1/ptm/m/n/10 A vec-tor of step sizes for the finite-difference ap-prox-i-ma -tion to the gra-di-ent, on Underfull \hbox (badness 2343) in paragraph at lines 19073--19077 []\T1/ptm/m/n/10 Relative con-ver-gence tol-er-ance. The al-go-rithm stops if i t is un-able to re-duce Underfull \hbox (badness 3471) in paragraph at lines 19073--19077 \T1/ptm/m/n/10 the value by a fac-tor of []\T1/zi4/m/sl/10 reltol * (abs(val) + reltol) []\T1/ptm/m/n/10 at a step. De-faults to Underfull \hbox (badness 2662) in paragraph at lines 19081--19085 []\T1/ptm/m/n/10 The fre-quency of re-ports for the []\T1/zi4/m/sl/10 "BFGS"[]\ T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 "L-BFGS-B" []\T1/ptm/m/n/10 and []\T1/zi4/m/s l/10 "SANN" []\T1/ptm/m/n/10 meth-ods if [1736] [1737] [1738] Underfull \vbox (badness 10000) has occurred while \output is active [1739] Overfull \hbox (15.73795pt too wide) in paragraph at lines 19306--19306 []\T1/zi4/m/n/9 ## 1-D minimization: "Brent" or optimize() being preferred.. b ut NM may be ok and "unavoidable",[] Overfull \hbox (3.75941pt too wide) in paragraph at lines 19309--19309 []\T1/zi4/m/n/9 system.time(ro <- optim(1, function(x) (x-pi)^2, control=list( warn.1d.NelderMead = FALSE)))[] [1740] [1741] [1742] [1743] [1744] [1745] [1746] Underfull \hbox (badness 1337) in paragraph at lines 19771--19774 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1747] [1748] [1749] [1750] [1751] [1752] [1753] [1754] [1755] Underfull \hbox (badness 10000) in paragraph at lines 20240--20246 \T1/zi4/m/sl/10 legend = "Cook\TS1/zi4/m/n/10 '\T1/zi4/m/sl/10 s distance", lty = cook.lty, col = cook.col, text.col [1756] [1757] [1758] [1759] [1760] [1761] [1762] Underfull \hbox (badness 1194) in paragraph at lines 20667--20670 []\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting of the con-fi-dence [1763] [1764] [1765] [1766] [1767] [1768] Underfull \hbox (badness 2503) in paragraph at lines 21045--21048 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of []\T1/zi4/m/sl/10 "two.sided"[]\T1/ptm/m/n/10 , Underfull \hbox (badness 3919) in paragraph at lines 21072--21074 []\T1/ptm/m/n/10 the char-ac-ter string []\T1/zi4/m/sl/10 "Exact Poisson test" []\T1/ptm/m/n/10 or []\T1/zi4/m/sl/10 "Comparison of Poisson [1769] [1770] [1771] [1772] [1773] [1774] [1775] [1776] [1777] [1778] [1779] [1780] [1781] [1782] [1783] [1784] [1785] [1786] Underfull \hbox (badness 10000) in paragraph at lines 22150--22156 []\T1/ptm/m/n/10 For time-series pre-dic-tion, [][][]\T1/zi4/m/sl/10 predict.ar [][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 predict.Arima[][][][]\T1/ptm/m/n /10 , [][][]\T1/zi4/m/sl/10 predict.arima0[][][][]\T1/ptm/m/n/10 , [1787] [1788] [1789] [1790] [1791] [1792] [1793] [1794] [1795] [1796] [1797] [1798] [1799] [1800] [1801] [1802] [1803] [1804] [1805] [1806] [1807] [1808] [1809] [1810] [1811] Underfull \hbox (badness 1337) in paragraph at lines 23626--23632 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1812] [1813] [1814] [1815] [1816] [1817] [1818] [1819] Underfull \hbox (badness 1436) in paragraph at lines 24116--24119 \T1/ptm/m/n/10 per-cent-ages. In \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions up t o 4.0.x, this had been set to []\T1/zi4/m/sl/10 max(2, [1820] Underfull \hbox (badness 10000) in paragraph at lines 24254--24255 []\T1/ptm/m/n/10 Wikipedia: [][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . o rg / wiki / Quantile # Estimating _ quantiles _ from _ a _ [1821] [1822] [1823] [1824] [1825] [1826] [1827] [1828] [1829] [1830] [1831] [1832] [1833] [1834] [1835] [1836] Underfull \hbox (badness 1824) in paragraph at lines 25224--25230 []\T1/ptm/m/n/10 Here, all the NAs in []\T1/zi4/m/sl/10 x []\T1/ptm/m/n/10 are first re-placed by al-ter- Underfull \hbox (badness 1033) in paragraph at lines 25224--25230 \T1/ptm/m/n/10 nat-ing $\OMS/cmsy/m/n/10 ^^F\OML/cmm/m/it/10 B$ \T1/ptm/m/n/10 where $\OML/cmm/m/it/10 B$ \T1/ptm/m/n/10 is a ``Big'' num-ber (with $\OT1/cmr/ m/n/10 2\OML/cmm/m/it/10 B < M\OMS/cmsy/m/n/10 ^^C$\T1/ptm/m/n/10 , where [1837] Underfull \hbox (badness 10000) in paragraph at lines 25245--25248 []\T1/ptm/m/n/10 Apart from the end val-ues, the re-sult []\T1/zi4/m/sl/10 y = runmed(x, k) []\T1/ptm/m/n/10 sim-ply has []\T1/zi4/m/sl/10 y[j] = [1838] [1839] [1840] [1841] [1842] [1843] [1844] [1845] [1846] Underfull \hbox (badness 2165) in paragraph at lines 25820--25825 []\T1/ptm/m/n/10 Each of the fol-low-ing are []\T1/zi4/m/sl/10 "selfStart" []\T 1/ptm/m/n/10 mod-els (with ex-am-ples) [][][]\T1/zi4/m/sl/10 SSasymp[][][][]\T1 /ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 SSasympOff[][][][]\T1/ptm/m/n/10 , [1847] [1848] [1849] [1850] Underfull \hbox (badness 1867) in paragraph at lines 26030--26032 []\T1/ptm/m/n/10 potentially fur-ther ar-gu-ments passed to and from meth-ods. Passed to Underfull \hbox (badness 10000) in paragraph at lines 26046--26050 []\T1/ptm/m/n/10 where []\T1/zi4/m/sl/10 NN <- [][]nobs[][][](object, use.fallb ack = use.fallback) []\T1/ptm/m/n/10 and []\T1/zi4/m/sl/10 PP <- [1851] [1852] [1853] [1854] [1855] [1856] [1857] [1858] [1859] [1860] [1861] [1862] [1863] [1864] [1865] [1866] [1867] [1868] [1869] [1870] [1871] [1872] [1873] [1874] [1875] Underfull \vbox (badness 10000) has occurred while \output is active [1876] [1877] Underfull \hbox (badness 3514) in paragraph at lines 27698--27703 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/zi4/m/sl/10 inp ut[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1878] [1879] [1880] [1881] Overfull \hbox (2.23795pt too wide) in paragraph at lines 27932--27932 [] \T1/zi4/m/n/9 quote({f(t[0.5]) == frac(phi[1],2)}~{} %=>% {}~~{t[0.5] == frac(log(2), e^{phi[2]})}),[] Underfull \hbox (badness 3514) in paragraph at lines 27968--27974 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/zi4/m/sl/10 inp ut[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1882] Overfull \hbox (14.22568pt too wide) in paragraph at lines 28028--28028 [] \T1/zi4/m/n/9 control = list(scaleOffset=1, printEval=TRUE, tol= 1e-11, nDcentral=TRUE), trace=TRUE)[] [1883] [1884] [1885] [1886] Underfull \hbox (badness 3514) in paragraph at lines 28201--28206 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/zi4/m/sl/10 inp ut[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1887] Underfull \hbox (badness 3514) in paragraph at lines 28288--28293 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/zi4/m/sl/10 inp ut[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1888] Underfull \hbox (badness 3514) in paragraph at lines 28353--28358 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/zi4/m/sl/10 inp ut[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1889] [1890] Underfull \hbox (badness 3514) in paragraph at lines 28447--28452 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/zi4/m/sl/10 inp ut[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1891] [1892] Underfull \hbox (badness 6691) in paragraph at lines 28539--28544 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/zi4/m/sl/10 x[] \T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1893] [1894] [1895] [1896] [1897] [1898] [1899] [1900] Underfull \hbox (badness 4024) in paragraph at lines 29026--29029 []\T1/ptm/m/n/10 the span (in lags) of the loess win-dow for trend ex-trac-tion , which [1901] [1902] [1903] [1904] [1905] [1906] [1907] [1908] [1909] [1910] Underfull \hbox (badness 5431) in paragraph at lines 29629--29631 []\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above []\T1 /zi4/m/sl/10 cov.unscaled[]\T1/ptm/m/n/10 , if [1911] [1912] [1913] Underfull \hbox (badness 5431) in paragraph at lines 29839--29842 []\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above []\T1 /zi4/m/sl/10 cov.unscaled[]\T1/ptm/m/n/10 , if [1914] [1915] [1916] [1917] [1918] [1919] Underfull \hbox (badness 1337) in paragraph at lines 30154--30158 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1920] [1921] Underfull \hbox (badness 1127) in paragraph at lines 30291--30294 []\T1/ptm/m/n/10 non-centrality pa-ram-e-ter $\OML/cmm/m/it/10 ^^N$\T1/ptm/m/n/ 10 ; cur-rently ex-cept for []\T1/zi4/m/sl/10 rt()[]\T1/ptm/m/n/10 , ac-cu-rate only for [1922] [1923] [1924] Underfull \hbox (badness 1616) in paragraph at lines 30497--30500 []\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial resid-u-als, when [1925] [1926] [1927] [1928] [1929] [1930] [1931] [1932] [1933] [1934] [1935] [1936] [1937] [1938] [1939] [1940] [1941] [1942] [1943] [1944] [1945] Underfull \hbox (badness 3557) in paragraph at lines 31724--31728 []\T1/ptm/m/n/10 Setting []\T1/zi4/m/sl/10 extendInt []\T1/ptm/m/n/10 to a non- []\T1/zi4/m/sl/10 "no" []\T1/ptm/m/n/10 string, means search-ing for the cor-re ct []\T1/zi4/m/sl/10 interval = [1946] [1947] [1948] Underfull \vbox (badness 10000) has occurred while \output is active [1949] [1950] [1951] Underfull \hbox (badness 1337) in paragraph at lines 32091--32095 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1952] [1953] [1954] [1955] [1956] [1957] [1958] [1959] [1960] Underfull \hbox (badness 1337) in paragraph at lines 32619--32623 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1961] [1962] [1963] Overfull \hbox (0.71648pt too wide) in paragraph at lines 32827--32827 []\T1/zi4/m/n/9 wilcox.test( 4:2, 3:1, paired=TRUE) # Warning: canno t compute exact p-value with ties[] [1964] [1965] [1966] Overfull \hbox (19.71954pt too wide) in paragraph at lines 32988--32988 [] \T1/zi4/m/sl/10 frequency = NULL, deltat = NULL, extend = FALSE, ts.ep s = getOption("ts.eps"), ...)[] [1967] [1968] [1969] [1970] [1971]) (./stats4-pkg.tex [1972] Chapter 11. [1973] [1974] [1975] Underfull \vbox (badness 10000) has occurred while \output is active [1976] Underfull \vbox (badness 10000) has occurred while \output is active [1977] [1978] [1979] [1980] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.show.Rdas h.methods}) has been already used, duplicate ignored \relax l.503 ...Package \pkg{stats4}}{show.Rdash.methods} [1981] [1982] [1983]) (./tcltk-pkg.tex [1984] Chapter 12. [1985] [1986] [1987] [1988] [1989] [1990] [1991] Underfull \vbox (badness 10000) has occurred while \output is active [1992] Underfull \vbox (badness 10000) has occurred while \output is active [1993] Underfull \hbox (badness 1546) in paragraph at lines 672--679 []\T1/zi4/m/sl/10 tcl []\T1/ptm/m/n/10 pro-vides a generic in-ter-face to call- ing any Tk or Tcl com-mand by sim-ply run-ning [1994] [1995] [1996] [1997] [1998] Underfull \vbox (badness 10000) has occurred while \output is active [1999] [2000] [2001] [2002] [2003] [2004] [2005] [2006]) (./tools-pkg.tex Chapter 13. [2007] LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined (Font) using `T1/zi4/m/n' instead on input line 72. [2008] Underfull \hbox (badness 3039) in paragraph at lines 167--170 []\T1/zi4/m/sl/10 assertWarning() []\T1/ptm/m/n/10 as-serts that a warn-ing wil l be sig-nalled, but \T1/ptm/m/it/10 not \T1/ptm/m/n/10 an er-ror, whereas [2009] [2010] Underfull \hbox (badness 1308) in paragraph at lines 288--301 []\T1/ptm/m/n/10 At a min-i-mum, the en-vi-ron-ment should con-tain rou-tines t o ren-der each of the 12 types Underfull \hbox (badness 4967) in paragraph at lines 288--301 \T1/ptm/m/n/10 of bib-li-o-graphic en-try sup-ported by [][][]\T1/zi4/m/sl/10 b ibentry[][][] []\T1/ptm/m/n/10 as well as sev-eral other rou-tines de- Underfull \hbox (badness 10000) in paragraph at lines 288--301 []\T1/zi4/m/sl/10 formatIncollection[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 format InProceedings[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 formatManual[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 formatMastersthesis[]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 288--301 []\T1/zi4/m/sl/10 formatMisc[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 formatPhdthesi s[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 formatProceedings[]\T1/ptm/m/n/10 , []\T1 /zi4/m/sl/10 formatTechreport []\T1/ptm/m/n/10 and [2011] [2012] Underfull \hbox (badness 3039) in paragraph at lines 392--394 []\T1/zi4/m/sl/10 NULL []\T1/ptm/m/n/10 or char-ac-ter; name of vi-gnette en-gi ne to use. Over-rides any [2013] Underfull \hbox (badness 1142) in paragraph at lines 464--468 \T1/ptm/m/n/10 If given, vi-gnette source files are by de-fault looked for in s ub-di-rec-tory [2014] [2015] [2016] [2017] [2018] [2019] [2020] [2021] [2022] [2023] [2024] [2025] [2026] Underfull \hbox (badness 1014) in paragraph at lines 1220--1222 []\T1/ptm/m/n/10 a log-i-cal in-di-cat-ing whether to also sum-ma-rize the re-v erse de-pen-den-cies Underfull \hbox (badness 7238) in paragraph at lines 1226--1228 []\T1/ptm/m/n/10 a char-ac-ter string giv-ing the path to the di-rec-tory of a pre-vi-ous [2027] Underfull \hbox (badness 10000) in paragraph at lines 1263--1266 []\T1/ptm/m/n/10 Results and tim-ings can con-ve-niently be sum-ma-rized us-ing Overfull \hbox (15.52087pt too wide) in paragraph at lines 1263--1266 []\T1/zi4/m/sl/10 summarize_check_packages_in_dir_results []\T1/ptm/m/n/10 and []\T1/zi4/m/sl/10 summarize_check_packages_in_dir_timings[]\T1/ptm/m/n/10 , [2028] [2029] [2030] [2031] [2032] [2033] Underfull \hbox (badness 10000) in paragraph at lines 1637--1640 []\T1/ptm/m/n/10 Internal func-tions []\T1/zi4/m/sl/10 CRAN_aliases_db[]\T1/ptm /m/n/10 , []\T1/zi4/m/sl/10 CRAN_archive_db[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 CRAN_current_db []\T1/ptm/m/n/10 and [2034] [2035] Underfull \hbox (badness 4096) in paragraph at lines 1756--1764 \T1/zi4/m/sl/10 "Imports", "LinkingTo", "Suggests", "Enhances")[]\T1/ptm/m/n/10 . Char-ac-ter string Underfull \hbox (badness 1082) in paragraph at lines 1766--1768 []\T1/ptm/m/n/10 a char-ac-ter vec-tor of \T1/phv/m/n/10 R \T1/ptm/m/n/10 li-br ary trees, or []\T1/zi4/m/sl/10 NULL []\T1/ptm/m/n/10 for all known trees (see [2036] [2037] [2038] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.GSC}) has been already used, duplicate ignored \relax l.1967 \aliasA{GSC}{find\_gs\_cmd}{GSC} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.R.Rul.GSC MD}) has been already used, duplicate ignored \relax l.1968 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD} [2039] [2040] [2041] [2042] [2043] [2044] [2045] [2046] Underfull \hbox (badness 3386) in paragraph at lines 2442--2445 []\T1/ptm/m/n/10 The de-fault method of []\T1/zi4/m/sl/10 as.Rconcordance []\T1 /ptm/m/n/10 searches for strings match-ing the pat-tern of [2047] [2048] Underfull \hbox (badness 4096) in paragraph at lines 2582--2590 \T1/zi4/m/sl/10 "Imports", "LinkingTo", "Suggests", "Enhances")[]\T1/ptm/m/n/10 . Char-ac-ter string [2049] [2050] [2051] [2052] [2053] [2054] [2055] [2056] [2057] [2058] [2059] [2060] [2061] [2062] [2063] Underfull \hbox (badness 1424) in paragraph at lines 3516--3518 []\T1/zi4/m/sl/10 NULL []\T1/ptm/m/n/10 or a named (by top-ics) char-ac-ter vec -tor of links, as re-turned by [2064] [2065] [2066] [2067] [2068] [2069] [2070] [2071] [2072] [2073] [2074] Underfull \hbox (badness 10000) in paragraph at lines 4232--4234 []\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run , [2075] [2076] [2077] Underfull \hbox (badness 10000) in paragraph at lines 4388--4391 []\T1/ptm/m/n/10 Where sup-ported ([]\T1/zi4/m/sl/10 texi2dvi []\T1/ptm/m/n/10 5.0 and later; []\T1/zi4/m/sl/10 texify.exe []\T1/ptm/m/n/10 from MiK-TeX), op- tion [2078] [2079] [2080] [2081] [2082] Underfull \hbox (badness 1796) in paragraph at lines 4745--4750 []\T1/ptm/m/n/10 Users should ex-pect sig-nif-i-cantly smaller speedups over [] \T1/zi4/m/sl/10 write_PACKAGES []\T1/ptm/m/n/10 in the []\T1/zi4/m/sl/10 type = = [2083] [2084] Underfull \hbox (badness 1838) in paragraph at lines 4831--4837 []\T1/ptm/m/n/10 The re-main-ing steps are done only if file `\T1/zi4/m/sl/10 p o/\T1/ptm/m/sl/10 pkgname\T1/zi4/m/sl/10 .pot\T1/ptm/m/n/10 ' al-ready ex-ists. The Underfull \hbox (badness 10000) in paragraph at lines 4831--4837 \T1/ptm/m/n/10 `\T1/zi4/m/sl/10 src/*.{c,cc,cpp,m,mm}\T1/ptm/m/n/10 ' files in the pack-age are ex-am-ined to cre-ate a file [2085] [2086] [2087] [2088] Underfull \hbox (badness 2197) in paragraph at lines 5112--5122 []\T1/ptm/m/n/10 The de-fault cor-re-sponds to the fields needed by [][][]\T1/z i4/m/sl/10 available.packages[][][][]\T1/ptm/m/n/10 : [2089] Underfull \hbox (badness 1571) in paragraph at lines 5178--5182 []\T1/ptm/m/n/10 For a re-mote repos-i-tory there is a trade-off be-tween down- load speed and time spent by [2090] [2091] [2092] [2093]) (./utils-pkg.tex [2094] Chapter 14. [2095] Underfull \hbox (badness 2556) in paragraph at lines 47--52 []\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `[] \T1/zi4/m/sl/10 insertions[]\T1/ptm/m/n/10 ', [2096] [2097] [2098] [2099] [2100] [2101] [2102] [2103] [2104] [2105] Underfull \hbox (badness 10000) in paragraph at lines 728--734 []\T1/ptm/m/n/10 Functions []\T1/zi4/m/sl/10 aspell_package_Rd_files[]\T1/ptm/m /n/10 , []\T1/zi4/m/sl/10 aspell_package_vignettes[]\T1/ptm/m/n/10 , Underfull \hbox (badness 3343) in paragraph at lines 728--734 []\T1/zi4/m/sl/10 aspell_package_R_files []\T1/ptm/m/n/10 and []\T1/zi4/m/sl/10 aspell_package_C_files []\T1/ptm/m/n/10 per-form spell check-ing on the [2106] [2107] [2108] Underfull \hbox (badness 3861) in paragraph at lines 934--939 []\T1/ptm/m/n/10 Where pro-vided by the repos-i-tory, fields []\T1/zi4/m/sl/10 "OS_type"[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 "License"[]\T1/ptm/m/n/10 , []\T1 /zi4/m/sl/10 "License_is_FOSS"[]\T1/ptm/m/n/10 , [2109] [2110] [2111] Underfull \hbox (badness 10000) in paragraph at lines 1139--1141 []\T1/ptm/m/n/10 logical in-di-cat-ing if biben-tries should be sorted, us-ing [2112] [2113] [2114] Underfull \vbox (badness 10000) has occurred while \output is active [2115] [2116] [2117] [2118] [2119] Underfull \hbox (badness 1371) in paragraph at lines 1666--1668 []\T1/ptm/m/n/10 additional named ar-gu-ments such as []\T1/zi4/m/sl/10 method []\T1/ptm/m/n/10 and []\T1/zi4/m/sl/10 ccaddress []\T1/ptm/m/n/10 to pass to [2120] [2121] [2122] [2123] [2124] [2125] [2126] [2127] [2128] [2129] [2130] [2131] Underfull \hbox (badness 2057) in paragraph at lines 2386--2388 []\T1/ptm/m/n/10 None for []\T1/zi4/m/sl/10 chooseCRANmirror()[]\T1/ptm/m/n/10 , this func-tion is in-voked for its side ef-fect of up-dat-ing [2132] Underfull \hbox (badness 2150) in paragraph at lines 2461--2468 []\T1/ptm/m/n/10 If the ob-ject re-turned by []\T1/zi4/m/sl/10 citation() []\T1 /ptm/m/n/10 con-tains only one ref-er-ence, the as-so-ci-ated print Underfull \hbox (badness 1400) in paragraph at lines 2461--2468 \T1/ptm/m/n/10 method shows both a text ver-sion and a Bib-TeX en-try for it. I f a pack-age has more [2133] [2134] [2135] Underfull \vbox (badness 3803) has occurred while \output is active [2136] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.clipboard }) has been already used, duplicate ignored \relax l.2738 ... the Clipboard in MS Windows}{clipboard} [2137] [2138] [2139] [2140] [2141] [2142] [2143] [2144] [2145] [2146] [2147] [2148] [2149] [2150] [2151] [2152] [2153] [2154] [2155] [2156] [2157] Underfull \hbox (badness 6842) in paragraph at lines 4048--4053 []\T1/ptm/m/n/10 Support for method []\T1/zi4/m/sl/10 "libcurl" []\T1/ptm/m/n/1 0 was op-tional on Win-dows prior to \T1/phv/m/n/10 R \T1/ptm/m/n/10 4.2.0: use [2158] Underfull \hbox (badness 1430) in paragraph at lines 4111--4115 []\T1/ptm/m/n/10 The level of de-tail pro-vided dur-ing trans-fer can be set by the []\T1/zi4/m/sl/10 quiet []\T1/ptm/m/n/10 ar-gu-ment and the [2159] Underfull \hbox (badness 1184) in paragraph at lines 4182--4198 []\T1/ptm/m/n/10 On Win-dows with []\T1/zi4/m/sl/10 method = "libcurl"[]\T1/ptm /m/n/10 , the CA root cer-tifi-cates are pro-vided by the OS Underfull \hbox (badness 1019) in paragraph at lines 4182--4198 \T1/ptm/m/n/10 con-tain-ing `[]\T1/zi4/m/sl/10 "Schannel"[]\T1/ptm/m/n/10 '. If it does not, for ver-i-fi-ca-tion to be on the en-vi-ron-ment vari- Underfull \hbox (badness 1668) in paragraph at lines 4182--4198 \T1/ptm/m/n/10 able []\T1/zi4/m/sl/10 CURL_CA_BUNDLE []\T1/ptm/m/n/10 must be s et to a path to a cer-tifi-cate bun-dle file, usu-ally named [2160] [2161] Underfull \hbox (badness 10000) in paragraph at lines 4332--4334 []\T1/ptm/m/n/10 additional ar-gu-ments to be passed to [][][]\T1/zi4/m/sl/10 d ownload.file[][][] []\T1/ptm/m/n/10 and [2162] [2163] [2164] [2165] [2166] [2167] [2168] [2169] [2170] [2171] [2172] [2173] [2174] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.format}) has been already used, duplicate ignored \relax l.5111 ...mat Unordered and Ordered Lists}{format} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.format.1} ) has been already used, duplicate ignored \relax l.5111 ...mat Unordered and Ordered Lists}{format} [2175] [2176] [2177] [2178] [2179] [2180] [2181] [2182] Underfull \hbox (badness 1622) in paragraph at lines 5634--5638 []\T1/ptm/m/n/10 This func-tion will search for Win-dows han-dles, for pass-ing to ex-ter-nal GUIs or to the [2183] [2184] [2185] [2186] [2187] [2188] Underfull \hbox (badness 1448) in paragraph at lines 6019--6024 []\T1/ptm/m/n/10 External pointer ob-jects are com-pared as ref-er-ence ob-ject s, cor-re-spond-ing to call-ing [2189] [2190] [2191] [2192] [2193] [2194] [2195] [2196] Underfull \hbox (badness 1371) in paragraph at lines 6567--6569 []\T1/ptm/m/n/10 additional named ar-gu-ments such as []\T1/zi4/m/sl/10 method []\T1/ptm/m/n/10 and []\T1/zi4/m/sl/10 ccaddress []\T1/ptm/m/n/10 to pass to [2197] [2198] Underfull \hbox (badness 1502) in paragraph at lines 6656--6662 []\T1/ptm/m/n/10 a char-ac-ter string to be matched in the help page `key-words '. `Key- Underfull \hbox (badness 2103) in paragraph at lines 6656--6662 \T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are listed in file [2199] [2200] Underfull \hbox (badness 10000) in paragraph at lines 6833--6842 []\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de x, Underfull \hbox (badness 3354) in paragraph at lines 6833--6842 \T1/ptm/m/n/10 `\T1/ptm/m/sl/10 R_DOC_DIR\T1/zi4/m/sl/10 /html/packages.html\T1 /ptm/m/n/10 ', which can be re-made by [][][]\T1/zi4/m/sl/10 make.packages.html [][][]()[]\T1/ptm/m/n/10 . [2201] Underfull \hbox (badness 2150) in paragraph at lines 6895--6898 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion to search. See [2202] [2203] Underfull \hbox (badness 3118) in paragraph at lines 7034--7036 []\T1/ptm/m/n/10 For de-tails of the lock-ing which is done, see the sec-tion ` Lock-ing' in the help for [2204] [2205] [2206] Underfull \hbox (badness 1325) in paragraph at lines 7213--7217 []\T1/ptm/m/n/10 a ma-trix as re-turned by [][][]\T1/zi4/m/sl/10 available.pack ages[][][] []\T1/ptm/m/n/10 list-ing pack-ages avail-able [2207] Underfull \hbox (badness 1424) in paragraph at lines 7306--7309 []\T1/ptm/m/n/10 logical: if true, re-duce the amount of out-put. This is \T1/p tm/m/it/10 not \T1/ptm/m/n/10 passed to [2208] Underfull \hbox (badness 3219) in paragraph at lines 7378--7385 []\T1/ptm/m/n/10 An al-ter-na-tive (and the cur-rent de-fault) is []\T1/zi4/m/s l/10 "both" []\T1/ptm/m/n/10 which means `use bi-nary if avail- Underfull \hbox (badness 5175) in paragraph at lines 7378--7385 \T1/ptm/m/n/10 able and cur-rent, oth-er-wise try source'. The ac-tion if there are source pack-ages Underfull \hbox (badness 1342) in paragraph at lines 7378--7385 \T1/ptm/m/n/10 which are pre-ferred but may con-tain code which needs to be com -piled is con-trolled by Underfull \hbox (badness 1596) in paragraph at lines 7378--7385 [][][]\T1/zi4/m/sl/10 getOption[][][]("install.packages.compile.from.source")[] \T1/ptm/m/n/10 . []\T1/zi4/m/sl/10 type = "both" []\T1/ptm/m/n/10 will be silen tly Underfull \hbox (badness 2932) in paragraph at lines 7386--7389 []\T1/ptm/m/n/10 Using pack-ages with []\T1/zi4/m/sl/10 type = "source" []\T1/p tm/m/n/10 al-ways works pro-vided the pack-age con-tains no [2209] [2210] Underfull \hbox (badness 1024) in paragraph at lines 7515--7518 []\T1/ptm/m/n/10 For other repos-i-to-ries, us-ing []\T1/zi4/m/sl/10 available. packages(filters = "OS_type")[\T1/ptm/m/sl/10 pkgname\T1/zi4/m/sl/10 , ] []\T1/ ptm/m/n/10 will Underfull \hbox (badness 10000) in paragraph at lines 7548--7553 [][][]\T1/zi4/m/sl/10 update.packages[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/s l/10 available.packages[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 download. packages[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 installed.packages[][][] []\T1/ptm/m/n/10 , [2211] Underfull \hbox (badness 5133) in paragraph at lines 7607--7611 []\T1/ptm/m/n/10 a char-ac-ter vec-tor giv-ing the fields to ex-tract from each pack-age's [2212] [2213] [2214] [2215] [2216] [2217] [2218] [2219] [2220] [2221] [2222] Underfull \hbox (badness 10000) in paragraph at lines 8271--8273 []\T1/ptm/m/n/10 typically the re-sult of []\T1/zi4/m/sl/10 methods(..)[]\T1/pt m/m/n/10 , an \T1/phv/m/n/10 R \T1/ptm/m/n/10 ob-ject of S3 class [2223] [2224] [2225] [2226] [2227] [2228] [2229] [2230] [2231] [2232] [2233] [2234] [2235] Underfull \hbox (badness 2310) in paragraph at lines 9058--9063 []\T1/ptm/m/n/10 If a `\T1/zi4/m/sl/10 DESCRIPTION\T1/ptm/m/n/10 ' file for the given pack-age is found and can suc-cess-fully be read, [2236] [2237] [2238] [2239] [2240] [2241] [2242] [2243] [2244] Underfull \hbox (badness 1248) in paragraph at lines 9629--9633 []\T1/zi4/m/sl/10 R CMD build []\T1/ptm/m/n/10 builds \T1/phv/m/n/10 R \T1/ptm/ m/n/10 source tar-balls. The name(s) of the pack-ages are taken from the [2245] Underfull \hbox (badness 1789) in paragraph at lines 9707--9709 []\T1/ptm/m/n/10 See `Writ-ing R Ex-ten-sions' and the `R for Win-dows FAQ' for more dis-cus-sion of the [2246] [2247] [2248] [2249] Underfull \hbox (badness 2600) in paragraph at lines 9931--9934 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the name of the help topic; de-faults to [2250] [2251] [2252] [2253] [2254] [2255] [2256] [2257] [2258] Underfull \hbox (badness 1097) in paragraph at lines 10568--10571 []\T1/ptm/m/n/10 The name []\T1/zi4/m/sl/10 "clipboard" []\T1/ptm/m/n/10 may al so be used on Win-dows, in which case [2259] [2260] Underfull \hbox (badness 3000) in paragraph at lines 10704--10709 [][][]\T1/zi4/m/sl/10 scan[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 type.c onvert[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 read.fwf[][][] []\T1/ptm/m /n/10 for read-ing \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ixed \T1/ptm/m/it/10 w\T1/pt m/m/n/10 idth \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ormatted in-put; [][][]\T1/zi4/m/ sl/10 read.table[][][][]\T1/ptm/m/n/10 ; [2261] [2262] [2263] [2264] [2265] [2266] [2267] [2268] [2269] Underfull \hbox (badness 2134) in paragraph at lines 11299--11304 [][][]\T1/zi4/m/sl/10 scan[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 type.c onvert[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 read.fwf[][][] []\T1/ptm/m /n/10 for read-ing \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ixed \T1/ptm/m/it/10 w\T1/pt m/m/n/10 idth \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ormatted in-put; [][][]\T1/zi4/m/ sl/10 write.table[][][][]\T1/ptm/m/n/10 ; [2270] Underfull \hbox (badness 10000) in paragraph at lines 11355--11360 []\T1/ptm/m/n/10 The `hive' con-tain-ing the key. The ab-bre-vi-a-tions are for Underfull \hbox (badness 10000) in paragraph at lines 11355--11360 []\T1/zi4/m/sl/10 HKEY_LOCAL_MACHINE[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 HKEY_C LASSES_ROOT[]\T1/ptm/m/n/10 . []\T1/zi4/m/sl/10 HKEY_CURRENT_USER[]\T1/ptm/m/n/ 10 , [2271] [2272] [2273] [2274] [2275] [2276] [2277] [2278] Underfull \hbox (badness 1824) in paragraph at lines 11853--11857 \T1/zi4/m/sl/10 / / en . wikipedia . org / w / index . php ? title = Roman _ nu merals & oldid = 1188781837$[][]\T1/ptm/m/n/10 . Ac-cessed [2279] [2280] [2281] [2282] [2283] [2284] [2285] Underfull \hbox (badness 4060) in paragraph at lines 12299--12302 []\T1/ptm/m/n/10 If `[]\T1/zi4/m/sl/10 --default-packages[]\T1/ptm/m/n/10 ' is not used, then []\T1/zi4/m/sl/10 Rscript []\T1/ptm/m/n/10 checks the en-vi-ron- ment vari-able Overfull \hbox (18.77168pt too wide) in paragraph at lines 12322--12322 []\T1/zi4/m/n/9 Rscript --default-packages=methods,datasets,utils,grDevices,gr aphics,stats -e \TS1/zi4/m/n/9 '\T1/zi4/m/n/9 sessionInfo()\TS1/zi4/m/n/9 '[] [2286] [2287] [2288] [2289] Underfull \hbox (badness 2150) in paragraph at lines 12577--12579 [][][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / wiki / Ctags$[][]\T1/ ptm/m/n/10 , [][]$\T1/zi4/m/sl/10 https : / / www . gnu . org / software / emac s / manual / [2290] [2291] [2292] [2293] Underfull \hbox (badness 10000) in paragraph at lines 12797--12801 []\T1/ptm/m/n/10 The de-fault for []\T1/zi4/m/sl/10 stylepath []\T1/ptm/m/n/10 is now taken from the en-vi-ron-ment vari-able Underfull \hbox (badness 10000) in paragraph at lines 12830--12836 []\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y ou can add a [2294] Underfull \hbox (badness 2762) in paragraph at lines 12845--12851 \T1/ptm/m/n/10 UTF-8 lo-cales (note that pdf-TeX as-sumes UTF-8 by de-fault sin ce 2018). Ei-ther set [2295] [2296] Underfull \hbox (badness 1009) in paragraph at lines 13020--13032 []\T1/ptm/m/n/10 Before each code chunk is eval-u-ated, zero or more hook func- tions can be ex-e-cuted. If Underfull \hbox (badness 4779) in paragraph at lines 13060--13062 []\T1/ptm/m/n/10 The file `\T1/zi4/m/sl/10 Rconsole\T1/ptm/m/n/10 ' con-fig-ure s the R GUI ([]\T1/zi4/m/sl/10 Rgui[]\T1/ptm/m/n/10 ) con-sole un-der MS Win-do ws and [2297] Underfull \hbox (badness 1077) in paragraph at lines 13090--13097 \T1/ptm/m/n/10 (strip-ping any trail-ing slash), oth-er-wise to the Win-dows `p er-sonal' di-rec-tory, oth-er-wise to [2298] [2299] [2300] [2301] [2302] [2303] Underfull \hbox (badness 3780) in paragraph at lines 13515--13521 []\T1/ptm/m/n/10 A Bio-con-duc-tor mir-ror can be se-lected by set-ting [][][]\ T1/zi4/m/sl/10 options[][][]("BioC_mirror")[]\T1/ptm/m/n/10 , e.g. via [2304] Underfull \hbox (badness 2635) in paragraph at lines 13533--13536 []\T1/ptm/m/n/10 Repository `[]\T1/zi4/m/sl/10 CRAN[]\T1/ptm/m/n/10 ' is treate d spe-cially: the value is taken from the cur-rent set-ting of [2305] [2306] [2307] Underfull \hbox (badness 2302) in paragraph at lines 13743--13745 []\T1/ptm/m/n/10 Convert file paths to the short form. This is an in-ter-face t o the Win-dows API call [2308] [2309] [2310] [2311] [2312] Underfull \hbox (badness 4441) in paragraph at lines 14042--14047 []\T1/ptm/m/n/10 logical; if []\T1/zi4/m/sl/10 TRUE []\T1/ptm/m/n/10 (de-fault) , [][][]\T1/zi4/m/sl/10 deparse[][][](control = \T1/ptm/m/sl/10 control\T1/zi4/ m/sl/10 ) []\T1/ptm/m/n/10 will not have Underfull \hbox (badness 5970) in paragraph at lines 14051--14054 []\T1/ptm/m/n/10 the page width to be used. The de-fault is the cur-rently ac-t ive [2313] [2314] [2315] [2316] [2317] [2318] [2319] Underfull \hbox (badness 2932) in paragraph at lines 14482--14489 []\T1/ptm/m/n/10 If []\T1/zi4/m/sl/10 syntax = NULL []\T1/ptm/m/n/10 (the de-fa ult) then the avail-able syn-tax ob-jects are con-sulted in turn, Underfull \hbox (badness 1688) in paragraph at lines 14482--14489 \T1/ptm/m/n/10 and se-lected if their []\T1/zi4/m/sl/10 extension []\T1/ptm/m/n /10 com-po-nent matches (as a reg-exp) the file name. Ob- [2320] [2321] [2322] [2323] Underfull \hbox (badness 6510) in paragraph at lines 14794--14798 []\T1/ptm/m/n/10 When ar-gu-ment []\T1/zi4/m/sl/10 tar []\T1/ptm/m/n/10 is set to the com-mand []\T1/zi4/m/sl/10 tar []\T1/ptm/m/n/10 on ma-cOS, en-vi-ron-men t vari-able [2324] Underfull \hbox (badness 10000) in paragraph at lines 14801--14804 [][][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / wiki / Tar _ (file _ format)$[][]\T1/ptm/m/n/10 , [][]$\T1/zi4/m/sl/10 https : / / pubs . opengroup . org / Underfull \hbox (badness 2245) in paragraph at lines 14801--14804 \T1/zi4/m/sl/10 onlinepubs / 9699919799 / utilities / pax . html # tag _ 20 _ 9 2 _ 13 _ 06$[][] \T1/ptm/m/n/10 for the way the POSIX [2325] [2326] [2327] [2328] [2329] [2330] [2331] [2332] [2333] [2334] Underfull \hbox (badness 10000) in paragraph at lines 15474--15479 []\T1/ptm/m/n/10 Arguments such as []\T1/zi4/m/sl/10 destdir []\T1/ptm/m/n/10 a nd []\T1/zi4/m/sl/10 dependencies []\T1/ptm/m/n/10 to be passed to Underfull \hbox (badness 3861) in paragraph at lines 15474--15479 [][][]\T1/zi4/m/sl/10 install.packages[][][] []\T1/ptm/m/n/10 and []\T1/zi4/m/s l/10 ignore_repo_cache[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 max_repo_cache_age [ ]\T1/ptm/m/n/10 and Underfull \hbox (badness 1052) in paragraph at lines 15480--15482 []\T1/ptm/m/n/10 character, in-di-cat-ing the type of pack-age to down-load and in-stall. See Underfull \hbox (badness 10000) in paragraph at lines 15539--15542 [][][]\T1/zi4/m/sl/10 install.packages[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/ sl/10 available.packages[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 download .packages[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 installed.packages[][][ ][]\T1/ptm/m/n/10 , [2335] [2336] [2337] [2338] [2339] [2340] [2341] [2342] [2343] [2344] [2345] [2346] [2347] [2348] [2349] [2350]) [2351] [2352] (./boot-pkg.tex Chapter 15. [2353] [2354] [2355] [2356] [2357] [2358] [2359] [2360] [2361] [2362] [2363] Underfull \hbox (badness 1297) in paragraph at lines 799--809 []\T1/ptm/m/n/10 Where random-number gen-er-a-tion is done in the worker pro-ce sses, the de-fault be-haviour Underfull \hbox (badness 1881) in paragraph at lines 826--828 []\T1/ptm/m/n/10 Davison, A.C., Hink-ley, D.V. and Schecht-man, E. (1986) Ef-fi -cient boot-strap sim-u-la-tion. [2364] [2365] Underfull \vbox (badness 10000) has occurred while \output is active [2366] [2367] [2368] Underfull \hbox (badness 2150) in paragraph at lines 1105--1111 []\T1/ptm/m/n/10 The ob-served value of the statis-tic of in-ter-est. The de-fa ult value is [2369] [2370] [2371] [2372] [2373] Underfull \hbox (badness 1571) in paragraph at lines 1445--1447 []\T1/ptm/m/n/10 Rawlings, J.O. (1988) \T1/ptm/m/it/10 Ap-plied Re-gres-sion An al-y-sis\T1/ptm/m/n/10 . Wadsworth and Brooks/Cole Statis- [2374] [2375] [2376] [2377] [2378] [2379] Underfull \hbox (badness 1005) in paragraph at lines 1800--1807 []\T1/ptm/m/n/10 The sim-u-la-tion type. Pos-si-ble types are []\T1/zi4/m/sl/10 "ordinary" []\T1/ptm/m/n/10 (case re-sam-pling), [2380] [2381] [2382] [2383] Underfull \hbox (badness 7379) in paragraph at lines 2084--2086 []\T1/ptm/m/n/10 The length of time (in months) that the res-i-dent spent at Ch an-ning House. [2384] [2385] [2386] [2387] Underfull \hbox (badness 1565) in paragraph at lines 2338--2343 []\T1/ptm/m/n/10 The ob-served value of the statis-tic of in-ter-est on the ori g-i-nal data set [2388] Underfull \hbox (badness 1881) in paragraph at lines 2432--2434 []\T1/ptm/m/n/10 Davison, A.C., Hink-ley, D.V. and Schecht-man, E. (1986) Ef-fi -cient boot-strap sim-u-la-tion. [2389] Underfull \hbox (badness 2970) in paragraph at lines 2536--2540 []\T1/ptm/m/n/10 The un-bi-ased es-ti-ma-tor uses a mul-ti-plier of []\T1/zi4/m /sl/10 n/((n-1)*(n-2)) []\T1/ptm/m/n/10 where []\T1/zi4/m/sl/10 n []\T1/ptm/m/n /10 is the sam-ple Underfull \hbox (badness 2310) in paragraph at lines 2536--2540 \T1/ptm/m/n/10 size, if []\T1/zi4/m/sl/10 unbiased []\T1/ptm/m/n/10 is []\T1/zi 4/m/sl/10 FALSE []\T1/ptm/m/n/10 then a mul-ti-plier of []\T1/zi4/m/sl/10 1/n [ ]\T1/ptm/m/n/10 is used. This is mul-ti-plied by [2390] [2391] [2392] [2393] [2394] [2395] [2396] [2397] [2398] [2399] [2400] [2401] [2402] [2403] [2404] [2405] [2406] [2407] [2408] [2409] [2410] [2411] [2412] [2413] [2414] [2415] [2416] [2417] [2418] [2419] [2420] [2421] [2422] [2423] [2424] [2425] [2426] [2427] Underfull \hbox (badness 3000) in paragraph at lines 4959--4962 []\T1/ptm/m/n/10 The in-dex of the statis-tic of in-ter-est within the out-put of a call to [2428] [2429] [2430] [2431] Underfull \hbox (badness 2293) in paragraph at lines 5238--5241 []\T1/ptm/m/n/10 An in-te-ger giv-ing the num-ber of classes to be used in the boot-strap Underfull \hbox (badness 1668) in paragraph at lines 5238--5241 \T1/ptm/m/n/10 his-togram. The de-fault is the in-te-ger be-tween 10 and 100 cl os-est to [2432] [2433] [2434] [2435] [2436] [2437] [2438] [2439] [2440] [2441] [2442] [2443] Underfull \hbox (badness 4954) in paragraph at lines 6021--6024 []\T1/ptm/m/n/10 The re-turned value is an ob-ject of class []\T1/zi4/m/sl/10 " saddle.distn"[]\T1/ptm/m/n/10 . See the help file for [2444] [2445] [2446] [2447] [2448] [2449] [2450] [2451] [2452] [2453] [2454] Underfull \hbox (badness 1596) in paragraph at lines 6742--6746 []\T1/ptm/m/n/10 A char-ac-ter string in-di-cat-ing the type of sec-ond ar-gu-m ent ex-pected by [2455] [2456] [2457] [2458] [2459] Underfull \vbox (badness 3803) has occurred while \output is active [2460] [2461] [2462] [2463] [2464]) (./class-pkg.tex Chapter 16. [2465] [2466] [2467] [2468] [2469] [2470] [2471] [2472] [2473] [2474] [2475] [2476] [2477] [2478] [2479] [2480] [2481]) (./cluster-pkg.tex [2482] Chapter 17. [2483] [2484] [2485] [2486] [2487] [2488] [2489] [2490] [2491] [2492] [2493] [2494] Underfull \hbox (badness 1412) in paragraph at lines 782--787 []\T1/ptm/m/n/10 Kaufman and Rousseeuw (see [][][]\T1/zi4/m/sl/10 agnes[][][][] \T1/ptm/m/n/10 ), orig-i-nally. Met-ric []\T1/zi4/m/sl/10 "jaccard"[]\T1/ptm/m/ n/10 : Kamil Ko-zlowski [2495] [2496] Underfull \hbox (badness 10000) in paragraph at lines 882--884 []\T1/ptm/m/n/10 list with sil-hou-ette width in-for-ma-tion for the best sam-p le, see [2497] [2498] Underfull \hbox (badness 10000) in paragraph at lines 992--994 []\T1/ptm/m/n/10 simply cor-re-sponds to the global max-i-mum, i.e., is Underfull \hbox (badness 1342) in paragraph at lines 1006--1010 []\T1/ptm/m/n/10 This, the de-fault, has been pro-posed by Mar-tin Maech-ler in 2012, [2499] [2500] Underfull \vbox (badness 3803) has occurred while \output is active [2501] [2502] [2503] [2504] [2505] Underfull \hbox (badness 10000) in paragraph at lines 1474--1477 [2506] [2507] Underfull \hbox (badness 2503) in paragraph at lines 1583--1586 []\T1/ptm/m/n/10 an ob-ject of class []\T1/zi4/m/sl/10 "hclust" []\T1/ptm/m/n/1 0 or []\T1/zi4/m/sl/10 "twins"[]\T1/ptm/m/n/10 , i.e., typ-i-cally the re-sult of [2508] Underfull \hbox (badness 4954) in paragraph at lines 1680--1682 []\T1/ptm/b/n/10 A\T1/ptm/m/n/10 symmetric bi-nary vari-able, aka []\T1/zi4/m/s l/10 "A" []\T1/ptm/m/n/10 in re-sult []\T1/zi4/m/sl/10 Types[]\T1/ptm/m/n/10 , see [2509] Underfull \hbox (badness 7667) in paragraph at lines 1694--1698 []\T1/ptm/b/n/10 I\T1/ptm/m/n/10 nterval scaled -- the \T1/ptm/b/n/10 de-fault \T1/ptm/m/n/10 for all nu-meric Underfull \hbox (badness 10000) in paragraph at lines 1694--1698 \T1/ptm/m/n/10 (incl []\T1/zi4/m/sl/10 integer[]\T1/ptm/m/n/10 ) columns of []\ T1/zi4/m/sl/10 x[]\T1/ptm/m/n/10 , aka []\T1/zi4/m/sl/10 "I" []\T1/ptm/m/n/10 i n re-sult []\T1/zi4/m/sl/10 Types[]\T1/ptm/m/n/10 , see [2510] [2511] Overfull \hbox (5.24408pt too wide) in paragraph at lines 1866--1866 []\T1/zi4/m/n/9 summary(dA123 <- daisy(flowerN)) # .. all 3 logicals treated * A*symmetric binary (w/ warning)[] Overfull \hbox (11.23795pt too wide) in paragraph at lines 1877--1877 []\T1/zi4/m/n/9 ## Still, using Euclidean/Manhattan distance for {0-1} *is* id entical to treating them as "N" :[] [2512] [2513] [2514] [2515] [2516] Underfull \hbox (badness 10000) in paragraph at lines 2212--2215 [2517] Underfull \hbox (badness 10000) in paragraph at lines 2223--2229 [][][]\T1/zi4/m/sl/10 predict.ellipsoid[][][] []\T1/ptm/m/n/10 which is also th e [][][]\T1/zi4/m/sl/10 predict[][][] []\T1/ptm/m/n/10 method for []\T1/zi4/m/s l/10 ellipsoid []\T1/ptm/m/n/10 ob-jects. [2518] [2519] [2520] Underfull \hbox (badness 6675) in paragraph at lines 2457--2459 []\T1/ptm/m/n/10 list with sil-hou-ette in-for-ma-tion of the near-est crisp cl us-ter-ing, see [2521] [2522] [2523] [2524] [2525] [2526] [2527] [2528] [2529] [2530] Underfull \hbox (badness 2980) in paragraph at lines 3059--3063 [][][]\T1/zi4/m/sl/10 agnes[][][] []\T1/ptm/m/n/10 for back-ground and ref-er-e nces; [][][]\T1/zi4/m/sl/10 pam.object[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/ sl/10 clara[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 daisy[][][][]\T1/ptm/ m/n/10 , [][][]\T1/zi4/m/sl/10 partition.object[][][][]\T1/ptm/m/n/10 , [2531] [2532] [2533] [2534] [2535] [2536] Underfull \hbox (badness 1142) in paragraph at lines 3406--3409 []\T1/ptm/m/n/10 graphical pa-ram-e-ters (see [][][]\T1/zi4/m/sl/10 par[][][][] \T1/ptm/m/n/10 ) may also be sup-plied and are passed to [2537] Underfull \hbox (badness 1142) in paragraph at lines 3525--3528 []\T1/ptm/m/n/10 graphical pa-ram-e-ters (see [][][]\T1/zi4/m/sl/10 par[][][][] \T1/ptm/m/n/10 ) may also be sup-plied and are passed to [2538] [2539] [2540] [2541] Underfull \hbox (badness 2582) in paragraph at lines 3748--3753 [][][]\T1/zi4/m/sl/10 partition.object[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/ sl/10 clusplot.partition[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 clusplot .default[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 pam[][][][]\T1/ptm/m/n/1 0 , [][][]\T1/zi4/m/sl/10 pam.object[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl /10 clara[][][][]\T1/ptm/m/n/10 , [2542] Underfull \hbox (badness 2698) in paragraph at lines 3810--3815 []\T1/ptm/m/n/10 Note that cur-rently the method func-tion sim-ply calls []\T1/ zi4/m/sl/10 plot([][]as.hclust[][][](x), ...)[]\T1/ptm/m/n/10 , which Underfull \hbox (badness 4792) in paragraph at lines 3810--3815 \T1/ptm/m/n/10 dis-patches to [][][]\T1/zi4/m/sl/10 plot.hclust[][][](..)[]\T1/ ptm/m/n/10 . If more flex-i-ble plots are needed, con-sider []\T1/zi4/m/sl/10 x x <- [2543] Underfull \hbox (badness 10000) in paragraph at lines 3883--3885 []\T1/ptm/m/n/10 Available as `\T1/zi4/m/sl/10 pluton.dat\T1/ptm/m/n/10 ' from the archive of the Uni-ver-sity of Antwer-pen, [2544] [2545] [2546] [2547] Underfull \hbox (badness 10000) in paragraph at lines 4097--4099 []\T1/ptm/m/n/10 a []\T1/zi4/m/sl/10 dissimilarity []\T1/ptm/m/n/10 ob-ject or a []\T1/zi4/m/sl/10 summary.dissimilarity []\T1/ptm/m/n/10 one for [2548] [2549] [2550] [2551] Underfull \hbox (badness 2626) in paragraph at lines 4326--4331 []\T1/ptm/m/n/10 arguments passed [][][]\T1/zi4/m/sl/10 barplot[][][]()[]\T1/pt m/m/n/10 ; note that the de-fault used to be []\T1/zi4/m/sl/10 col = [2552] Underfull \hbox (badness 1383) in paragraph at lines 4403--4408 []\T1/ptm/m/n/10 While []\T1/zi4/m/sl/10 silhouette() []\T1/ptm/m/n/10 is \T1/p tm/m/it/10 in-trin-sic \T1/ptm/m/n/10 to the [][][]\T1/zi4/m/sl/10 partition[][ ][] []\T1/ptm/m/n/10 clus-ter-ings, and hence has a (triv-ial) [2553] [2554] [2555] [2556] [2557] [2558] [2559] [2560] Underfull \hbox (badness 10000) in paragraph at lines 4844--4846 []\T1/ptm/m/n/10 Sample data set ac-com-pa-ny-ing the ref-er-ence be-low (file `\T1/zi4/m/sl/10 xclara.dat\T1/ptm/m/n/10 ' in side [2561]) (./codetools-pkg.tex [2562] Chapter 18. [2563] [2564] [2565] [2566] [2567]) (./foreign-pkg.tex [2568] Chapter 19. Underfull \hbox (badness 10000) in paragraph at lines 33--37 []\T1/ptm/m/n/10 SAS Tech-ni-cal Sup-port doc-u-ment TS-140: ``The Record Lay-o ut of Underfull \hbox (badness 10000) in paragraph at lines 33--37 \T1/ptm/m/n/10 a Data Set in SAS Trans-port (XPORT) For-mat'' avail-able as [][ ]$\T1/zi4/m/sl/10 https : Underfull \hbox (badness 10000) in paragraph at lines 33--37 \T1/zi4/m/sl/10 / / support . sas . com / content / dam / SAS / support / en / technical-[]papers / Underfull \hbox (badness 10000) in paragraph at lines 33--37 \T1/zi4/m/sl/10 record-[]layout-[]of-[]a-[]sas-[]version-[]5-[]or-[]6-[]data-[] set-[]in-[]sas-[]transport-[]xport-[]format . [2569] Underfull \hbox (badness 10000) in paragraph at lines 78--80 []\T1/ptm/m/n/10 Attribute-Relation File For-mat [][]$\T1/zi4/m/sl/10 https : / / waikato . github . io / weka-[]wiki / formats _ and _ [2570] [2571] [2572] [2573] [2574] [2575] [2576] [2577] Underfull \hbox (badness 2846) in paragraph at lines 502--511 []\T1/ptm/m/n/10 character: what to do with du-pli-cated value la-bels for dif- fer-ent lev- Underfull \hbox (badness 5417) in paragraph at lines 502--511 \T1/ptm/m/n/10 els. For []\T1/zi4/m/sl/10 "append" []\T1/ptm/m/n/10 (the de-fau lt), the first orig-i-nal value la-bel is Underfull \hbox (badness 6001) in paragraph at lines 502--511 \T1/ptm/m/n/10 kept while fur-ther du-pli-cated la-bels are re-named to []\T1/z i4/m/sl/10 paste0(label, [2578] Overfull \hbox (6.73795pt too wide) in paragraph at lines 620--620 []\T1/zi4/m/n/9 ### Expect lots of warnings as value labels (corresponding to R factor labels) are uncomplete,[] [2579] [2580] [2581] [2582] Underfull \hbox (badness 10000) in paragraph at lines 808--809 [2583] Underfull \hbox (badness 10000) in paragraph at lines 865--869 []\T1/ptm/m/n/10 SAS Tech-ni-cal Sup-port doc-u-ment TS-140: ``The Record Lay-o ut of Underfull \hbox (badness 10000) in paragraph at lines 865--869 \T1/ptm/m/n/10 a Data Set in SAS Trans-port (XPORT) For-mat'' avail-able at [][ ]$\T1/zi4/m/sl/10 https : Underfull \hbox (badness 10000) in paragraph at lines 865--869 \T1/zi4/m/sl/10 / / support . sas . com / content / dam / SAS / support / en / technical-[]papers / Underfull \hbox (badness 10000) in paragraph at lines 865--869 \T1/zi4/m/sl/10 record-[]layout-[]of-[]a-[]sas-[]version-[]5-[]or-[]6-[]data-[] set-[]in-[]sas-[]transport-[]xport-[]format . [2584] [2585] Underfull \hbox (badness 10000) in paragraph at lines 986--988 []\T1/ptm/m/n/10 Attribute-Relation File For-mat [][]$\T1/zi4/m/sl/10 https : / / waikato . github . io / weka-[]wiki / formats _ and _ [2586] [2587] [2588] [2589] Underfull \hbox (badness 10000) in paragraph at lines 1265--1271 []\T1/ptm/m/n/10 The work for this func-tion is done by []\T1/zi4/m/sl/10 forei gn:::writeForeignStata[]\T1/ptm/m/n/10 , [2590] [2591]) (./KernSmooth-pkg.tex [2592] Chapter 20. [2593] [2594] [2595] [2596] [2597] [2598] [2599] [2600] [2601] [2602] [2603]) (./lattice-pkg.tex [2604] Chapter 21. [2605] Underfull \hbox (badness 1484) in paragraph at lines 114--118 []\T1/ptm/m/n/10 Bell Lab's Trel-lis Page con-tains sev-eral doc-u-ments out-li n-ing the use of Trel-lis graph-ics; Underfull \hbox (badness 10000) in paragraph at lines 114--118 \T1/zi4/m/sl/10 20081020164041 / http : / / cm . bell-[]labs . com / cm / ms / departments / sia / project / trellis / [2606] [2607] [2608] Underfull \vbox (badness 10000) has occurred while \output is active [2609] [2610] [2611] [2612] [2613] [2614] [2615] [2616] [2617] [2618] [2619] [2620] [2621] [2622] Underfull \hbox (badness 1062) in paragraph at lines 1395--1399 \T1/ptm/m/n/10 no-ta-tion for the x and y axes re-spec-tively. See doc-u-men-ta -tion for [2623] [2624] Underfull \hbox (badness 1803) in paragraph at lines 1563--1580 [][][]\T1/zi4/m/sl/10 Lattice[][][] []\T1/ptm/m/n/10 for an overview of the pac k-age, as well as [][][]\T1/zi4/m/sl/10 barchart.table[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 print.trellis[][][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1563--1580 [][][]\T1/zi4/m/sl/10 panel.stripplot[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/s l/10 panel.superpose[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 panel.loess[ ][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 panel.average[][][][]\T1/ptm/m/n/ 10 , [][][]\T1/zi4/m/sl/10 strip.default[][][][]\T1/ptm/m/n/10 , [2625] [2626] [2627] Underfull \hbox (badness 3009) in paragraph at lines 1705--1707 []\T1/ptm/m/n/10 additional ar-gu-ments passed to [][][]\T1/zi4/m/sl/10 xyplot[ ][][][]\T1/ptm/m/n/10 , which may pass them on to Underfull \hbox (badness 6808) in paragraph at lines 1735--1739 []\T1/ptm/m/n/10 graphical ar-gu-ments, which are pro-cessed and even-tu-ally p assed to [2628] [2629] [2630] [2631] [2632] [2633] Underfull \hbox (badness 10000) in paragraph at lines 2137--2140 []\T1/ptm/m/n/10 When []\T1/zi4/m/sl/10 breaks []\T1/ptm/m/n/10 is un-spec-i-fi ed, the value of [2634] [2635] [2636] [2637] [2638] [2639] [2640] [2641] [2642] Underfull \vbox (badness 10000) has occurred while \output is active [2643] [2644] Underfull \hbox (badness 2781) in paragraph at lines 2871--2873 []\T1/ptm/m/n/10 A color ramp spec-i-fi-ca-tion, as in the []\T1/zi4/m/sl/10 co l.regions []\T1/ptm/m/n/10 ar-gu-ment in [2645] [2646] Underfull \hbox (badness 2486) in paragraph at lines 3021--3025 []\T1/ptm/m/n/10 Other use-ful ar-gu-ments are men-tioned in the help page for the de-fault panel func-tion [2647] [2648] [2649] [2650] [2651] [2652] [2653] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.parallel} ) has been already used, duplicate ignored \relax l.3506 \aliasA{parallel}{B\_08\_splom}{parallel} [2654] [2655] Underfull \hbox (badness 2368) in paragraph at lines 3644--3644 []\T1/zi4/m/sl/10 auto.key[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 prepanel[]\T1/pt m/m/n/10 , []\T1/zi4/m/sl/10 scales[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 strip[] \T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 groups[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 x lab[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 xlim[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/1 0 ylab[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 ylim[]\T1/ptm/m/n/10 , [2656] [2657] [2658] [2659] [2660] Underfull \hbox (badness 5696) in paragraph at lines 3992--3996 []\T1/ptm/m/n/10 A pos-si-ble use of this ar-gu-ment is to change the de-fault set-tings Underfull \hbox (badness 10000) in paragraph at lines 3992--3996 \T1/ptm/m/n/10 by spec-i-fy-ing []\T1/zi4/m/sl/10 lattice.options(default.theme = "col.whitebg")[]\T1/ptm/m/n/10 . Underfull \hbox (badness 2435) in paragraph at lines 3992--3996 \T1/ptm/m/n/10 For back-compatibility, this is ini-tially (when lat-tice is loa ded) set to [2661] [2662] [2663] Underfull \hbox (badness 1389) in paragraph at lines 4175--4183 \T1/ptm/m/n/10 based on HCL palettes, but cus-tomiza-tion of the palettes is al -lowed. Ear-lier be-haviour [2664] Underfull \hbox (badness 1173) in paragraph at lines 4251--4255 []\T1/ptm/m/n/10 A char-ac-ter string giv-ing the name of a com-po-nent. If un- spec-i-fied in Underfull \hbox (badness 3219) in paragraph at lines 4278--4280 []\T1/ptm/m/n/10 A log-i-cal flag, in-di-cat-ing whether a warn-ing should be i s-sued when [2665] [2666] [2667] Underfull \hbox (badness 3492) in paragraph at lines 4478--4488 []\T1/ptm/m/n/10 A color spec-i-fi-ca-tion. []\T1/zi4/m/sl/10 col []\T1/ptm/m/n /10 is used for com-po-nents []\T1/zi4/m/sl/10 "plot.symbol"[]\T1/ptm/m/n/10 , [2668] Underfull \hbox (badness 10000) in paragraph at lines 4503--4506 []\T1/ptm/m/n/10 fill color, ap-pli-ca-ble for com-po-nents []\T1/zi4/m/sl/10 p lot.symbol[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 plot.polygon[]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4506--4508 []\T1/ptm/m/n/10 border color, ap-pli-ca-ble for com-po-nents []\T1/zi4/m/sl/10 plot.polygon []\T1/ptm/m/n/10 and [2669] [2670] [2671] [2672] [2673] [2674] [2675] [2676] [2677] [2678] Underfull \hbox (badness 6157) in paragraph at lines 5232--5235 []\T1/zi4/m/sl/10 plot.shingle []\T1/ptm/m/n/10 dis-plays the ranges of shin-gl es via rect-an-gles. []\T1/zi4/m/sl/10 print.shingle []\T1/ptm/m/n/10 and [2679] [2680] [2681] [2682] [2683] [2684] [2685] [2686] Underfull \hbox (badness 10000) in paragraph at lines 5684--5687 []\T1/ptm/m/n/10 logical, spec-i-fy-ing whether the la-bels etc should be hor-i -zon-tal. Underfull \hbox (badness 5592) in paragraph at lines 5684--5687 []\T1/zi4/m/sl/10 horizontal=FALSE []\T1/ptm/m/n/10 is use-ful for strips on th e left of pan-els us-ing [2687] [2688] [2689] [2690] [2691] Underfull \hbox (badness 4805) in paragraph at lines 6045--6049 []\T1/ptm/m/n/10 logical, whether the view-port be-ing as-signed fo-cus should be high- Underfull \hbox (badness 10000) in paragraph at lines 6056--6063 []\T1/ptm/m/n/10 For []\T1/zi4/m/sl/10 panel.identify.qqmath[]\T1/ptm/m/n/10 , ex-tra pa-ram-e-ters are passed on to Underfull \hbox (badness 1226) in paragraph at lines 6056--6063 []\T1/zi4/m/sl/10 panel.identify[]\T1/ptm/m/n/10 . For []\T1/zi4/m/sl/10 panel. identify[]\T1/ptm/m/n/10 , ex-tra ar-gu-ments are treated as Underfull \hbox (badness 2418) in paragraph at lines 6056--6063 \T1/ptm/m/n/10 graph-i-cal pa-ram-e-ters and are used for la-belling. For []\T1 /zi4/m/sl/10 trellis.focus Underfull \hbox (badness 10000) in paragraph at lines 6056--6063 []\T1/ptm/m/n/10 and []\T1/zi4/m/sl/10 trellis.switchFocus[]\T1/ptm/m/n/10 , th ese are used (in com-bi-na-tion with Underfull \hbox (badness 1259) in paragraph at lines 6056--6063 [][][]\T1/zi4/m/sl/10 lattice.options[][][][]\T1/ptm/m/n/10 ) for high-light-in g the cho-sen view-port if so re-quested. [2692] [2693] [2694] [2695] Underfull \hbox (badness 4242) in paragraph at lines 6356--6361 []\T1/ptm/m/n/10 Graphical pa-ram-e-ters for the bars. By de-fault, the trel-li s pa-ram-e- Underfull \hbox (badness 2529) in paragraph at lines 6356--6361 \T1/ptm/m/n/10 ter []\T1/zi4/m/sl/10 plot.polygon []\T1/ptm/m/n/10 is used if t here is no group-ing vari-able, oth-er-wise [2696] [2697] Underfull \hbox (badness 2310) in paragraph at lines 6472--6477 []\T1/ptm/m/n/10 Creates Box and Whisker plot of []\T1/zi4/m/sl/10 x []\T1/ptm/ m/n/10 for ev-ery level of []\T1/zi4/m/sl/10 y []\T1/ptm/m/n/10 (or the other w ay round if [2698] [2699] [2700] [2701] [2702] [2703] [2704] [2705] [2706] [2707] [2708] [2709] [2710] Underfull \hbox (badness 3168) in paragraph at lines 7330--7334 []\T1/ptm/m/n/10 to know what ar-gu-ments this func-tion is passed when called. Use [2711] [2712] [2713] [2714] Underfull \hbox (badness 2012) in paragraph at lines 7601--7604 []\T1/ptm/m/n/10 Further ar-gu-ments, of-ten graph-i-cal pa-ram-e-ters, even-tu -ally passed on to [2715] [2716] [2717] [2718] Underfull \hbox (badness 3333) in paragraph at lines 7808--7810 []\T1/ptm/m/n/10 default colours are ob-tained from []\T1/zi4/m/sl/10 plot.symb ol []\T1/ptm/m/n/10 and []\T1/zi4/m/sl/10 plot.line []\T1/ptm/m/n/10 us-ing Underfull \hbox (badness 2318) in paragraph at lines 7836--7844 []\T1/zi4/m/sl/10 "spline" []\T1/ptm/m/n/10 adds a cu-bic smooth-ing spline fit (same as [][][]\T1/zi4/m/sl/10 panel.spline[][][][]\T1/ptm/m/n/10 ). [2719] [2720] [2721] Underfull \vbox (badness 10000) has occurred while \output is active [2722] [2723] [2724] [2725] Underfull \hbox (badness 1436) in paragraph at lines 8309--8315 []\T1/ptm/m/n/10 A log-i-cal flag de-ter-min-ing whether the de-fault graph-i-c al pa-ram-e-ters for [2726] [2727] [2728] [2729] [2730] [2731] [2732] [2733] Underfull \hbox (badness 10000) in paragraph at lines 8878--8881 []\T1/ptm/m/n/10 Extra ar-gu-ments. Passed down to []\T1/zi4/m/sl/10 panel.supe rpose []\T1/ptm/m/n/10 from [2734] Underfull \hbox (badness 1092) in paragraph at lines 8924--8926 []\T1/ptm/m/n/10 Deepayan Sarkar \T1/zi4/m/sl/10 \T1/ptm/m/n/10 ([]\T1/zi4/m/sl/10 panel.superpose.2 []\T1/ptm/m/n/10 orig-i-n ally con- [2735] [2736] [2737] Underfull \hbox (badness 3895) in paragraph at lines 9085--9088 []\T1/ptm/m/n/10 details of his-togram cal-cu-la-tions. []\T1/zi4/m/sl/10 type []\T1/ptm/m/n/10 has a dif-fer-ent mean-ing in Underfull \hbox (badness 6625) in paragraph at lines 9095--9095 []\T1/zi4/m/sl/10 perspective[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 distance[]\T1 /ptm/m/n/10 , []\T1/zi4/m/sl/10 xlim[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 ylim[] \T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 zlim[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 scr een[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 R.mat[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/ 10 aspect[]\T1/ptm/m/n/10 , [2738] Underfull \hbox (badness 1515) in paragraph at lines 9160--9164 []\T1/ptm/m/n/10 numeric vec-tor of length two, rep-re-sent-ing prob-a-bil-i-ti es. If used with [2739] [2740] Underfull \hbox (badness 6316) in paragraph at lines 9266--9271 []\T1/ptm/m/n/10 which packet (counted ac-cord-ing to the packet or-der, de-scr ibed in Underfull \hbox (badness 5908) in paragraph at lines 9283--9286 []\T1/ptm/m/n/10 list, sim-i-lar to those pro-duced by []\T1/zi4/m/sl/10 xscale .components.default []\T1/ptm/m/n/10 and [2741] [2742] Underfull \vbox (badness 10000) has occurred while \output is active [2743] [2744] [2745] Underfull \hbox (badness 2418) in paragraph at lines 9574--9578 []\T1/ptm/m/n/10 returns a list with sev-eral com-po-nents, in-clud-ing []\T1/z i4/m/sl/10 left, right, left.name, right.name, [2746] [2747] [2748] [2749] [2750] [2751] Underfull \hbox (badness 2310) in paragraph at lines 10018--10022 []\T1/ptm/m/n/10 Factor with lev-els []\T1/zi4/m/sl/10 "Svansota"[]\T1/ptm/m/n/ 10 , []\T1/zi4/m/sl/10 "No. 462"[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 "Manchuria "[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 "No. 475"[]\T1/ptm/m/n/10 , []\T1/zi4/m/s l/10 "Velvet"[]\T1/ptm/m/n/10 , Underfull \hbox (badness 3701) in paragraph at lines 10023--10026 []\T1/ptm/m/n/10 Factor with 6 lev-els: []\T1/zi4/m/sl/10 "Grand Rapids"[]\T1/p tm/m/n/10 , []\T1/zi4/m/sl/10 "Duluth"[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 "Uni versity Farm"[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 "Morris"[]\T1/ptm/m/n/10 , [2752] [2753] [2754] [2755] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.melanoma} ) has been already used, duplicate ignored \relax l.10249 \aliasA{melanoma}{H\_melanoma}{melanoma} [2756] [2757] [2758] [2759] Underfull \hbox (badness 4144) in paragraph at lines 10473--10476 []\T1/ptm/m/n/10 Rural Health Re-form Pol-icy Re-search Cen-ter. _Ex-plor-ing R u-ral and Ur-ban Mor-tal- Underfull \hbox (badness 1509) in paragraph at lines 10473--10476 \T1/ptm/m/n/10 ity Dif-fer-ences_, Au-gust 2015 Bethesda, MD. [][]$\T1/zi4/m/sl /10 https : / / ruralhealth . und . edu / projects / [2760]) (./MASS-pkg.tex Chapter 22. [2761] [2762] [2763] [2764] [2765] [2766] [2767] [2768] [2769] [2770] [2771] [2772] [2773] [2774] [2775] [2776] [2777] [2778] [2779] [2780] [2781] [2782] [2783] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.confint.g lm}) has been already used, duplicate ignored \relax l.1477 ...{confint.glm}{confint-MASS}{confint.glm} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.confint.n ls}) has been already used, duplicate ignored \relax l.1478 ...{confint.nls}{confint-MASS}{confint.nls} [2784] [2785] [2786] [2787] [2788] [2789] [2790] [2791] [2792] [2793] [2794] [2795] [2796] [2797] [2798] [2799] [2800] [2801] [2802] Underfull \hbox (badness 10000) in paragraph at lines 2785--2790 []\T1/zi4/m/sl/10 "geometric"[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 "log-normal"[ ]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 "lognormal"[]\T1/ptm/m/n/10 , []\T1/zi4/m/s l/10 "logistic"[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 "negative [2803] [2804] [2805] Underfull \hbox (badness 4686) in paragraph at lines 2957--2959 []\T1/ptm/m/n/10 An early ter-mi-na-tion cri-te-rion. If any par-tial de-nom-i- na-tor ex-ceeds [2806] [2807] [2808] [2809] [2810] [2811] [2812] [2813] [2814] [2815] [2816] [2817] [2818] [2819] [2820] [2821] [2822] [2823] [2824] [2825] [2826] [2827] [2828] [2829] [2830] [2831] [2832] Underfull \hbox (badness 1117) in paragraph at lines 4732--4735 []\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo rm []\T1/zi4/m/sl/10 response ~ [2833] Underfull \hbox (badness 1117) in paragraph at lines 4811--4814 []\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo rm []\T1/zi4/m/sl/10 response ~ [2834] [2835] [2836] [2837] [2838] [2839] [2840] [2841] [2842] [2843] [2844] [2845] [2846] [2847] [2848] [2849] [2850] [2851] [2852] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.npk}) has been already used, duplicate ignored \relax l.6080 ...sical N, P, K Factorial Experiment}{npk} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.npk.1}) h as been already used, duplicate ignored \relax l.6080 ...sical N, P, K Factorial Experiment}{npk} [2853] [2854] [2855] [2856] [2857] [2858] Underfull \vbox (badness 10000) has occurred while \output is active [2859] [2860] [2861] [2862] [2863] [2864] [2865] [2866] Underfull \hbox (badness 1117) in paragraph at lines 6981--6988 []\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo rm []\T1/zi4/m/sl/10 response ~ [2867] Underfull \hbox (badness 3138) in paragraph at lines 7052--7058 []\T1/ptm/m/n/10 The log-log and com-ple-men-tary log-log links are the in-crea s-ing func-tions $\OML/cmm/m/it/10 F[]\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 p\OT1/c mr/m/n/10 ) = [2868] [2869] [2870] Underfull \hbox (badness 1910) in paragraph at lines 7231--7234 []\T1/ptm/m/n/10 the di-men-sion of the space to be used. If this is less than []\T1/zi4/m/sl/10 min(p, [2871] [2872] [2873] [2874] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.profile.g lm}) has been already used, duplicate ignored \relax l.7508 ... for Profiling glm Objects}{profile.glm} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.profile.g lm.1}) has been already used, duplicate ignored \relax l.7508 ... for Profiling glm Objects}{profile.glm} [2875] [2876] [2877] [2878] Underfull \hbox (badness 4686) in paragraph at lines 7803--7805 []\T1/ptm/m/n/10 An early ter-mi-na-tion cri-te-rion. If any par-tial de-nom-i- na-tor ex-ceeds [2879] [2880] [2881] [2882] [2883] [2884] [2885] [2886] [2887] [2888] [2889] [2890] [2891] [2892] [2893] [2894] [2895] [2896] [2897] [2898] [2899] [2900] [2901] [2902] [2903] [2904] [2905] [2906] [2907] [2908] [2909] [2910] [2911] [2912] [2913] [2914] [2915] [2916] [2917] [2918]) (./Matrix-pkg.tex Chapter 23. Underfull \hbox (badness 10000) in paragraph at lines 35--38 []\T1/ptm/m/n/10 Note that the cur-rent im-ple-men-ta-tion de-tails are sub-jec t to change, and if you Underfull \hbox (badness 10000) in paragraph at lines 35--38 \T1/ptm/m/n/10 con-sider work-ing with these classes, please con-tact the pack- age main-tain-ers [2919] Underfull \hbox (badness 1769) in paragraph at lines 89--92 []\T1/ptm/m/n/10 This is cur-rently ex-per-i-men-tal and not yet used for our o wn code. Please con-tact us [2920] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.all.equal }) has been already used, duplicate ignored \relax l.182 ...{all.equal}{all.equal-methods}{all.equal} [2921] Underfull \hbox (badness 3098) in paragraph at lines 264--266 []\T1/ptm/m/n/10 optional ar-gu-ments passed to the de-fault method for generic func-tion [2922] [2923] [2924] [2925] Underfull \hbox (badness 5119) in paragraph at lines 492--496 []\T1/ptm/m/n/10 logical; if true the re-sult will be sym-met-ric (in-her-it-in g from class [2926] Underfull \hbox (badness 2035) in paragraph at lines 590--593 []\T1/ptm/m/n/10 The value of []\T1/zi4/m/sl/10 bdiag() []\T1/ptm/m/n/10 in-her -its from class [][][]\T1/zi4/m/sl/10 CsparseMatrix[][][][]\T1/ptm/m/n/10 , whe reas []\T1/zi4/m/sl/10 .bdiag() []\T1/ptm/m/n/10 re-turns a [2927] [2928] [2929] [2930] Underfull \hbox (badness 5817) in paragraph at lines 913--916 []\T1/ptm/m/n/10 Class [][][]\T1/zi4/m/sl/10 BunchKaufmanFactorization[][][][]\ T1/ptm/m/n/10 , di-rectly. Class [][][]\T1/zi4/m/sl/10 MatrixFactorization[][][ ][]\T1/ptm/m/n/10 , by class Underfull \hbox (badness 6758) in paragraph at lines 919--924 []\T1/ptm/m/n/10 Objects can be gen-er-ated di-rectly by calls of the form []\T 1/zi4/m/sl/10 new("BunchKaufman", ...) Underfull \hbox (badness 2961) in paragraph at lines 919--924 []\T1/ptm/m/n/10 or []\T1/zi4/m/sl/10 new("pBunchKaufman", ...)[]\T1/ptm/m/n/10 , but they are more typ-i-cally ob-tained as the value of [2931] [2932] Underfull \hbox (badness 10000) in paragraph at lines 1081--1086 []\T1/ptm/m/n/10 An ob-ject rep-re-sent-ing the fac-tor-iza-tion, in-her-it-ing from vir-tual class [2933] [2934] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.cbind2.Rd ash.methods}) has been already used, duplicate ignored \relax l.1185 ... on cbind2/rbind2}{cbind2.Rdash.methods} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.cbind2}) has been already used, duplicate ignored \relax l.1186 \aliasA{cbind2}{cbind2-methods}{cbind2} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.rbind2}) has been already used, duplicate ignored \relax l.1195 \aliasA{rbind2}{cbind2-methods}{rbind2} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.rbind2.Rd ash.methods}) has been already used, duplicate ignored \relax l.1204 ...s}{cbind2-methods}{rbind2.Rdash.methods} [2935] Underfull \hbox (badness 10000) in paragraph at lines 1322--1329 []\T1/ptm/m/n/10 The im-ple-men-ta-tion of class []\T1/zi4/m/sl/10 CHMfactor [] \T1/ptm/m/n/10 is based on CHOLMOD's C-level [2936] [2937] [2938] [2939] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.chol}) ha s been already used, duplicate ignored \relax l.1625 \aliasA{chol}{chol-methods}{chol} [2940] Underfull \hbox (badness 6220) in paragraph at lines 1656--1658 []\T1/ptm/m/n/10 Methods for [][][]\T1/zi4/m/sl/10 sparseMatrix[][][] []\T1/ptm /m/n/10 are built on CHOLMOD rou-tines []\T1/zi4/m/sl/10 cholmod_analyze []\T1/ ptm/m/n/10 and [2941] Underfull \hbox (badness 2334) in paragraph at lines 1730--1734 []\T1/ptm/m/n/10 The LA-PACK source code, in-clud-ing doc-u-men-ta-tion; see [] []$\T1/zi4/m/sl/10 https : / / netlib . org / lapack / Underfull \hbox (badness 1616) in paragraph at lines 1730--1734 \T1/zi4/m/sl/10 double / dpstrf . f$[][]\T1/ptm/m/n/10 , [][]$\T1/zi4/m/sl/10 h ttps : / / netlib . org / lapack / double / dpotrf . f$[][]\T1/ptm/m/n/10 , and [][]$\T1/zi4/m/sl/10 https : / / netlib . [2942] Underfull \vbox (badness 10000) has occurred while \output is active [2943] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.chol2inv} ) has been already used, duplicate ignored \relax l.1854 ...sA{chol2inv}{chol2inv-methods}{chol2inv} [2944] [2945] Underfull \hbox (badness 10000) in paragraph at lines 2005--2008 []\T1/ptm/m/n/10 Class [][][]\T1/zi4/m/sl/10 CholeskyFactorization[][][][]\T1/p tm/m/n/10 , di-rectly. Class [][][]\T1/zi4/m/sl/10 MatrixFactorization[][][][]\ T1/ptm/m/n/10 , by class Underfull \hbox (badness 7722) in paragraph at lines 2011--2019 []\T1/ptm/m/n/10 Objects can be gen-er-ated di-rectly by calls of the form []\T 1/zi4/m/sl/10 new("Cholesky", ...) []\T1/ptm/m/n/10 or Underfull \hbox (badness 1990) in paragraph at lines 2051--2060 []\T1/ptm/m/n/10 In \T1/ptm/b/n/10 Ma-trix []\T1/zi4/m/sl/10 < 1.6-0[]\T1/ptm/m /n/10 , class []\T1/zi4/m/sl/10 Cholesky []\T1/ptm/m/n/10 ex-tended [][][]\T1/z i4/m/sl/10 dtrMatrix[][][] []\T1/ptm/m/n/10 and class []\T1/zi4/m/sl/10 pCholes ky []\T1/ptm/m/n/10 ex-tended Underfull \hbox (badness 2334) in paragraph at lines 2066--2070 []\T1/ptm/m/n/10 The LA-PACK source code, in-clud-ing doc-u-men-ta-tion; see [] []$\T1/zi4/m/sl/10 https : / / netlib . org / lapack / Underfull \hbox (badness 1616) in paragraph at lines 2066--2070 \T1/zi4/m/sl/10 double / dpstrf . f$[][]\T1/ptm/m/n/10 , [][]$\T1/zi4/m/sl/10 h ttps : / / netlib . org / lapack / double / dpotrf . f$[][]\T1/ptm/m/n/10 , and [][]$\T1/zi4/m/sl/10 https : / / netlib . [2946] [2947] Underfull \hbox (badness 6220) in paragraph at lines 2185--2187 []\T1/ptm/m/n/10 Methods for [][][]\T1/zi4/m/sl/10 sparseMatrix[][][] []\T1/ptm /m/n/10 are built on CHOLMOD rou-tines []\T1/zi4/m/sl/10 cholmod_analyze []\T1/ ptm/m/n/10 and [2948] [2949] Underfull \hbox (badness 2334) in paragraph at lines 2315--2319 []\T1/ptm/m/n/10 The LA-PACK source code, in-clud-ing doc-u-men-ta-tion; see [] []$\T1/zi4/m/sl/10 https : / / netlib . org / lapack / Underfull \hbox (badness 1616) in paragraph at lines 2315--2319 \T1/zi4/m/sl/10 double / dpstrf . f$[][]\T1/ptm/m/n/10 , [][]$\T1/zi4/m/sl/10 h ttps : / / netlib . org / lapack / double / dpotrf . f$[][]\T1/ptm/m/n/10 , and [][]$\T1/zi4/m/sl/10 https : / / netlib . [2950] Underfull \vbox (badness 10000) has occurred while \output is active [2951] Underfull \vbox (badness 10000) has occurred while \output is active [2952] Underfull \vbox (badness 10000) has occurred while \output is active [2953] [2954] [2955] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.colMeans} ) has been already used, duplicate ignored \relax l.2696 ...asA{colMeans}{colSums-methods}{colMeans} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.colSums}) has been already used, duplicate ignored \relax l.2704 \aliasA{colSums}{colSums-methods}{colSums} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.rowMeans} ) has been already used, duplicate ignored \relax l.2711 ...asA{rowMeans}{colSums-methods}{rowMeans} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.rowSums}) has been already used, duplicate ignored \relax l.2719 \aliasA{rowSums}{colSums-methods}{rowSums} [2956] [2957] Underfull \hbox (badness 3547) in paragraph at lines 2888--2891 []\T1/ptm/m/n/10 a num-ber $\OML/cmm/m/it/10 > \OT1/cmr/m/n/10 0$\T1/ptm/m/n/10 , the es-ti-mated (1-norm) con-di-tion num-ber $[]$; when [2958] [2959] [2960] [2961] [2962] [2963] [2964] Underfull \hbox (badness 1983) in paragraph at lines 3390--3398 []\T1/ptm/m/n/10 and [][][]\T1/zi4/m/sl/10 unpackedMatrix[][][][]\T1/ptm/m/n/10 . Al-ter-na-tively into the (cur-rently) three sub-classes [][][]\T1/zi4/m/sl/ 10 ddenseMatrix[][][][]\T1/ptm/m/n/10 , [2965] [2966] [2967] [2968] Underfull \hbox (badness 2717) in paragraph at lines 3712--3716 []\T1/ptm/m/n/10 However this means that a ma-trix typ-i-cally can be stored in more than one pos-si-ble [2969] [2970] Underfull \hbox (badness 3417) in paragraph at lines 3828--3830 []\T1/zi4/m/sl/10 .sparseDiagonal() []\T1/ptm/m/n/10 ex-ists pri-mar-ily to lev er-age ef-fi-cient C-level meth-ods avail-able for [2971] Underfull \hbox (badness 8019) in paragraph at lines 3933--3935 []\T1/zi4/m/sl/10 signature(x = "nMatrix")[]\T1/ptm/m/n/10 , se-man-ti-cally eq uiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion [][][]\T1/zi4/m/sl/1 0 which[][][](x, Underfull \hbox (badness 10000) in paragraph at lines 3936--3940 []\T1/zi4/m/sl/10 signature(x = "diagonalMatrix")[]\T1/ptm/m/n/10 : all these g roup meth-ods re-turn a [2972] [2973] [2974] [2975] [2976] Underfull \hbox (badness 1902) in paragraph at lines 4263--4265 [][][]\T1/zi4/m/sl/10 drop0[][][](x, tol=1e-10) []\T1/ptm/m/n/10 is some-times prefer-able to (and more ef-fi-cient than) []\T1/zi4/m/sl/10 zapsmall(x, Underfull \hbox (badness 2020) in paragraph at lines 4300--4303 []\T1/ptm/m/n/10 a typ-i-cally sparse ma-trix; in-ter-nally co-erced to ei-ther []\T1/zi4/m/sl/10 "[][]dgCMatrix[][][]" []\T1/ptm/m/n/10 or [2977] [2978] [2979] Underfull \hbox (badness 4378) in paragraph at lines 4503--4512 []\T1/ptm/m/n/10 or [][][]\T1/zi4/m/sl/10 chol[][][]() []\T1/ptm/m/n/10 is typ- i-cally used, e.g., see []\T1/zi4/m/sl/10 selectMethod("coerce", c(from="dsyMat rix", [2980] [2981] [2982] [2983] [2984] Underfull \hbox (badness 10000) in paragraph at lines 4834--4837 []\T1/ptm/m/n/10 Class []\T1/zi4/m/sl/10 "dMatrix"[]\T1/ptm/m/n/10 , by class [ ]\T1/zi4/m/sl/10 "dsparseMatrix"[]\T1/ptm/m/n/10 ; class []\T1/zi4/m/sl/10 "spa rseMatrix"[]\T1/ptm/m/n/10 , by classes [2985] Underfull \hbox (badness 4518) in paragraph at lines 4929--4932 []\T1/zi4/m/sl/10 signature(x = "dspMatrix", type = "character")[]\T1/ptm/m/n/1 0 , or []\T1/zi4/m/sl/10 x = "dsyMatrix" []\T1/ptm/m/n/10 or []\T1/zi4/m/sl/10 type = Underfull \hbox (badness 3690) in paragraph at lines 4932--4935 []\T1/zi4/m/sl/10 signature(x = "dspMatrix", type = "character")[]\T1/ptm/m/n/1 0 , or []\T1/zi4/m/sl/10 x = "dsyMatrix" []\T1/ptm/m/n/10 or []\T1/zi4/m/sl/10 type = [2986] [2987] Underfull \hbox (badness 2318) in paragraph at lines 5035--5039 []\T1/ptm/m/n/10 Class []\T1/zi4/m/sl/10 "dgCMatrix"[]\T1/ptm/m/n/10 , di-rectl y. Class []\T1/zi4/m/sl/10 "triangularMatrix"[]\T1/ptm/m/n/10 , di-rectly. Clas s []\T1/zi4/m/sl/10 "dMatrix"[]\T1/ptm/m/n/10 , [2988] [2989] Underfull \hbox (badness 3240) in paragraph at lines 5151--5155 []\T1/zi4/m/sl/10 signature(x = "dtpMatrix", logarithm = "logical")[]\T1/ptm/m/ n/10 : the [][][]\T1/zi4/m/sl/10 determinant[][][](x) [2990] [2991] [2992] Underfull \hbox (badness 10000) in paragraph at lines 5399--5401 []\T1/ptm/m/n/10 a ma-trix fac-tor-iza-tion, typ-i-cally in-her-it-ing from vir -tual class [2993] [2994] Underfull \hbox (badness 10000) in paragraph at lines 5522--5529 []\T1/zi4/m/sl/10 signature(x = "CHMfactor")[]\T1/ptm/m/n/10 : as []\T1/zi4/m/s l/10 expand2[]\T1/ptm/m/n/10 , but re-turn-ing []\T1/zi4/m/sl/10 list(P, L)[]\T 1/ptm/m/n/10 . Underfull \hbox (badness 1776) in paragraph at lines 5522--5529 []\T1/zi4/m/sl/10 expand(x)[["P"]] []\T1/ptm/m/n/10 and []\T1/zi4/m/sl/10 expan d2(x)[["P1"]] []\T1/ptm/m/n/10 rep-re-sent the same per-mu-ta-tion ma-trix Underfull \hbox (badness 10000) in paragraph at lines 5529--5544 []\T1/zi4/m/sl/10 signature(x = "sparseLU")[]\T1/ptm/m/n/10 : as []\T1/zi4/m/sl /10 expand2[]\T1/ptm/m/n/10 , but re-turn-ing []\T1/zi4/m/sl/10 list(P, L, U, Q )[]\T1/ptm/m/n/10 . Underfull \hbox (badness 10000) in paragraph at lines 5544--5549 []\T1/zi4/m/sl/10 signature(x = "denseLU")[]\T1/ptm/m/n/10 : as []\T1/zi4/m/sl/ 10 expand2[]\T1/ptm/m/n/10 , but re-turn-ing []\T1/zi4/m/sl/10 list(L, U, P)[]\ T1/ptm/m/n/10 . Underfull \hbox (badness 1142) in paragraph at lines 5544--5549 []\T1/zi4/m/sl/10 expand(x)[["P"]] []\T1/ptm/m/n/10 and []\T1/zi4/m/sl/10 expan d2(x)[["P1."]] []\T1/ptm/m/n/10 are iden-ti-cal mod-ulo []\T1/zi4/m/sl/10 Dimna mes[]\T1/ptm/m/n/10 . The [2995] [2996] [2997] [2998] [2999] [3000] [3001] Underfull \hbox (badness 1087) in paragraph at lines 5987--5993 []\T1/ptm/m/n/10 a string whose first three char-ac-ters spec-ify the class of the re-sult. It Underfull \hbox (badness 10000) in paragraph at lines 6000--6002 []\T1/ptm/m/n/10 a string in []\T1/zi4/m/sl/10 c("trace", "sumLog", "prod", "mi n", "max", "range", [3002] [3003] [3004] [3005] Underfull \hbox (badness 1931) in paragraph at lines 6262--6264 []\T1/ptm/m/n/10 a string spec-i-fy-ing how the []\T1/zi4/m/sl/10 zero.print [] \T1/ptm/m/n/10 codes should be aligned, see [3006] [3007] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.image}) h as been already used, duplicate ignored \relax l.6399 \aliasA{image}{image-methods}{image} [3008] Underfull \hbox (badness 1005) in paragraph at lines 6476--6481 []\T1/ptm/m/n/10 color for the bor-der of each rect-an-gle. []\T1/zi4/m/sl/10 N A []\T1/ptm/m/n/10 means no bor-der is drawn. Underfull \hbox (badness 1189) in paragraph at lines 6476--6481 \T1/ptm/m/n/10 When []\T1/zi4/m/sl/10 NULL []\T1/ptm/m/n/10 as by de-fault, []\ T1/zi4/m/sl/10 border.col <- if(lwd < .01) NA else NULL []\T1/ptm/m/n/10 is Underfull \hbox (badness 5862) in paragraph at lines 6495--6498 []\T1/ptm/m/n/10 All meth-ods cur-rently end up call-ing the method for the [][ ][]\T1/zi4/m/sl/10 dgTMatrix[][][] []\T1/ptm/m/n/10 class. Use [3009] Overfull \hbox (42.75635pt too wide) in paragraph at lines 6545--6545 []\T1/zi4/m/n/9 image(USCounties, c(1,100), c(1,100), useAbs=FALSE, lwd=3, bor der.col = adjustcolor("skyblue", 1/2))[] [3010] [3011] [3012] [3013] Underfull \hbox (badness 1509) in paragraph at lines 6810--6812 []\T1/ptm/m/n/10 an in-te-ger off-set, in-di-cat-ing that the re-sult should be a per-mu-ta-tion of [3014] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.anyNA}) h as been already used, duplicate ignored \relax l.6888 \aliasA{anyNA}{is.na-methods}{anyNA} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.is.finite }) has been already used, duplicate ignored \relax l.6895 ...asA{is.finite}{is.na-methods}{is.finite} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.is.infini te}) has been already used, duplicate ignored \relax l.6903 ...is.infinite}{is.na-methods}{is.infinite} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.is.na}) h as been already used, duplicate ignored \relax l.6911 \aliasA{is.na}{is.na-methods}{is.na} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.is.nan}) has been already used, duplicate ignored \relax l.6918 \aliasA{is.nan}{is.na-methods}{is.nan} [3015] [3016] [3017] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.isSymmetr ic}) has been already used, duplicate ignored \relax l.7077 ...etric}{isSymmetric-methods}{isSymmetric} Overfull \hbox (26.39984pt too wide) in paragraph at lines 7124--7124 []\T1/zi4/m/sl/10 isSymmetric(object, checkDN = TRUE, tol = 100 * .Machine$dou ble.eps, tol1 = 8 * tol, ...)[] [3018] [3019] [3020] [3021] [3022] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.kronecker }) has been already used, duplicate ignored \relax l.7453 ...kronecker}{kronecker-methods}{kronecker} [3023] [3024] [3025 pdfTeX warning (ext4): destination with the same identifier (name{Rfn.*,ndiMatr ix,Matrix.Rdash.method}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.7718 \end{Description} ] Underfull \hbox (badness 2478) in paragraph at lines 7736--7741 []\T1/ptm/m/n/10 Class []\T1/zi4/m/sl/10 "ldenseMatrix"[]\T1/ptm/m/n/10 , di-re ctly. Class []\T1/zi4/m/sl/10 "lMatrix"[]\T1/ptm/m/n/10 , by class []\T1/zi4/m/ sl/10 "ldenseMatrix"[]\T1/ptm/m/n/10 . Class Underfull \hbox (badness 10000) in paragraph at lines 7744--7747 []\T1/ptm/m/n/10 Currently, mainly [][][]\T1/zi4/m/sl/10 t[][][]() []\T1/ptm/m/ n/10 and co-er-cion meth-ods (for [][][]\T1/zi4/m/sl/10 as[][][](.)[]\T1/ptm/m/ n/10 ); use, e.g., [3026] [3027] [3028] Underfull \hbox (badness 10000) in paragraph at lines 7968--7971 []\T1/ptm/m/n/10 Currently, mainly [][][]\T1/zi4/m/sl/10 t[][][]() []\T1/ptm/m/ n/10 and co-er-cion meth-ods (for [][][]\T1/zi4/m/sl/10 as[][][](.)[]\T1/ptm/m/ n/10 ; use, e.g., [3029] Underfull \hbox (badness 10000) in paragraph at lines 8029--8032 []\T1/ptm/m/n/10 Currently, mainly [][][]\T1/zi4/m/sl/10 t[][][]() []\T1/ptm/m/ n/10 and co-er-cion meth-ods (for [][][]\T1/zi4/m/sl/10 as[][][](.)[]\T1/ptm/m/ n/10 ; use, e.g., [3030] [3031] [3032] [3033] pdfTeX warning (ext4): destination with the same identifier (name{Rfn..Rpcent.* .Rpcent.}) has been already used, duplicate ignored \relax l.8310 ...*\%}{matmult-methods}{.Rpcent.*.Rpcent.} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.crossprod }) has been already used, duplicate ignored \relax l.8384 ...A{crossprod}{matmult-methods}{crossprod} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.tcrosspro d}) has been already used, duplicate ignored \relax l.8460 ...tcrossprod}{matmult-methods}{tcrossprod} [3034] Underfull \hbox (badness 10000) in paragraph at lines 8618--8623 []\T1/zi4/m/sl/10 signature(x = "dtrMatrix", y = "matrix") []\T1/ptm/m/n/10 and other sig-na-tures (use Underfull \hbox (badness 5359) in paragraph at lines 8618--8623 []\T1/zi4/m/sl/10 showMethods("%*%", class="dtrMatrix")[]\T1/ptm/m/n/10 ): ma-t rix mul-ti-pli-ca-tion. Mul-ti-pli-ca-tion Underfull \hbox (badness 10000) in paragraph at lines 8627--8629 []\T1/zi4/m/sl/10 signature(x = "CsparseMatrix", y = "missing") []\T1/ptm/m/n/1 0 re-turns []\T1/zi4/m/sl/10 t(x) %*% x []\T1/ptm/m/n/10 as an Underfull \hbox (badness 10000) in paragraph at lines 8629--8631 []\T1/zi4/m/sl/10 signature(x = "TsparseMatrix", y = "missing") []\T1/ptm/m/n/1 0 re-turns []\T1/zi4/m/sl/10 t(x) %*% x []\T1/ptm/m/n/10 as an [3035] [3036] [3037] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.det}) has been already used, duplicate ignored \relax l.8856 \aliasA{det}{Matrix-class}{det} [3038] Underfull \hbox (badness 1527) in paragraph at lines 8933--8935 []\T1/zi4/m/sl/10 signature(x = "Matrix")[]\T1/ptm/m/n/10 : sim-ply de-fined as []\T1/zi4/m/sl/10 prod(dim(x)) []\T1/ptm/m/n/10 (and hence of mode Underfull \hbox (badness 4846) in paragraph at lines 8941--8944 []\T1/zi4/m/sl/10 signature(object = "Matrix")[]\T1/ptm/m/n/10 : draws an [][][ ]\T1/zi4/m/sl/10 image[][][] []\T1/ptm/m/n/10 of the ma-trix en-tries, us-ing Underfull \hbox (badness 10000) in paragraph at lines 8946--8949 [3039] [3040] [3041] Underfull \hbox (badness 10000) in paragraph at lines 9148--9150 []\T1/zi4/m/sl/10 signature(x = "MatrixFactorization", logarithm = "missing")[] \T1/ptm/m/n/10 : sets Underfull \hbox (badness 10000) in paragraph at lines 9154--9156 []\T1/zi4/m/sl/10 signature(x = "MatrixFactorization", value = "NULL")[]\T1/ptm /m/n/10 : re-turns []\T1/zi4/m/sl/10 x []\T1/ptm/m/n/10 with Underfull \hbox (badness 10000) in paragraph at lines 9156--9158 []\T1/zi4/m/sl/10 signature(x = "MatrixFactorization", value = "list")[]\T1/ptm /m/n/10 : re-turns []\T1/zi4/m/sl/10 x []\T1/ptm/m/n/10 with [3042] Underfull \hbox (badness 10000) in paragraph at lines 9193--9196 []\T1/ptm/m/n/10 Generic func-tions [][][]\T1/zi4/m/sl/10 expand1[][][] []\T1/p tm/m/n/10 and [][][]\T1/zi4/m/sl/10 expand2[][][] []\T1/ptm/m/n/10 for con-stru ct-ing ma-trix fac-tors from [3043] Underfull \hbox (badness 10000) in paragraph at lines 9311--9313 []\T1/ptm/m/n/10 logical in-di-cat-ing if []\T1/zi4/m/sl/10 X <- (X + t(X))/2 [ ]\T1/ptm/m/n/10 should be done, af-ter []\T1/zi4/m/sl/10 X <- [3044] [3045] [3046] Underfull \hbox (badness 2478) in paragraph at lines 9507--9512 []\T1/ptm/m/n/10 Class []\T1/zi4/m/sl/10 "ndenseMatrix"[]\T1/ptm/m/n/10 , di-re ctly. Class []\T1/zi4/m/sl/10 "lMatrix"[]\T1/ptm/m/n/10 , by class []\T1/zi4/m/ sl/10 "ndenseMatrix"[]\T1/ptm/m/n/10 . Class [3047] Underfull \hbox (badness 10000) in paragraph at lines 9515--9518 []\T1/ptm/m/n/10 Currently, mainly [][][]\T1/zi4/m/sl/10 t[][][]() []\T1/ptm/m/ n/10 and co-er-cion meth-ods (for [][][]\T1/zi4/m/sl/10 as[][][](.)[]\T1/ptm/m/ n/10 ); use, e.g., [3048] [3049] Underfull \hbox (badness 5924) in paragraph at lines 9696--9698 []\T1/ptm/m/n/10 fast sim-ple meth-ods pdfTeX warning (ext4): destination with the same identifier (name{Rfn.norm}) ha s been already used, duplicate ignored \relax l.9738 \aliasA{norm}{norm-methods}{norm} [3050] [3051] [3052] [3053] Underfull \hbox (badness 10000) in paragraph at lines 10031--10034 []\T1/ptm/m/n/10 Currently, mainly [][][]\T1/zi4/m/sl/10 t[][][]() []\T1/ptm/m/ n/10 and co-er-cion meth-ods (for [][][]\T1/zi4/m/sl/10 as[][][](.)[]\T1/ptm/m/ n/10 ; use, e.g., [3054] Underfull \hbox (badness 10000) in paragraph at lines 10095--10098 []\T1/ptm/m/n/10 Currently, mainly [][][]\T1/zi4/m/sl/10 t[][][]() []\T1/ptm/m/ n/10 and co-er-cion meth-ods (for [][][]\T1/zi4/m/sl/10 as[][][](.)[]\T1/ptm/m/ n/10 ; use, e.g., [3055] [3056] [3057] Underfull \hbox (badness 4242) in paragraph at lines 10295--10298 [][][]\T1/zi4/m/sl/10 pack[][][] []\T1/ptm/m/n/10 and [][][]\T1/zi4/m/sl/10 unp ack[][][][]\T1/ptm/m/n/10 ; its vir-tual "com-ple-ment" []\T1/zi4/m/sl/10 "[][] unpackedMatrix[][][]"[]\T1/ptm/m/n/10 ; its proper sub-classes [3058] Underfull \hbox (badness 3547) in paragraph at lines 10383--10386 []\T1/zi4/m/sl/10 signature(x = "pMatrix", y = "Matrix") []\T1/ptm/m/n/10 and o th-ers listed by []\T1/zi4/m/sl/10 showMethods("%*%", [3059] [3060] [3061] [3062] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.qr}) has been already used, duplicate ignored \relax l.10601 \aliasA{qr}{qr-methods}{qr} [3063] [3064] Underfull \vbox (badness 10000) has occurred while \output is active [3065] [3066] Underfull \hbox (badness 7186) in paragraph at lines 10845--10851 []\T1/ptm/m/n/10 for a dense ma-trix, this is the rank of [][][]\T1/zi4/m/sl/10 qr[][][](x, tol, [3067] [3068] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.rcond}) h as been already used, duplicate ignored \relax l.11002 \aliasA{rcond}{rcond-methods}{rcond} [3069] [3070] [3071] [3072] Underfull \hbox (badness 2351) in paragraph at lines 11284--11292 []\T1/ptm/m/n/10 The al-go-rithm first sam-ples ``en-coded'' $\OT1/cmr/m/n/10 ( \OML/cmm/m/it/10 i; j\OT1/cmr/m/n/10 )$\T1/ptm/m/n/10 s with-out re-place-ment, via one di-men-sional Underfull \hbox (badness 1509) in paragraph at lines 11284--11292 \T1/ptm/m/n/10 in-dices, if not []\T1/zi4/m/sl/10 symmetric [][]sample.int[][][ ](nrow*ncol, nnz)[]\T1/ptm/m/n/10 , then---if []\T1/zi4/m/sl/10 rand.x []\T1/pt m/m/n/10 is not []\T1/zi4/m/sl/10 NULL[]\T1/ptm/m/n/10 --- [3073] [3074] Underfull \hbox (badness 10000) in paragraph at lines 11441--11444 []\T1/ptm/m/n/10 Class [][][]\T1/zi4/m/sl/10 SchurFactorization[][][][]\T1/ptm/ m/n/10 , di-rectly. Class [][][]\T1/zi4/m/sl/10 MatrixFactorization[][][][]\T1/ ptm/m/n/10 , by class [3075] [3076] [3077] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.solve}) h as been already used, duplicate ignored \relax l.11630 \aliasA{solve}{solve-methods}{solve} [3078] [3079] Underfull \hbox (badness 5316) in paragraph at lines 11816--11821 []\T1/ptm/m/n/10 Methods for dense []\T1/zi4/m/sl/10 a []\T1/ptm/m/n/10 are bui lt on 14 LA-PACK rou-tines: class []\T1/zi4/m/sl/10 d..Matrix[]\T1/ptm/m/n/10 , where [3080] Underfull \hbox (badness 10000) in paragraph at lines 11916--11919 []\T1/ptm/m/n/10 Construct a sparse model or ``de-sign'' ma-trix, from a for-mu la and data frame [3081] Underfull \hbox (badness 10000) in paragraph at lines 11952--11955 []\T1/ptm/m/n/10 character string or []\T1/zi4/m/sl/10 NULL []\T1/ptm/m/n/10 or (co-er-ca-ble to) Underfull \hbox (badness 10000) in paragraph at lines 11963--11967 []\T1/ptm/m/n/10 should fac-tors have un-used lev-els dropped? The de-fault for [3082] [3083] [3084] [3085] [3086] [3087] [3088] [3089] Underfull \hbox (badness 10000) in paragraph at lines 12500--12508 []\T1/zi4/m/sl/10 (object = "sparseMatrix", uniqT=FALSE)[]\T1/ptm/m/n/10 : Re-t urns an ob-ject of S3 class Underfull \hbox (badness 1796) in paragraph at lines 12500--12508 []\T1/zi4/m/sl/10 "sparseSummary" []\T1/ptm/m/n/10 which is ba-si-cally a [][][ ]\T1/zi4/m/sl/10 data.frame[][][] []\T1/ptm/m/n/10 with columns []\T1/zi4/m/sl/ 10 (i,j,x) []\T1/ptm/m/n/10 (or just Underfull \hbox (badness 10000) in paragraph at lines 12525--12533 []\T1/zi4/m/sl/10 signature(from = "factor", to = "sparseMatrix")[]\T1/ptm/m/n/ 10 : Co-er-cion of a fac-tor to Underfull \hbox (badness 1112) in paragraph at lines 12525--12533 []\T1/zi4/m/sl/10 "sparseMatrix" []\T1/ptm/m/n/10 pro-duces the ma-trix of in-d i-ca-tor \T1/ptm/b/n/10 rows \T1/ptm/m/n/10 stored as an ob-ject of class [3090] [3091] [3092] [3093] [3094] Underfull \hbox (badness 5036) in paragraph at lines 12918--12920 []\T1/ptm/m/n/10 vector of the non zero en-tries; may be miss-ing in which case a [3095] [3096] Underfull \hbox (badness 2828) in paragraph at lines 13084--13087 []\T1/zi4/m/sl/10 signature(x = "sparseVector", mode = "character") []\T1/ptm/m /n/10 co-erces sparse vec-tors to Underfull \hbox (badness 2486) in paragraph at lines 13106--13109 []\T1/zi4/m/sl/10 signature(x = "sparseVector") []\T1/ptm/m/n/10 re-peat []\T1/ zi4/m/sl/10 x[]\T1/ptm/m/n/10 , with the same ar-gu-ment list []\T1/zi4/m/sl/10 (x, times, [3097] [3098] [3099] [3100] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.[<.Rdash. }) has been already used, duplicate ignored \relax l.13311 ...\Rdash{}}{subassign-methods}{[<.Rdash.} Underfull \hbox (badness 6910) in paragraph at lines 13398--13400 []\T1/ptm/m/n/10 is cur-rently a sim-ple fall-back [3101] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.[}) has b een already used, duplicate ignored \relax l.13445 \aliasA{[}{subscript-methods}{[} [3102] [3103] Underfull \hbox (badness 2057) in paragraph at lines 13656--13658 []\T1/ptm/m/n/10 These are generic func-tions with sev-eral meth-ods for dif-fe r-ent ma-trix classes, use e.g., Underfull \hbox (badness 10000) in paragraph at lines 13670--13675 []\T1/zi4/m/sl/10 skewpart(x) []\T1/ptm/m/n/10 re-turns a skew-symmetric ma-tri x, in-her-it-ing from [][][]\T1/zi4/m/sl/10 generalMatrix[][][][]\T1/ptm/m/n/10 , [3104] [3105] [3106] Underfull \hbox (badness 10000) in paragraph at lines 13826--13831 []\T1/ptm/m/n/10 Note that all []\T1/zi4/m/sl/10 new(.)[]\T1/ptm/m/n/10 , [][][ ]\T1/zi4/m/sl/10 spMatrix[][][] []\T1/ptm/m/n/10 and [][][]\T1/zi4/m/sl/10 spar seMatrix[][][](*, repr="T") []\T1/ptm/m/n/10 con-struc-tors for Underfull \hbox (badness 1831) in paragraph at lines 13832--13838 []\T1/ptm/m/n/10 For con-ve-nience, meth-ods for some op-er-a-tions such as []\ T1/zi4/m/sl/10 %*% []\T1/ptm/m/n/10 and []\T1/zi4/m/sl/10 crossprod []\T1/ptm/m /n/10 are de-fined [3107] [3108] [3109] Overfull \hbox (21.75807pt too wide) in paragraph at lines 14021--14027 []\T1/ptm/m/n/10 GAL lat-tice file `\T1/zi4/m/sl/10 usc_q.GAL\T1/ptm/m/n/10 ' ( re-trieved in 2008 from `\T1/zi4/m/sl/10 http://sal.uiuc.edu/weights/zips/usc.z ip\T1/ptm/m/n/10 ' [3110] [3111] [3112]) (./mgcv-pkg.tex Chapter 24. [3113] [3114] [3115] Underfull \hbox (badness 1142) in paragraph at lines 185--189 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from Underfull \hbox (badness 1043) in paragraph at lines 210--215 \T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known scale. [3116] [3117] [3118] [3119] [3120] Underfull \hbox (badness 10000) in paragraph at lines 379--386 [][][]\T1/zi4/m/sl/10 mgcv.parallel[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/ 10 mgcv-package[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 gamObject[][][][] \T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 gam.models[][][][]\T1/ptm/m/n/10 , [][][ ]\T1/zi4/m/sl/10 smooth.terms[][][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 7168) in paragraph at lines 379--386 [][][]\T1/zi4/m/sl/10 linear.functional.terms[][][][]\T1/ptm/m/n/10 , [][][]\T1 /zi4/m/sl/10 s[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 te[][][] [][]predi ct.gam[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 plot.gam[][][][]\T1/ptm/m/ n/10 , [][][]\T1/zi4/m/sl/10 summary.gam[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/ m/sl/10 gam.side[][][][]\T1/ptm/m/n/10 , [3121] [3122] [3123] [3124] [3125] [3126] Underfull \hbox (badness 1406) in paragraph at lines 704--705 []\T1/ptm/m/n/10 The MKL BLAS is mut-lithreaded by de-fault. Un-der linux set-t ing en-vi-ron-ment vari-able [3127] [3128] Underfull \hbox (badness 1158) in paragraph at lines 814--816 []\T1/ptm/m/n/10 Choosing the ba-sis di-men-sion, and check-ing the choice, whe n us-ing pe-nal-ized re-gres-sion [3129] Underfull \hbox (badness 1259) in paragraph at lines 877--878 []\T1/ptm/m/n/10 Wood, S.N. (2017) Gen-er-al-ized Ad-di-tive Mod-els: An In-tro -duc-tion with R (2nd edi-tion). [3130] Underfull \vbox (badness 10000) has occurred while \output is active [3131] [3132] [3133] [3134] [3135] [3136] [3137] Underfull \hbox (badness 1281) in paragraph at lines 1272--1273 []\T1/zi4/m/sl/10 deviance[]\T1/ptm/m/n/10 ,[]\T1/zi4/m/sl/10 martingale[]\T1/p tm/m/n/10 ,[]\T1/zi4/m/sl/10 score[]\T1/ptm/m/n/10 , or []\T1/zi4/m/sl/10 schoe nfeld []\T1/ptm/m/n/10 resid-u-als can be ex-tracted. See Klein amd [3138] [3139] Underfull \vbox (badness 10000) has occurred while \output is active [3140] [3141] [3142] Underfull \vbox (badness 10000) has occurred while \output is active [3143] [3144] [3145] [3146] [3147] [3148] [3149] [3150] [3151] [3152] [3153] [3154] [3155] [3156] [3157] Underfull \vbox (badness 2302) has occurred while \output is active [3158] [3159] [3160] [3161] [3162] Underfull \hbox (badness 1142) in paragraph at lines 2604--2608 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from Underfull \hbox (badness 1043) in paragraph at lines 2630--2636 \T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known scale. [3163] [3164] [3165] [3166] [3167] [3168] [3169] Underfull \vbox (badness 10000) has occurred while \output is active [3170] Underfull \vbox (badness 10000) has occurred while \output is active [3171] [3172] [3173] [3174] [3175] [3176] [3177] [3178] [3179] [3180] [3181] [3182] [3183] [3184] [3185] [3186] [3187] [3188] Underfull \hbox (badness 10000) in paragraph at lines 4071--4075 []\T1/ptm/m/n/10 Random ef-fects can be added to []\T1/zi4/m/sl/10 gam []\T1/pt m/m/n/10 mod-els us-ing []\T1/zi4/m/sl/10 s(...,bs="re") []\T1/ptm/m/n/10 terms (see [3189] [3190] Underfull \vbox (badness 10000) has occurred while \output is active [3191] Underfull \vbox (badness 10000) has occurred while \output is active [3192] [3193] Underfull \hbox (badness 1184) in paragraph at lines 4358--4362 []\T1/ptm/m/n/10 list of the square root penal-ties: last en-try is root of fix ed penalty, if [3194] [3195] [3196] [3197] [3198] [3199] [3200] [3201] [3202] [3203] [3204] [3205] [3206] Underfull \hbox (badness 1142) in paragraph at lines 5081--5085 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from [3207] [3208] Underfull \hbox (badness 1231) in paragraph at lines 5185--5187 []\T1/zi4/m/sl/10 gamm []\T1/ptm/m/n/10 per-forms poorly with bi-nary data, sin ce it uses PQL. It is bet-ter to use []\T1/zi4/m/sl/10 gam []\T1/ptm/m/n/10 wit h [3209] [3210] Underfull \vbox (badness 10000) has occurred while \output is active [3211] Underfull \vbox (badness 10000) has occurred while \output is active [3212] [3213] [3214] [3215] Underfull \hbox (badness 2181) in paragraph at lines 5626--5627 []\T1/ptm/m/n/10 one sided for-mula con-tain-ing vari-ables needed for pre-dic- tion, used by [3216] [3217] [3218] [3219] [3220] [3221] [3222] [3223] [3224] Underfull \vbox (badness 3803) has occurred while \output is active [3225] Underfull \hbox (badness 10000) in paragraph at lines 6130--6131 []\T1/ptm/m/n/10 A pre-fit gam ob-ject, as pro-duced by []\T1/zi4/m/sl/10 gam(. ..,fit=FALSE) []\T1/ptm/m/n/10 or [3226] [3227] [3228] [3229] [3230] [3231] [3232] [3233] [3234] [3235] [3236] Underfull \hbox (badness 1142) in paragraph at lines 6715--6719 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from [3237] [3238] [3239] [3240] Underfull \vbox (badness 3803) has occurred while \output is active [3241] [3242] [3243] [3244] Underfull \hbox (badness 1087) in paragraph at lines 7087--7088 []\T1/ptm/m/n/10 If []\T1/zi4/m/sl/10 rho []\T1/ptm/m/n/10 and []\T1/zi4/m/sl/1 0 theta []\T1/ptm/m/n/10 were sup-plied then deriva-tives are w.r.t. these. In this case, and if [3245] [3246] [3247] Underfull \vbox (badness 10000) has occurred while \output is active [3248] Underfull \vbox (badness 10000) has occurred while \output is active [3249] [3250] [3251] [3252] [3253] [3254] [3255] [3256] [3257] [3258] [3259] Underfull \vbox (badness 4805) has occurred while \output is active [3260] [3261] [3262] Underfull \hbox (badness 1242) in paragraph at lines 8046--8047 []\T1/ptm/m/n/10 Development of mgcv ver-sion 1.8 was part funded by EP-SRC gra nts EP/K005251/1 and Underfull \hbox (badness 1122) in paragraph at lines 8072--8073 []\T1/ptm/m/n/10 When us-ing [][][]\T1/zi4/m/sl/10 NCV[][][] []\T1/ptm/m/n/10 w ith [][][]\T1/zi4/m/sl/10 gam[][][] []\T1/ptm/m/n/10 worth-while per-for-mance im-prove-ments are avail-able by set-ting [3263] [3264] [3265] [3266] [3267] [3268] [3269] [3270] [3271] [3272] [3273] [3274] [3275] [3276] [3277] Underfull \hbox (badness 6001) in paragraph at lines 8785--8787 []\T1/ptm/m/n/10 Simon N. Wood \T1/zi4/m/sl/10 \T1/p tm/m/n/10 mod-i-fied from Ven-ables and Rip-ley's [3278] [3279] [3280] [3281] [3282] [3283] [3284] [3285] [3286] [3287] [3288] Underfull \vbox (badness 10000) has occurred while \output is active [3289] [3290] Underfull \hbox (badness 1038) in paragraph at lines 9533--9536 []\T1/ptm/m/n/10 The fol-low-ing func-tions are pro-vided: []\T1/zi4/m/sl/10 Di m.pdIndot[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 coef.pdIdnot[]\T1/ptm/m/n/10 , [] \T1/zi4/m/sl/10 corMatrix.pdIdnot[]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 9533--9536 []\T1/zi4/m/sl/10 logDet.pdIdnot[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 pdConstruc t.pdIdnot[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 pdFactor.pdIdnot[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 pdMatrix.pdIdnot[]\T1/ptm/m/n/10 , [3291] Underfull \hbox (badness 10000) in paragraph at lines 9589--9592 []\T1/ptm/m/n/10 These func-tions ([]\T1/zi4/m/sl/10 pdTens[]\T1/ptm/m/n/10 , [ ]\T1/zi4/m/sl/10 pdConstruct.pdTens[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 pdFacto r.pdTens[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 pdMatrix.pdTens[]\T1/ptm/m/n/10 , [3292] [3293] [3294] [3295] [3296] [3297] [3298] [3299] [3300] [3301] [3302] [3303] Underfull \hbox (badness 1852) in paragraph at lines 10261--10264 []\T1/ptm/m/n/10 To fa-cil-i-tate plot-ting with [][][]\T1/zi4/m/sl/10 termplot [][][][]\T1/ptm/m/n/10 , if []\T1/zi4/m/sl/10 object []\T1/ptm/m/n/10 pos-sesse s an at-tribute []\T1/zi4/m/sl/10 "para.only" []\T1/ptm/m/n/10 and [3304] [3305] [3306] Underfull \hbox (badness 1852) in paragraph at lines 10430--10433 []\T1/ptm/m/n/10 To fa-cil-i-tate plot-ting with [][][]\T1/zi4/m/sl/10 termplot [][][][]\T1/ptm/m/n/10 , if []\T1/zi4/m/sl/10 object []\T1/ptm/m/n/10 pos-sesse s an at-tribute []\T1/zi4/m/sl/10 "para.only" []\T1/ptm/m/n/10 and [3307] [3308] Underfull \vbox (badness 10000) has occurred while \output is active [3309] Underfull \vbox (badness 10000) has occurred while \output is active [3310] Underfull \hbox (badness 1205) in paragraph at lines 10670--10671 []\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a tes at which Underfull \hbox (badness 2689) in paragraph at lines 10670--10671 \T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are as for Underfull \hbox (badness 1975) in paragraph at lines 10676--10681 []\T1/ptm/m/n/10 Smooth terms in a GAM for-mula are turned into smooth spec-i-f i-ca-tion ob-jects of class [3311] [3312] Underfull \hbox (badness 1205) in paragraph at lines 10760--10761 []\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a tes at which Underfull \hbox (badness 2689) in paragraph at lines 10760--10761 \T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are as for [3313] [3314] Underfull \vbox (badness 3803) has occurred while \output is active [3315] Underfull \hbox (badness 1253) in paragraph at lines 10959--10961 []\T1/ptm/m/n/10 Note that the op-ti-mized smooth-ing pa-ram-e-ter se-lec-tion cri-te-rion re-ported is one of GCV, [3316] [3317] [3318] [3319] [3320] [3321] Underfull \hbox (badness 4792) in paragraph at lines 11220--11223 []\T1/ptm/m/n/10 Alternatively, but less straight-for-wardly, the []\T1/zi4/m/s l/10 paraPen []\T1/ptm/m/n/10 ar-gu-ment to [][][]\T1/zi4/m/sl/10 gam[][][] []\ T1/ptm/m/n/10 can be used: Underfull \hbox (badness 10000) in paragraph at lines 11220--11223 \T1/ptm/m/n/10 see [][][]\T1/zi4/m/sl/10 gam.models[][][][]\T1/ptm/m/n/10 . If smooth-ing pa-ram-e-ter es-ti-ma-tion is by ML or REML (e.g. [3322] [3323] Underfull \hbox (badness 10000) in paragraph at lines 11327--11330 []\T1/ptm/m/n/10 the type of resid-u-als wanted. Usu-ally one of []\T1/zi4/m/sl /10 "deviance"[]\T1/ptm/m/n/10 , [3324] [3325] [3326] [3327] [3328] [3329] [3330] [3331] [3332] [3333] [3334] [3335] Underfull \vbox (badness 10000) has occurred while \output is active [3336] [3337] Underfull \hbox (badness 3861) in paragraph at lines 12118--12121 []\T1/ptm/m/n/10 INTERNAL rou-tine to ap-ply ini-tial Sl re-parameterization to model ma-trix X, or, if [3338] [3339] [3340] Underfull \hbox (badness 1320) in paragraph at lines 12233--12238 \T1/ptm/m/n/10 and []\T1/zi4/m/sl/10 b.orig = D*b.repara []\T1/ptm/m/n/10 (wher e []\T1/zi4/m/sl/10 b.orig []\T1/ptm/m/n/10 is the orig-i-nal pa-ram-e-ter vec- tor). If ma- [3341] [3342] Underfull \hbox (badness 1975) in paragraph at lines 12339--12344 []\T1/ptm/m/n/10 Smooth terms in a GAM for-mula are turned into smooth spec-i-f i-ca-tion ob-jects of class [3343] Underfull \hbox (badness 1762) in paragraph at lines 12428--12440 \T1/ptm/m/n/10 plate re-gres-sion splines: see [][][]\T1/zi4/m/sl/10 tprs[][][] []\T1/ptm/m/n/10 ); []\T1/zi4/m/sl/10 ts.smooth.spec []\T1/ptm/m/n/10 (thin pla te re-gres-sion splines with [3344] [3345] [3346] Underfull \vbox (badness 3803) has occurred while \output is active [3347] Underfull \hbox (badness 7667) in paragraph at lines 12640--12646 [][][]\T1/zi4/m/sl/10 gam[][][] []\T1/ptm/m/n/10 can use adap-tive smooths of o ne or two vari-ables, spec-i-fied via terms like [3348] Underfull \hbox (badness 10000) in paragraph at lines 12681--12682 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3349] [3350] [3351] [3352] Underfull \vbox (badness 3803) has occurred while \output is active [3353] Underfull \hbox (badness 10000) in paragraph at lines 12958--12960 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3354] [3355] [3356] Underfull \hbox (badness 10000) in paragraph at lines 13088--13089 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3357] [3358] Underfull \hbox (badness 1436) in paragraph at lines 13224--13231 \T1/ptm/m/n/10 nest-ing of the smooth within the fac-tor. Note how-ever that: i ) []\T1/zi4/m/sl/10 gamm []\T1/ptm/m/n/10 only al-lows one [3359] [3360] Underfull \hbox (badness 10000) in paragraph at lines 13323--13324 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3361] [3362] [3363] [3364] [3365] [3366] [3367] [3368] Underfull \vbox (badness 10000) has occurred while \output is active [3369] [3370] [3371] [3372] Underfull \hbox (badness 10000) in paragraph at lines 13924--13930 []\T1/ptm/m/n/10 A smooth spec-i-fi-ca-tion ob-ject as pro-duced by a Underfull \hbox (badness 1292) in paragraph at lines 13924--13930 []\T1/zi4/m/sl/10 s(...,bs="so",xt=list(bnd=bnd,...)) []\T1/ptm/m/n/10 term in a []\T1/zi4/m/sl/10 gam []\T1/ptm/m/n/10 for-mula. Note [3373] [3374] [3375] Underfull \vbox (badness 10000) has occurred while \output is active [3376] Underfull \vbox (badness 10000) has occurred while \output is active [3377] [3378] Underfull \hbox (badness 10000) in paragraph at lines 14268--14269 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3379] [3380] [3381] [3382] Overfull \hbox (35.26862pt too wide) in paragraph at lines 14480--14480 []\T1/zi4/m/n/9 b <- gam(y ~ s(x)+s(f1,x,bs="sz")+s(f2,x,bs="sz")+s(f1,f2,x,bs ="sz",id=1),data=dat,method="REML")[] [3383] [3384] Underfull \hbox (badness 3895) in paragraph at lines 14626--14629 [][][]\T1/zi4/m/sl/10 gam[][][] []\T1/ptm/m/n/10 can use isotropic smooths of a ny num-ber of vari-ables, spec-i-fied via terms like [3385] Underfull \hbox (badness 10000) in paragraph at lines 14671--14673 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3386] [3387] [3388] [3389] [3390] [3391] Underfull \hbox (badness 1371) in paragraph at lines 14951--14957 []\T1/zi4/m/sl/10 bs="ad" []\T1/ptm/m/n/10 Uni-vari-ate and bi-vari-ate adap-ti ve smooths are avail-able (see Underfull \hbox (badness 10000) in paragraph at lines 14962--14964 []\T1/zi4/m/sl/10 bs="fs" []\T1/ptm/m/n/10 A spe-cial smoother class (see Underfull \hbox (badness 1132) in paragraph at lines 14962--14964 [][][]\T1/zi4/m/sl/10 smooth.construct.fs.smooth.spec[][][][]\T1/ptm/m/n/10 ) i s avail-able for the case in which a smooth is [3392] Underfull \hbox (badness 6461) in paragraph at lines 14996--15000 [][][]\T1/zi4/m/sl/10 s[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 te[][][][ ]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 t2[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi 4/m/sl/10 tprs[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 Duchon.spline[][][ ][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 cubic.regression.spline[][][][]\T1/pt m/m/n/10 , [][][]\T1/zi4/m/sl/10 p.spline[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4 /m/sl/10 d.spline[][][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 14996--15000 [][][]\T1/zi4/m/sl/10 mrf[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 soap[][ ][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 Spherical.Spline[][][][]\T1/ptm/m/n /10 , [][][]\T1/zi4/m/sl/10 adaptive.smooth[][][][]\T1/ptm/m/n/10 , [][][]\T1/z i4/m/sl/10 user.defined.smooth[][][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 14996--15000 [][][]\T1/zi4/m/sl/10 smooth.construct.re.smooth.spec[][][][]\T1/ptm/m/n/10 , [ ][][]\T1/zi4/m/sl/10 smooth.construct.gp.smooth.spec[][][][]\T1/ptm/m/n/10 , [3393] [3394] [3395] [3396] Underfull \hbox (badness 2326) in paragraph at lines 15200--15207 []\T1/ptm/m/n/10 These wrap-per func-tions ex-ist to al-low smooths spec-i-fied us-ing [][][]\T1/zi4/m/sl/10 smooth.construct[][][] []\T1/ptm/m/n/10 and [3397] Underfull \hbox (badness 2158) in paragraph at lines 15285--15285 []\T1/ptm/m/it/10 Extract smooth-ing pa-ram-e-ter es-ti-ma-tor co-vari-ance ma- trix from [3398] [3399] [3400] [3401] [3402] [3403] [3404] [3405] [3406] [3407] [3408] [3409] [3410] [3411] [3412] [3413] [3414] [3415] [3416] [3417] [3418] [3419] [3420] [3421] [3422] [3423] [3424] Overfull \hbox (21.42029pt too wide) in paragraph at lines 16847--16847 []\T1/zi4/m/sl/10 vcov(object, sandwich=FALSE, freq = FALSE, dispersion = NULL ,unconditional=FALSE, ...)[] [3425] [3426] [3427] Underfull \hbox (badness 1796) in paragraph at lines 16960--16963 []\T1/ptm/m/n/10 other op-tions to pass on to [][][]\T1/zi4/m/sl/10 persp[][][] []\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 image[][][] []\T1/ptm/m/n/10 or [][][] \T1/zi4/m/sl/10 contour[][][][]\T1/ptm/m/n/10 . In par-tic-u-lar [3428] [3429] [3430] [3431] [3432] [3433] Underfull \vbox (badness 3803) has occurred while \output is active [3434] [3435] [3436]) (./nlme-pkg.tex Chapter 25. [3437] [3438] [3439] [3440] [3441] [3442] [3443] [3444] [3445] [3446] [3447] [3448] [3449] [3450] [3451] [3452] [3453] [3454] [3455] [3456] [3457] [3458] [3459] [3460] [3461] [3462] [3463] [3464] [3465] [3466] [3467] [3468] [3469] [3470] [3471] [3472] [3473] Underfull \hbox (badness 10000) in paragraph at lines 2238--2244 [][][]\T1/zi4/m/sl/10 ACF.lme[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 cor ARMA[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 corClasses[][][][]\T1/ptm/m/ n/10 , [][][]\T1/zi4/m/sl/10 Dim.corSpatial[][][][]\T1/ptm/m/n/10 , [][][]\T1/z i4/m/sl/10 Initialize.corStruct[][][][]\T1/ptm/m/n/10 , [3474] [3475] [3476] [3477] [3478] [3479] [3480] [3481] [3482] [3483] [3484] [3485] [3486] [3487] [3488] [3489] [3490] [3491] [3492] [3493] [3494] [3495] [3496] [3497] [3498] [3499] [3500] [3501] [3502] [3503] [3504] [3505] [3506] [3507] [3508] [3509] Underfull \hbox (badness 1067) in paragraph at lines 4372--4377 \T1/ptm/m/n/10 ma-trix), []\T1/zi4/m/sl/10 fitted []\T1/ptm/m/n/10 (fit-ted val -ues), and []\T1/zi4/m/sl/10 residuals []\T1/ptm/m/n/10 (resid-u-als). De-fault s to [3510] [3511] [3512] [3513] [3514] [3515] [3516] [3517] [3518] [3519] [3520] [3521] [3522] Underfull \hbox (badness 10000) in paragraph at lines 5116--5120 [][][]\T1/zi4/m/sl/10 getCovariate.corStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/ zi4/m/sl/10 getCovariate.data.frame[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/ 10 getCovariate.varFunc[][][][]\T1/ptm/m/n/10 , [3523] [3524] [3525] [3526] [3527] [3528] [3529] [3530] Underfull \hbox (badness 10000) in paragraph at lines 5540--5543 [][][]\T1/zi4/m/sl/10 getGroups.corStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4 /m/sl/10 getGroups.data.frame[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 get Groups.gls[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 getGroups.lmList[][][] []\T1/ptm/m/n/10 , [3531] [3532] [3533] [3534] [3535] [3536] [3537] Underfull \hbox (badness 10000) in paragraph at lines 5915--5920 [][][]\T1/zi4/m/sl/10 getGroupsFormula.gls[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi 4/m/sl/10 getGroupsFormula.lmList[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 getGroupsFormula.lme[][][][]\T1/ptm/m/n/10 , [3538] [3539] [3540] [3541] [3542] Underfull \hbox (badness 1490) in paragraph at lines 6194--6205 [][][]\T1/zi4/m/sl/10 corClasses[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 glsControl[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 glsObject[][][][]\T1/p tm/m/n/10 , [][][]\T1/zi4/m/sl/10 glsStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/z i4/m/sl/10 plot.gls[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 predict.gls[] [][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 qqnorm.gls[][][][]\T1/ptm/m/n/10 , [3543] Underfull \hbox (badness 10000) in paragraph at lines 6258--6260 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is [3544] [3545] [3546] [3547] [3548] [3549] [3550] Underfull \hbox (badness 10000) in paragraph at lines 6667--6669 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is [3551] [3552] [3553] [3554] Underfull \hbox (badness 10000) in paragraph at lines 6936--6943 [][][]\T1/zi4/m/sl/10 formula[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 gap ply[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 gsummary[][][][]\T1/ptm/m/n/1 0 , [][][]\T1/zi4/m/sl/10 lme[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 plo t.nffGroupedData[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 plot.nfnGroupedD ata[][][][]\T1/ptm/m/n/10 , [3555] [3556] [3557] [3558] Underfull \hbox (badness 10000) in paragraph at lines 7196--7202 [][][]\T1/zi4/m/sl/10 Initialize.corStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi 4/m/sl/10 Initialize.glsStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 In itialize.lmeStruct[][][][]\T1/ptm/m/n/10 , [3559] [3560] [3561] [3562] [3563] [3564] [3565] [3566] [3567] [3568] [3569] [3570] [3571] [3572] [3573] [3574] [3575] [3576] [3577] [3578] [3579] Underfull \hbox (badness 10000) in paragraph at lines 8466--8468 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is [3580] [3581] [3582] [3583] [3584] Underfull \hbox (badness 10000) in paragraph at lines 8751--8758 [][][]\T1/zi4/m/sl/10 lm[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 lme.lmLi st[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 plot.lmList[][][][]\T1/ptm/m/n /10 , [][][]\T1/zi4/m/sl/10 pooledSD[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl /10 predict.lmList[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 residuals.lmLi st[][][][]\T1/ptm/m/n/10 , [3585] [3586] [3587] [3588] [3589] [3590] [3591] [3592] [3593] Underfull \hbox (badness 10000) in paragraph at lines 9266--9273 [][][]\T1/zi4/m/sl/10 lme[][][][]\T1/ptm/m/n/10 ,[][][]\T1/zi4/m/sl/10 gls[][][ ][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 logLik.corStruct[][][][]\T1/ptm/m/n/1 0 , [][][]\T1/zi4/m/sl/10 logLik.glsStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi 4/m/sl/10 logLik.lmeStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 logLik .lmList[][][][]\T1/ptm/m/n/10 , [3594] [3595] [3596] [3597] [3598] [3599] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Matrix}) has been already used, duplicate ignored \relax l.9628 ...rA{Matrix}{Assign Matrix Values}{Matrix} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Matrix.1} ) has been already used, duplicate ignored \relax l.9628 ...rA{Matrix}{Assign Matrix Values}{Matrix} [3600] [3601] [3602] [3603] [3604] [3605] [3606] [3607] [3608] [3609] [3610] [3611] [3612] Underfull \hbox (badness 1596) in paragraph at lines 10395--10421 []\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a two-sided for-mula o f the form [3613] [3614] Underfull \hbox (badness 1490) in paragraph at lines 10511--10517 [][][]\T1/zi4/m/sl/10 nlmeControl[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 nlme.nlsList[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 nlmeObject[][][][]\ T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 nlsList[][][][]\T1/ptm/m/n/10 , [][][]\T1 /zi4/m/sl/10 nlmeStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 pdClasses [][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 reStruct[][][][]\T1/ptm/m/n/10 , [3615] [3616] [3617] [3618] Underfull \hbox (badness 10000) in paragraph at lines 10752--10754 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is [3619] [3620] [3621] [3622] [3623] [3624] [3625] [3626] [3627] [3628] [3629] [3630] [3631] [3632] [3633] [3634] [3635] [3636] [3637] [3638] [3639] [3640] [3641] [3642] [3643] [3644] [3645] [3646] [3647] [3648] [3649] [3650] [3651] [3652] [3653] [3654] [3655] [3656] [3657] [3658] [3659] [3660] [3661] [3662] [3663] [3664] [3665] Underfull \hbox (badness 1286) in paragraph at lines 13655--13662 []\T1/ptm/m/n/10 an op-tional log-i-cal func-tion or func-tion. If []\T1/zi4/m/ sl/10 TRUE []\T1/ptm/m/n/10 and ei-ther []\T1/zi4/m/sl/10 inner []\T1/ptm/m/n/1 0 or [3666] [3667] [3668] [3669] [3670] [3671] [3672] [3673] [3674] [3675] [3676] [3677] [3678] [3679] [3680] [3681] [3682] [3683] [3684] [3685] [3686] [3687] [3688] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.random.ef fects}) has been already used, duplicate ignored \relax l.15098 ...Extract Random Effects}{random.effects} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.random.ef fects.1}) has been already used, duplicate ignored \relax l.15098 ...Extract Random Effects}{random.effects} [3689] [3690] [3691] [3692] [3693] [3694] [3695] [3696] [3697] [3698] [3699] [3700] [3701] Underfull \hbox (badness 1067) in paragraph at lines 15840--15845 \T1/ptm/m/n/10 ma-trix), []\T1/zi4/m/sl/10 fitted []\T1/ptm/m/n/10 (fit-ted val -ues), and []\T1/zi4/m/sl/10 residuals []\T1/ptm/m/n/10 (resid-u-als). De-fault s to [3702] [3703] [3704] [3705] Underfull \hbox (badness 1448) in paragraph at lines 16083--16092 \T1/ptm/m/n/10 Op-tions in-clude []\T1/zi4/m/sl/10 "response" []\T1/ptm/m/n/10 for the "raw" resid-u-als (ob-served - fit-ted), [3706] [3707] [3708] [3709] [3710] [3711] [3712] [3713] [3714] [3715] [3716] Underfull \hbox (badness 1728) in paragraph at lines 16786--16789 []\T1/ptm/m/n/10 an op-tional log-i-cal value used to con-trol the amount of ou t-put in the [3717] [3718] [3719] [3720] [3721] Underfull \hbox (badness 8056) in paragraph at lines 17120--17129 \T1/zi4/m/sl/10 Symmetry" []\T1/ptm/m/n/10 for []\T1/zi4/m/sl/10 pdCompSymm[]\T 1/ptm/m/n/10 , []\T1/zi4/m/sl/10 "Diagonal" []\T1/ptm/m/n/10 for []\T1/zi4/m/sl /10 pdDiag[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 "Multiple of Underfull \hbox (badness 10000) in paragraph at lines 17120--17129 \T1/zi4/m/sl/10 an Identity" []\T1/ptm/m/n/10 for []\T1/zi4/m/sl/10 pdIdent[]\T 1/ptm/m/n/10 , []\T1/zi4/m/sl/10 "General Positive-Definite, Natural Underfull \hbox (badness 5756) in paragraph at lines 17120--17129 \T1/zi4/m/sl/10 Parametrization" []\T1/ptm/m/n/10 for []\T1/zi4/m/sl/10 pdNatur al[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 "General Positive-Definite" []\T1/ptm/m/ n/10 for [3722] [3723] [3724] [3725] [3726] Underfull \hbox (badness 10000) in paragraph at lines 17441--17449 [][][]\T1/zi4/m/sl/10 varComb[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 var ConstPower[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 varConstProp[][][][]\T 1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 varExp[][][][]\T1/ptm/m/n/10 , [][][]\T1/z i4/m/sl/10 varFixed[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 varIdent[][][ ][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 varPower[][][][]\T1/ptm/m/n/10 , [3727] [3728] [3729] [3730] [3731] [3732] [3733] [3734] [3735] [3736] [3737] [3738] Underfull \hbox (badness 10000) in paragraph at lines 18153--18163 [][][]\T1/zi4/m/sl/10 Variogram.corExp[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/ sl/10 Variogram.corGaus[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 Variogram .corLin[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 Variogram.corRatio[][][][ ]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 18153--18163 [][][]\T1/zi4/m/sl/10 Variogram.corSpatial[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi 4/m/sl/10 Variogram.corSpher[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 Vari ogram.default[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 Variogram.gls[][][] []\T1/ptm/m/n/10 , [3739] [3740] [3741] [3742] [3743] [3744] Underfull \hbox (badness 5036) in paragraph at lines 18471--18480 [][][]\T1/zi4/m/sl/10 corSpatial[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 Variogram[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 Variogram.default[][][] []\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 Variogram.corExp[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 Variogram.corGaus[][][][]\T1/ptm/m/n/10 , [3745] [3746] [3747] [3748] [3749] [3750] [3751] [3752] [3753] [3754] [3755] [3756] [3757] [3758]) (./nnet-pkg.tex Chapter 26. [3759] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.multinom} ) has been already used, duplicate ignored \relax l.47 ...t Multinomial Log-linear Models}{multinom} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.multinom. 1}) has been already used, duplicate ignored \relax l.47 ...t Multinomial Log-linear Models}{multinom} Underfull \hbox (badness 1117) in paragraph at lines 79--88 []\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo rm []\T1/zi4/m/sl/10 response ~ [3760] [3761] [3762] [3763] [3764] [3765] [3766] [3767]) (./rpart-pkg.tex [3768] Chapter 27. [3769] [3770] [3771] [3772] [3773] [3774] [3775] [3776] [3777] [3778] [3779] Underfull \hbox (badness 10000) in paragraph at lines 771--775 []\T1/ptm/m/n/10 Logical. If []\T1/zi4/m/sl/10 TRUE []\T1/ptm/m/n/10 (de-fault) , adds to the la-bel Underfull \hbox (badness 1348) in paragraph at lines 771--775 \T1/zi4/m/sl/10 #events level1/ #events level2/ \T1/ptm/m/n/10 etc. for method []\T1/zi4/m/sl/10 class[]\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 n \T1/ptm/m/n/10 for [3780] [3781] [3782] [3783] [3784] [3785] [3786] [3787] [3788] [3789] [3790] [3791] [3792] [3793] [3794] [3795] [3796] [3797] [3798] [3799]) (./spatial-pkg.tex [3800] Chapter 28. [3801] [3802] [3803] [3804] [3805] [3806] Underfull \hbox (badness 10000) in paragraph at lines 423--427 [3807] [3808] [3809] [3810] [3811] [3812] [3813] [3814] [3815] [3816] [3817] [3818] [3819] [3820] [3821]) (./survival-pkg.tex [3822] Chapter 29. [3823] [3824] [3825] [3826] Underfull \hbox (badness 6412) in paragraph at lines 284--286 []\T1/ptm/m/n/10 an op-tional list or vec-tor of group-ing el-e-ments, each as long as [3827] [3828] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.aml}) has been already used, duplicate ignored \relax l.384 ... Myelogenous Leukemia survival data}{aml} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.aml.1}) h as been already used, duplicate ignored \relax l.384 ... Myelogenous Leukemia survival data}{aml} [3829] [3830] [3831] [3832] [3833] [3834] [3835] [3836] [3837] [3838] [3839] [3840] [3841] Underfull \hbox (badness 1097) in paragraph at lines 1205--1207 []\T1/ptm/m/n/10 F.J. Anscombe (1949). Trans-for-ma-tions of Pois-son, bi-no-mi al and negative-binomial data. [3842] [3843] [3844] [3845] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.colon}) h as been already used, duplicate ignored \relax l.1407 ...erapy for Stage B/C colon cancer}{colon} [3846] Underfull \hbox (badness 3679) in paragraph at lines 1455--1459 []\T1/ptm/m/n/10 Peter Hig-gins has pointed out a data in-con-sis-tency, re-vea led by []\T1/zi4/m/sl/10 table(colon$nodes, [3847] [3848] [3849] [3850] [3851] [3852] [3853] [3854] [3855] Underfull \hbox (badness 3250) in paragraph at lines 2145--2150 \T1/ptm/m/n/10 ing guides and prepend []\T1/zi4/m/sl/10 survival:: []\T1/ptm/m/ n/10 onto ev-er-thing, in-clud-ing the spe-cial terms, e.g., Underfull \hbox (badness 10000) in paragraph at lines 2145--2150 []\T1/zi4/m/sl/10 survival::coxph(survival:Surv(time, status) ~ age + survival: :strata(inst), [3856] [3857] [3858] [3859] [3860] [3861] [3862] [3863] [3864] [3865] [3866] [3867] [3868] [3869] [3870] [3871] [3872] [3873] [3874] [3875] [3876] [3877] [3878] [3879] Underfull \hbox (badness 1389) in paragraph at lines 3683--3685 []\T1/ptm/m/n/10 Often used to add the ex-pected sur-vival curve(s) to a Kaplan -Meier plot gen-er-ated with [3880] [3881] [3882] [3883] [3884] Overfull \hbox (467.89665pt too wide) in alignment at lines 3976--3976 [] [] [3885] [3886] [3887] [3888] [3889] [3890] [3891] [3892] [3893] [3894] [3895] [3896] [3897] [3898] [3899] [3900] [3901] [3902] [3903] [3904] [3905] [3906] [3907] [3908] [3909] [3910] [3911] [3912] [3913] Underfull \hbox (badness 5274) in paragraph at lines 5766--5768 []\T1/ptm/m/n/10 an ob-ject of class []\T1/zi4/m/sl/10 "summary.survfit"[]\T1/p tm/m/n/10 , which is the re-sult of the [3914] [3915] [3916] [3917] [3918] [3919] [3920] [3921] [3922] [3923] [3924] [3925] [3926] [3927] [3928] [3929] [3930] [3931] [3932] [3933] [3934] Underfull \hbox (badness 1281) in paragraph at lines 7046--7049 []\T1/ptm/m/n/10 type of resid-u-als, with choices of []\T1/zi4/m/sl/10 "respon se"[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 "deviance"[]\T1/ptm/m/n/10 , []\T1/zi4/ m/sl/10 "dfbeta"[]\T1/ptm/m/n/10 , [3935] [3936] [3937] [3938] [3939] [3940] [3941] [3942] [3943] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.solder}) has been already used, duplicate ignored \relax l.7635 ...ata from a soldering experiment}{solder} [3944] [3945] [3946] [3947] [3948] [3949] [3950] [3951] [3952] [3953] [3954] [3955] [3956] [3957] [3958] [3959] [3960] [3961] [3962] [3963] [3964] [3965] [3966] [3967] [3968] Underfull \hbox (badness 1038) in paragraph at lines 9294--9300 []\T1/ptm/m/n/10 op-tion does not cre-ate a curve, rather it re-trieves the pre -dicted sur-vival [3969] [3970] [3971] [3972] [3973] Underfull \hbox (badness 10000) in paragraph at lines 9652--9657 [][][]\T1/zi4/m/sl/10 survfit.formula[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/s l/10 survfit.coxph[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 survfit.object [][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 print.survfit[][][][]\T1/ptm/m/n /10 , [][][]\T1/zi4/m/sl/10 plot.survfit[][][][]\T1/ptm/m/n/10 , [3974] [3975] [3976] [3977] [3978] Underfull \hbox (badness 4441) in paragraph at lines 10042--10052 []\T1/ptm/m/n/10 by de-fault, the surv-fit rou-tines only re-turn in-for-ma-tio n at the [3979] [3980] [3981] Underfull \hbox (badness 1490) in paragraph at lines 10217--10226 [][][]\T1/zi4/m/sl/10 survfit.coxph[][][] []\T1/ptm/m/n/10 for sur-vival curves from Cox mod-els, [][][]\T1/zi4/m/sl/10 survfit.object[][][] []\T1/ptm/m/n/10 for a de-scrip-tion Underfull \hbox (badness 2213) in paragraph at lines 10217--10226 \T1/ptm/m/n/10 of the com-po-nents of a surv-fit ob-ject, [][][]\T1/zi4/m/sl/10 print.survfit[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 plot.survfit[][][] []\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 lines.survfit[][][][]\T1/ptm/m/n/10 , [3982] [3983] [3984] [3985] [3986] [3987] [3988] Underfull \hbox (badness 1354) in paragraph at lines 10715--10719 []\T1/ptm/m/n/10 survival times, for time de-pen-dent pre-dic-tion. It gives th e time range [3989] [3990] [3991] [3992] [3993] [3994] [3995] [3996] [3997] [3998] [3999] [4000] [4001] [4002] [4003] [4004] [4005] [4006] [4007] [4008] [4009] [4010] [4011] [4012] [4013] [4014]) (./fullrefman.ind [4015] [4016] [4017] [4018] [4019] [4020] [4021] [4022] [4023] [4024] [4025] [4026] [4027] [4028] [4029] [4030] [4031] [4032] [4033] [4034] [4035] [4036] [4037] [4038] [4039] [4040] [4041] [4042] [4043] [4044] Overfull \hbox (8.3567pt too wide) in paragraph at lines 2898--2900 []| \T1/zi4/m/it/10 smooth.construct.tensor.smooth.spec\T1/ptm/m/n/10 , [4045] [4046] [4047] [4048] [4049] [4050] [4051] Overfull \hbox (8.3567pt too wide) in paragraph at lines 3550--3552 []| \T1/zi4/m/it/10 smooth.construct.tensor.smooth.spec\T1/ptm/m/n/10 , [4052] [4053] [4054] [4055] [4056] [4057] [4058] [4059] [4060] [4061] [4062] Overfull \hbox (5.8567pt too wide) in paragraph at lines 4962--4964 []\T1/zi4/m/it/10 [,Matrix,lMatrix,missing,missing-method Overfull \hbox (0.8567pt too 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5502--5504 []\T1/zi4/m/it/10 %&%,RsparseMatrix,CsparseMatrix-method Overfull \hbox (0.8567pt too wide) in paragraph at lines 5504--5506 []\T1/zi4/m/it/10 %&%,RsparseMatrix,RsparseMatrix-method Overfull \hbox (0.8567pt too wide) in paragraph at lines 5506--5508 []\T1/zi4/m/it/10 %&%,RsparseMatrix,TsparseMatrix-method Overfull \hbox (5.8567pt too wide) in paragraph at lines 5510--5512 []\T1/zi4/m/it/10 %&%,RsparseMatrix,diagonalMatrix-method Overfull \hbox (0.8567pt too wide) in paragraph at lines 5516--5518 []\T1/zi4/m/it/10 %&%,TsparseMatrix,CsparseMatrix-method Overfull \hbox (0.8567pt too wide) in paragraph at lines 5518--5520 []\T1/zi4/m/it/10 %&%,TsparseMatrix,RsparseMatrix-method Overfull \hbox (0.8567pt too wide) in paragraph at lines 5520--5522 []\T1/zi4/m/it/10 %&%,TsparseMatrix,TsparseMatrix-method Overfull \hbox (5.8567pt too wide) in paragraph at lines 5524--5526 []\T1/zi4/m/it/10 %&%,TsparseMatrix,diagonalMatrix-method [4068] Overfull \hbox (5.8567pt too wide) in paragraph at lines 5544--5546 []\T1/zi4/m/it/10 %&%,diagonalMatrix,CsparseMatrix-method Overfull \hbox (5.8567pt too wide) in paragraph at lines 5546--5548 []\T1/zi4/m/it/10 %&%,diagonalMatrix,RsparseMatrix-method Overfull \hbox (5.8567pt too wide) in paragraph at lines 5548--5550 []\T1/zi4/m/it/10 %&%,diagonalMatrix,TsparseMatrix-method Overfull \hbox (10.8567pt too wide) in paragraph at lines 5552--5554 []\T1/zi4/m/it/10 %&%,diagonalMatrix,diagonalMatrix-method [4069] [4070] Overfull \hbox (15.01662pt too wide) in paragraph at lines 5821--5823 \T1/ptm/m/it/10 (\T1/zi4/m/it/10 smooth.construct.ad.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , [4071] Overfull \hbox (20.8567pt too wide) in paragraph at lines 5975--5977 []\T1/zi4/m/it/10 all.equal,sparseVector,sparseVector-method [4072] Overfull \hbox (10.8567pt too wide) in paragraph at lines 6229--6231 []\T1/zi4/m/it/10 Arith,CsparseMatrix,CsparseMatrix-method Overfull \hbox (0.8567pt too wide) in paragraph at lines 6237--6239 []\T1/zi4/m/it/10 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6363--6365 []\T1/zi4/m/it/10 Arith,triangularMatrix,diagonalMatrix-method [4074] [4075] [4076] Overfull \hbox (15.01662pt too wide) in paragraph at lines 7032--7034 \T1/ptm/m/it/10 (\T1/zi4/m/it/10 smooth.construct.bs.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , [4077] [4078] [4079] [4080] [4081] [4082] [4083] [4084] Overfull \hbox (30.8567pt too wide) in paragraph at lines 8545--8547 []\T1/zi4/m/it/10 coerce,diagonalMatrix,symmetricMatrix-method Overfull \hbox (35.8567pt too wide) in paragraph at lines 8547--8549 []\T1/zi4/m/it/10 coerce,diagonalMatrix,triangularMatrix-method [4085] Overfull \hbox (10.8567pt too wide) in paragraph at lines 8567--8569 []\T1/zi4/m/it/10 coerce,generalMatrix,packedMatrix-method [4086] Overfull \hbox (0.8567pt too wide) in paragraph at lines 8713--8715 []\T1/zi4/m/it/10 coerce,matrix.coo,CsparseMatrix-method Overfull \hbox (0.8567pt too wide) in paragraph at lines 8721--8723 []\T1/zi4/m/it/10 coerce,matrix.coo,RsparseMatrix-method Overfull \hbox (0.8567pt too wide) in paragraph at lines 8725--8727 []\T1/zi4/m/it/10 coerce,matrix.coo,TsparseMatrix-method Overfull \hbox (0.8567pt too wide) in paragraph at lines 8727--8729 []\T1/zi4/m/it/10 coerce,matrix.csc,CsparseMatrix-method Overfull \hbox (0.8567pt too wide) in paragraph at lines 8733--8735 []\T1/zi4/m/it/10 coerce,matrix.csc,RsparseMatrix-method Overfull \hbox (0.8567pt too wide) in paragraph at lines 8737--8739 []\T1/zi4/m/it/10 coerce,matrix.csc,TsparseMatrix-method Overfull \hbox (0.8567pt too wide) in paragraph at lines 8739--8741 []\T1/zi4/m/it/10 coerce,matrix.csr,CsparseMatrix-method Overfull \hbox (0.8567pt too wide) in paragraph at lines 8747--8749 []\T1/zi4/m/it/10 coerce,matrix.csr,RsparseMatrix-method Overfull \hbox (0.8567pt too wide) in paragraph at lines 8751--8753 []\T1/zi4/m/it/10 coerce,matrix.csr,TsparseMatrix-method [4087] Overfull \hbox (10.8567pt too wide) in paragraph at lines 8775--8777 []\T1/zi4/m/it/10 coerce,sparseVector,CsparseMatrix-method Overfull \hbox (0.8567pt too wide) in paragraph at lines 8777--8779 []\T1/zi4/m/it/10 coerce,sparseVector,denseMatrix-method Overfull \hbox (10.8567pt too wide) in paragraph at lines 8779--8781 []\T1/zi4/m/it/10 coerce,sparseVector,dsparseVector-method Overfull \hbox (10.8567pt too wide) in paragraph at lines 8781--8783 []\T1/zi4/m/it/10 coerce,sparseVector,generalMatrix-method Overfull \hbox (10.8567pt too wide) in paragraph at lines 8783--8785 []\T1/zi4/m/it/10 coerce,sparseVector,isparseVector-method Overfull \hbox (10.8567pt too wide) in paragraph at lines 8785--8787 []\T1/zi4/m/it/10 coerce,sparseVector,lsparseVector-method Overfull \hbox (10.8567pt too wide) in paragraph at lines 8789--8791 []\T1/zi4/m/it/10 coerce,sparseVector,nsparseVector-method Overfull \hbox (10.8567pt too wide) in paragraph at lines 8791--8793 []\T1/zi4/m/it/10 coerce,sparseVector,RsparseMatrix-method Overfull \hbox (5.8567pt too wide) in paragraph at lines 8793--8795 []\T1/zi4/m/it/10 coerce,sparseVector,sparseMatrix-method Overfull \hbox (10.8567pt too wide) in paragraph at lines 8795--8797 []\T1/zi4/m/it/10 coerce,sparseVector,TsparseMatrix-method Overfull \hbox (15.8567pt too wide) in paragraph at lines 8797--8799 []\T1/zi4/m/it/10 coerce,sparseVector,unpackedMatrix-method Overfull \hbox (10.8567pt too wide) in paragraph at lines 8799--8801 []\T1/zi4/m/it/10 coerce,sparseVector,zsparseVector-method [4088] Overfull \hbox (20.8567pt too wide) in paragraph at lines 8975--8977 []\T1/zi4/m/it/10 Compare,CsparseMatrix,CsparseMatrix-method [4089] Overfull \hbox (40.8567pt too wide) in paragraph at lines 9007--9009 []\T1/zi4/m/it/10 Compare,triangularMatrix,diagonalMatrix-method [4090] [4091] Overfull \hbox (30.8567pt too wide) in paragraph at lines 9552--9554 []\T1/zi4/m/it/10 crossprod,CsparseMatrix,CsparseMatrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 9554--9556 []\T1/zi4/m/it/10 crossprod,CsparseMatrix,denseMatrix-method Overfull \hbox (35.8567pt too wide) in paragraph at lines 9556--9558 []\T1/zi4/m/it/10 crossprod,CsparseMatrix,diagonalMatrix-method Overfull \hbox (0.8567pt too wide) in paragraph at lines 9560--9562 []\T1/zi4/m/it/10 crossprod,CsparseMatrix,missing-method Overfull \hbox (30.8567pt too wide) in paragraph at lines 9562--9564 []\T1/zi4/m/it/10 crossprod,CsparseMatrix,RsparseMatrix-method Overfull \hbox (30.8567pt too wide) in paragraph at lines 9564--9566 []\T1/zi4/m/it/10 crossprod,CsparseMatrix,TsparseMatrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 9568--9570 []\T1/zi4/m/it/10 crossprod,denseMatrix,CsparseMatrix-method Overfull \hbox (10.8567pt too wide) in paragraph at lines 9570--9572 []\T1/zi4/m/it/10 crossprod,denseMatrix,denseMatrix-method Overfull \hbox (25.8567pt too wide) in paragraph at lines 9572--9574 []\T1/zi4/m/it/10 crossprod,denseMatrix,diagonalMatrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 9578--9580 []\T1/zi4/m/it/10 crossprod,denseMatrix,RsparseMatrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 9580--9582 []\T1/zi4/m/it/10 crossprod,denseMatrix,TsparseMatrix-method Overfull \hbox (35.8567pt too wide) in paragraph at lines 9584--9586 []\T1/zi4/m/it/10 crossprod,diagonalMatrix,CsparseMatrix-method Overfull \hbox (25.8567pt too wide) in paragraph at lines 9586--9588 []\T1/zi4/m/it/10 crossprod,diagonalMatrix,denseMatrix-method Overfull \hbox (40.8567pt too wide) in paragraph at lines 9588--9590 []\T1/zi4/m/it/10 crossprod,diagonalMatrix,diagonalMatrix-method [4092] Overfull \hbox (0.8567pt too wide) in paragraph at lines 9590--9592 []\T1/zi4/m/it/10 crossprod,diagonalMatrix,matrix-method Overfull \hbox (5.8567pt too wide) in paragraph at lines 9592--9594 []\T1/zi4/m/it/10 crossprod,diagonalMatrix,missing-method Overfull \hbox (35.8567pt too wide) in paragraph at lines 9594--9596 []\T1/zi4/m/it/10 crossprod,diagonalMatrix,RsparseMatrix-method Overfull \hbox (35.8567pt too wide) in paragraph at lines 9596--9598 []\T1/zi4/m/it/10 crossprod,diagonalMatrix,TsparseMatrix-method Overfull \hbox (0.8567pt too wide) in paragraph at lines 9598--9600 []\T1/zi4/m/it/10 crossprod,diagonalMatrix,vector-method Overfull \hbox (0.8567pt too wide) in paragraph at lines 9614--9616 []\T1/zi4/m/it/10 crossprod,matrix,diagonalMatrix-method Overfull \hbox (30.8567pt too wide) in paragraph at lines 9636--9638 []\T1/zi4/m/it/10 crossprod,RsparseMatrix,CsparseMatrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 9638--9640 []\T1/zi4/m/it/10 crossprod,RsparseMatrix,denseMatrix-method Overfull \hbox (35.8567pt too wide) in paragraph at lines 9640--9642 []\T1/zi4/m/it/10 crossprod,RsparseMatrix,diagonalMatrix-method Overfull \hbox (0.8567pt too wide) in paragraph at lines 9644--9646 []\T1/zi4/m/it/10 crossprod,RsparseMatrix,missing-method Overfull \hbox (30.8567pt too wide) in paragraph at lines 9646--9648 []\T1/zi4/m/it/10 crossprod,RsparseMatrix,RsparseMatrix-method 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crossprod,TsparseMatrix,TsparseMatrix-method Overfull \hbox (0.8567pt too wide) in paragraph at lines 9684--9686 []\T1/zi4/m/it/10 crossprod,vector,diagonalMatrix-method [4093] Overfull \hbox (15.01662pt too wide) in paragraph at lines 9731--9733 \T1/ptm/m/it/10 (\T1/zi4/m/it/10 smooth.construct.cr.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (15.01662pt too wide) in paragraph at lines 9795--9797 \T1/ptm/m/it/10 (\T1/zi4/m/it/10 smooth.construct.cr.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (15.01662pt too wide) in paragraph at lines 9800--9802 \T1/ptm/m/it/10 (\T1/zi4/m/it/10 smooth.construct.ps.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (15.01662pt too wide) in paragraph at lines 9809--9811 \T1/ptm/m/it/10 (\T1/zi4/m/it/10 smooth.construct.bs.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , [4094] [4095] Overfull \hbox (5.8567pt too wide) in paragraph at lines 10174--10176 []\T1/zi4/m/it/10 determinant,BunchKaufman,logical-method Overfull 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[]\T1/zi4/m/it/10 dimnames<-,symmetricMatrix,NULL-method [4098] [4099] Overfull \hbox (15.01662pt too wide) in paragraph at lines 10967--10969 \T1/ptm/m/it/10 (\T1/zi4/m/it/10 smooth.construct.ds.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , [4100] [4101] [4102] [4103] [4104] Overfull \hbox (35.8567pt too wide) in paragraph at lines 11950--11952 []\T1/zi4/m/it/10 forceSymmetric,CsparseMatrix,character-method Overfull \hbox (25.8567pt too wide) in paragraph at lines 11952--11954 []\T1/zi4/m/it/10 forceSymmetric,CsparseMatrix,missing-method Overfull \hbox (25.8567pt too wide) in paragraph at lines 11954--11956 []\T1/zi4/m/it/10 forceSymmetric,denseMatrix,character-method Overfull \hbox (15.8567pt too wide) in paragraph at lines 11956--11958 []\T1/zi4/m/it/10 forceSymmetric,denseMatrix,missing-method Overfull \hbox (40.8567pt too wide) in paragraph at lines 11958--11960 []\T1/zi4/m/it/10 forceSymmetric,diagonalMatrix,character-method Overfull \hbox (30.8567pt too wide) in paragraph at 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forceSymmetric,TsparseMatrix,missing-method [4105] [4106] [4107] [4108] Overfull \hbox (15.01662pt too wide) in paragraph at lines 12969--12971 \T1/ptm/m/it/10 (\T1/zi4/m/it/10 smooth.construct.gp.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , [4109] [4110] [4111] [4112] [4113] [4114] [4115] [4116] Overfull \hbox (30.8567pt too wide) in paragraph at lines 14569--14571 []\T1/zi4/m/it/10 kronecker,CsparseMatrix,CsparseMatrix-method Overfull \hbox (35.8567pt too wide) in paragraph at lines 14571--14573 []\T1/zi4/m/it/10 kronecker,CsparseMatrix,diagonalMatrix-method Overfull \hbox (10.8567pt too wide) in paragraph at lines 14575--14577 []\T1/zi4/m/it/10 kronecker,denseMatrix,denseMatrix-method [4117] Overfull \hbox (35.8567pt too wide) in paragraph at lines 14579--14581 []\T1/zi4/m/it/10 kronecker,diagonalMatrix,CsparseMatrix-method Overfull \hbox (40.8567pt too wide) in paragraph at lines 14581--14583 []\T1/zi4/m/it/10 kronecker,diagonalMatrix,diagonalMatrix-method Overfull \hbox (15.8567pt 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kronecker,TsparseMatrix,diagonalMatrix-method Overfull \hbox (30.8567pt too wide) in paragraph at lines 14613--14615 []\T1/zi4/m/it/10 kronecker,TsparseMatrix,TsparseMatrix-method [4118] [4119] [4120] Overfull \hbox (10.8567pt too wide) in paragraph at lines 15451--15453 []\T1/zi4/m/it/10 Logic,CsparseMatrix,CsparseMatrix-method Overfull \hbox (5.8567pt too wide) in paragraph at lines 15459--15461 []\T1/zi4/m/it/10 Logic,ldenseMatrix,lsparseMatrix-method [4121] Overfull \hbox (5.8567pt too wide) in paragraph at lines 15481--15483 []\T1/zi4/m/it/10 Logic,lsparseMatrix,ldenseMatrix-method Overfull \hbox (10.8567pt too wide) in paragraph at lines 15483--15485 []\T1/zi4/m/it/10 Logic,lsparseMatrix,lsparseMatrix-method Overfull \hbox (10.8567pt too wide) in paragraph at lines 15485--15487 []\T1/zi4/m/it/10 Logic,lsparseVector,lsparseVector-method Overfull \hbox (0.8567pt too wide) in paragraph at lines 15517--15519 []\T1/zi4/m/it/10 Logic,sparseVector,sparseVector-method Overfull \hbox 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in paragraph at lines 17883--17885 \T1/ptm/m/it/10 (\T1/zi4/m/it/10 smooth.construct.ps.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , [4133] Overfull \hbox (33.3567pt too wide) in paragraph at lines 17918--17920 []\T1/zi4/m/it/10 package_native_routine_registration_skeleton\T1/ptm/m/n/10 , [4134] [4135] [4136] [4137] [4138] Overfull \hbox (15.01662pt too wide) in paragraph at lines 19274--19276 \T1/ptm/m/it/10 (\T1/zi4/m/it/10 smooth.construct.bs.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (15.01662pt too wide) in paragraph at lines 19281--19283 \T1/ptm/m/it/10 (\T1/zi4/m/it/10 smooth.construct.ds.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (15.01662pt too wide) in paragraph at lines 19283--19285 \T1/ptm/m/it/10 (\T1/zi4/m/it/10 smooth.construct.fs.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , [4139] Overfull \hbox (15.01662pt too wide) in paragraph at lines 19285--19287 \T1/ptm/m/it/10 (\T1/zi4/m/it/10 smooth.construct.gp.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (20.01662pt too wide) in paragraph at lines 19287--19289 \T1/ptm/m/it/10 (\T1/zi4/m/it/10 smooth.construct.mrf.smooth.spec\T1/ptm/m/it/1 0 )\T1/ptm/m/n/10 , Overfull \hbox (15.01662pt too wide) in paragraph at lines 19291--19293 \T1/ptm/m/it/10 (\T1/zi4/m/it/10 smooth.construct.re.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (20.01662pt too wide) in paragraph at lines 19297--19299 \T1/ptm/m/it/10 (\T1/zi4/m/it/10 smooth.construct.sos.smooth.spec\T1/ptm/m/it/1 0 )\T1/ptm/m/n/10 , Overfull \hbox (15.01662pt too wide) in paragraph at lines 19301--19303 \T1/ptm/m/it/10 (\T1/zi4/m/it/10 smooth.construct.sz.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , [4140] [4141] [4142] [4143] [4144] [4145] Overfull \hbox (20.8567pt too wide) in paragraph at lines 20397--20399 []\T1/zi4/m/it/10 R_AVAILABLE_PACKAGES_CACHE_CONTROL_MAX_AGE [4146] [4147] [4148] [4149] [4150] [4151] [4152] [4153] [4154] [4155] Overfull \hbox (15.01662pt too wide) in paragraph at lines 22362--22364 \T1/ptm/m/it/10 (\T1/zi4/m/it/10 smooth.construct.cr.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (15.01662pt too wide) in paragraph at lines 22364--22366 \T1/ptm/m/it/10 (\T1/zi4/m/it/10 smooth.construct.ps.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (15.01662pt too wide) in paragraph at lines 22367--22369 \T1/ptm/m/it/10 (\T1/zi4/m/it/10 smooth.construct.cr.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (15.01662pt too wide) in paragraph at lines 22384--22386 \T1/ptm/m/it/10 (\T1/zi4/m/it/10 smooth.construct.so.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (15.01662pt too wide) in paragraph at lines 22389--22391 \T1/ptm/m/it/10 (\T1/zi4/m/it/10 smooth.construct.so.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (15.01662pt too wide) in paragraph at lines 22401--22403 \T1/ptm/m/it/10 (\T1/zi4/m/it/10 smooth.construct.tp.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , [4156] Overfull \hbox (5.8567pt 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(\T1/zi4/m/it/10 smooth.construct.sos.smooth.spec\T1/ptm/m/it/1 0 )\T1/ptm/m/n/10 , [4159] [4160] Overfull \hbox (5.8567pt too wide) in paragraph at lines 23269--23271 []\T1/zi4/m/it/10 summarize_check_packages_in_dir_depends Overfull \hbox (5.8567pt too wide) in paragraph at lines 23271--23273 []\T1/zi4/m/it/10 summarize_check_packages_in_dir_results Overfull \hbox (5.8567pt too wide) in paragraph at lines 23273--23275 []\T1/zi4/m/it/10 summarize_check_packages_in_dir_timings [4161] [4162] [4163] [4164] Overfull \hbox (35.8567pt too wide) in paragraph at lines 24107--24109 []\T1/zi4/m/it/10 tcrossprod,CsparseMatrix,CsparseMatrix-method Overfull \hbox (25.8567pt too wide) in paragraph at lines 24109--24111 []\T1/zi4/m/it/10 tcrossprod,CsparseMatrix,denseMatrix-method Overfull \hbox (40.8567pt too wide) in paragraph at lines 24111--24113 []\T1/zi4/m/it/10 tcrossprod,CsparseMatrix,diagonalMatrix-method Overfull \hbox (0.8567pt too wide) in paragraph at lines 24113--24115 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Val-ues [8] [9] [10] [11] Underfull \hbox (badness 2556) in paragraph at lines 572--578 []\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `[] \T1/zi4/m/n/10 insertions[]\T1/ptm/m/n/10 ', [12] [13] [14] (/usr/local/share/texmf-dist/tex/latex/inconsolata/ts1zi4.fd) [15{/usr/local/share/texmf-dist/fonts/enc/dvips/inconsolata/i4-ts1.enc}] [16] [17] [18] [19] [20] [21] [22] [23] [24] [25] (/usr/local/share/texmf-dist/tex/latex-dev/base/t1cmtt.fd) (/usr/local/share/texmf-dist/tex/latex-dev/base/ts1cmtt.fd) [26{/usr/local/share/texmf-dist/fonts/enc/dvips/cm-super/cm-super-ts1.enc}] [27] [28] [29] [30] [31] [32] Underfull \vbox (badness 3803) has occurred while \output is active [33] [34] [35] [36] [37] [38] Overfull \hbox (26.27782pt too wide) in paragraph at lines 2261--2261 []\T1/zi4/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen t-date-and-times-in-MATLAB.html)[] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] Underfull \hbox (badness 1721) in paragraph at lines 2926--2930 [][][]\T1/zi4/m/n/10 assign[][][] []\T1/ptm/m/n/10 (and its in-verse [][][]\T1/ zi4/m/n/10 get[][][][]\T1/ptm/m/n/10 ), for ``sub-assign-ment'' such as []\T1/z i4/m/n/10 x[i] <- v[]\T1/ptm/m/n/10 , see [][][]\T1/zi4/m/n/10 [<-[][][][]\T1/p tm/m/n/10 ; fur-ther, [49] [50] [51] [52] [53] [54] [55] Underfull \hbox (badness 2538) in paragraph at lines 3404--3407 []\T1/zi4/m/n/10 unCfillPOSIXlt(x) []\T1/ptm/m/n/10 is a fast [][]prim-i-tive[] [][] ver-sion of []\T1/zi4/m/n/10 balancePOSIXlt(x, fill.only=TRUE, [56] [57] [58] [59] [60] [61] [62] [63] [64] [65] [66] [67] [68] Underfull \hbox (badness 10000) in paragraph at lines 4200--4202 []\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim -ited by set-ting [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] Underfull \hbox (badness 2521) in paragraph at lines 5551--5553 []\T1/ptm/m/n/10 a char-ac-ter vec-tor, or an ob-ject that can be co-erced to c har-ac-ter by [90] [91] [92] [93] [94] [95] [96] [97] [98] [99] [100] [101] [102] [103] [104] [105] [106] [107] [108] [109] Overfull \hbox (5.27168pt too wide) in paragraph at lines 6834--6834 []\T1/zi4/m/n/9 stopifnot(is.na(NpNA), is.na(NA_complex_), is.na(Re(NA_complex _)), is.na(Im(NA_complex_)))[] [110] [111] [112] [113] [114] [115] [116] [117] [118] [119] [120] [121] Underfull \hbox (badness 1303) in paragraph at lines 7730--7737 []\T1/zi4/m/n/10 file []\T1/ptm/m/n/10 can be used with []\T1/zi4/m/n/10 descri ption = "clipboard" []\T1/ptm/m/n/10 in mode []\T1/zi4/m/n/10 "r" []\T1/ptm/m/n /10 only. This reads the [122] Underfull \hbox (badness 2261) in paragraph at lines 7741--7746 \T1/zi4/m/n/10 / / github . com / astrand / xclip$[][]\T1/ptm/m/n/10 ) or []\T1 /zi4/m/n/10 xsel []\T1/ptm/m/n/10 ([][]$\T1/zi4/m/n/10 https : / / www . vergen et . net / ~conrad / software / [123] [124] Underfull \vbox (badness 10000) has occurred while \output is active [125] [126] [127] [128] [129] [130] [131] [132] [133] Underfull \hbox (badness 2096) in paragraph at lines 8474--8478 \T1/zi4/m/n/10 status _ codes$[][] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / List _ of _ FTP _ server _ return _ codes$ [][]\T1/ptm/m/n/10 . [134] [135] Underfull \hbox (badness 2351) in paragraph at lines 8589--8592 [][][]\T1/zi4/m/n/10 split[][][] []\T1/ptm/m/n/10 for split-ting a vari-able ac -cord-ing to a group fac-tor; [][][]\T1/zi4/m/n/10 factor[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 tabulate[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 t able[][][][]\T1/ptm/m/n/10 , [136] [137] [138] [139] [140] Underfull \hbox (badness 4479) in paragraph at lines 8906--8917 [][][]\T1/zi4/m/n/10 I[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 plot.data.f rame[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 print.data.frame[][][][]\T1/p tm/m/n/10 , [][][]\T1/zi4/m/n/10 row.names[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi 4/m/n/10 names[][][] []\T1/ptm/m/n/10 (for the col-umn names), [141] [142] [143] [144] [145] [146] Underfull \hbox (badness 1629) in paragraph at lines 9334--9346 []\T1/ptm/m/n/10 A few times have spe-cific is-sues. First, the leap sec-onds a re ig-nored, and real times Underfull \hbox (badness 2875) in paragraph at lines 9334--9346 []\T1/zi4/m/n/10 NA[]\T1/ptm/m/n/10 , and hence []\T1/zi4/m/n/10 as.POSIXct("19 69-12-31 23:59:59", tz = "UTC") []\T1/ptm/m/n/10 will give []\T1/zi4/m/n/10 "19 69-12-31 [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157] [158] [159] Underfull \hbox (badness 1178) in paragraph at lines 10200--10204 []\T1/ptm/m/n/10 If true, [][][]\T1/zi4/m/n/10 list[][][][]\T1/ptm/m/n/10 s and atomic vec-tors with non-[][][]\T1/zi4/m/n/10 NA[][][] []\T1/ptm/m/n/10 names (see [][][]\T1/zi4/m/n/10 names[][][][]\T1/ptm/m/n/10 ) are de- [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] [183] [184] [185] [186] [187] [188] [189] [190] [191] [192] [193] [194] [195] Underfull \hbox (badness 2744) in paragraph at lines 12540--12542 []\T1/ptm/m/n/10 Changing the cur-rent en-cod-ing from a run-ning R ses-sion ma y lead to con-fu-sion (see [196] [197] [198] [199] [200] [201] [202] [203] Underfull \vbox (badness 10000) has occurred while \output is active [204] [205] [206] [207] [208] [209] [210] [211] [212] [213] [214] [215] [216] [217] [218] [219] [220] [221] [222] [223] [224] [225] [226] [227] [228] Underfull \hbox (badness 2253) in paragraph at lines 14746--14748 []\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is done: see Underfull \hbox (badness 1490) in paragraph at lines 14781--14784 []\T1/ptm/m/n/10 Junction points and sym-bolic links are fol-lowed, so in-for-m a-tion is given about the [229] Underfull \hbox (badness 1565) in paragraph at lines 14863--14867 [][][]\T1/zi4/m/n/10 Sys.readlink[][][] []\T1/ptm/m/n/10 to find out about sym- bolic links, [][][]\T1/zi4/m/n/10 files[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m /n/10 file.access[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 list.files[][][] []\T1/ptm/m/n/10 , and [230] Underfull \hbox (badness 4927) in paragraph at lines 14914--14916 []\T1/ptm/m/n/10 It can also be used for en-vi-ron-ment paths such as []\T1/zi4 /m/n/10 PATH []\T1/ptm/m/n/10 and []\T1/zi4/m/n/10 R_LIBS []\T1/ptm/m/n/10 with []\T1/zi4/m/n/10 fsep = [231] [232] [233] Underfull \hbox (badness 1466) in paragraph at lines 15065--15068 []\T1/ptm/m/n/10 character vec-tors, con-tain-ing file names or paths. For []\T 1/zi4/m/n/10 file.copy []\T1/ptm/m/n/10 and [234] Underfull \hbox (badness 10000) in paragraph at lines 15196--15200 [][][]\T1/zi4/m/n/10 file.info[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 fil e.access[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 file.path[][][][]\T1/ptm/ m/n/10 , [][][]\T1/zi4/m/n/10 file.show[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m /n/10 list.files[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 unlink[][][][]\T1 /ptm/m/n/10 , [][][]\T1/zi4/m/n/10 basename[][][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 15207--15210 [][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][ ] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wik i / [235] [236] [237] [238] [239] Underfull \hbox (badness 3965) in paragraph at lines 15504--15508 []\T1/ptm/m/n/10 This is the same com-pu-ta-tion as for the em-pir-i-cal dis-tr i-bu-tion func-tion, and in-deed, [240] [241] [242] [243] [244] [245] [246] [247] Underfull \hbox (badness 5260) in paragraph at lines 16006--16006 []\T1/zi4/m/n/10 big.mark[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 big.interval[]\T1/ ptm/m/n/10 , []\T1/zi4/m/n/10 small.mark[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 sma ll.interval[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 decimal.mark[]\T1/ptm/m/n/10 , [248] [249] [250] [251] Underfull \hbox (badness 4429) in paragraph at lines 16296--16299 []\T1/ptm/m/n/10 an atomic nu-mer-i-cal or char-ac-ter ob-ject, pos-si-bly [][] []\T1/zi4/m/n/10 complex[][][] []\T1/ptm/m/n/10 only for [252] [253] Underfull \hbox (badness 10000) in paragraph at lines 16403--16405 []\T1/ptm/m/n/10 This works via []\T1/zi4/m/n/10 prettyNum()[]\T1/ptm/m/n/10 , which calls []\T1/zi4/m/n/10 .format.zeros(*, [254] Underfull \hbox (badness 2035) in paragraph at lines 16476--16480 []\T1/ptm/m/n/10 The de-fault for []\T1/zi4/m/n/10 decimal.mark []\T1/ptm/m/n/1 0 in []\T1/zi4/m/n/10 formatC() []\T1/ptm/m/n/10 was changed in \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.2.0: for use within [255] Underfull \vbox (badness 10000) has occurred while \output is active [256] [257] [258] [259] [260] [261] [262] [263] [264] Underfull \hbox (badness 2452) in paragraph at lines 17099--17103 []\T1/zi4/m/n/10 gctorture2 []\T1/ptm/m/n/10 can also be in-voked via en-vi-ron -ment vari-ables at the start of the \T1/phv/m/n/10 R \T1/ptm/m/n/10 ses- Underfull \hbox (badness 1147) in paragraph at lines 17099--17103 \T1/ptm/m/n/10 sion. []\T1/zi4/m/n/10 R_GCTORTURE []\T1/ptm/m/n/10 cor-re-spond s to the []\T1/zi4/m/n/10 step []\T1/ptm/m/n/10 ar-gu-ment, []\T1/zi4/m/n/10 R_ GCTORTURE_WAIT []\T1/ptm/m/n/10 to []\T1/zi4/m/n/10 wait[]\T1/ptm/m/n/10 , and [265] [266] [267] Underfull \hbox (badness 1092) in paragraph at lines 17273--17278 [][][]\T1/zi4/m/n/10 library.dynam[][][][]\T1/ptm/m/n/10 , or can be found af-t er the DLL has been loaded us-ing [268] [269] [270] Underfull \hbox (badness 6741) in paragraph at lines 17526--17530 \T1/ptm/m/n/10 Additionally, the list will have an ad-di-tional class, be-ing [ ]\T1/zi4/m/n/10 CRoutine[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 CallRoutine[]\T1/pt m/m/n/10 , [271] [272] [273] [274] [275] [276] [277] [278] [279] [280] [281] Underfull \vbox (badness 3803) has occurred while \output is active [282] Underfull \vbox (badness 10000) has occurred while \output is active [283] [284] [285] [286] [287] [288] [289] [290] [291] [292] Underfull \hbox (badness 1769) in paragraph at lines 18999--19002 []\T1/ptm/m/n/10 a char-ac-ter vec-tor, or an ob-ject to be con-verted to a cha r-ac-ter vec-tor [293] [294] [295] [296] [297] Underfull \hbox (badness 10000) in paragraph at lines 19308--19310 []\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/zi4/m/n/10 https : / / ww w . unicode . org / reports / tr35 / Underfull \hbox (badness 2088) in paragraph at lines 19314--19323 []\T1/ptm/m/n/10 For the spec-i-fi-ca-tions of `real' ICU lo-cales, see [][]$\T 1/zi4/m/n/10 https : / / unicode-[]org . github . io / icu / [298] [299] [300] [301] [302] [303] [304] [305] [306] [307] Underfull \hbox (badness 1442) in paragraph at lines 19922--19924 []\T1/ptm/m/n/10 the choice of de-fault graph-ics de-vice launched when needed and by [][][]\T1/zi4/m/n/10 dev.new[][][][]\T1/ptm/m/n/10 : see [308] Underfull \hbox (badness 2452) in paragraph at lines 20018--20044 [][][]\T1/zi4/m/n/10 as.character[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 as.complex[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 as.double[][][][]\T1/pt m/m/n/10 , [][][]\T1/zi4/m/n/10 as.integer[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi 4/m/n/10 as.logical[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 as.raw[][][][] \T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 as.vector[][][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 5726) in paragraph at lines 20018--20044 [][][]\T1/zi4/m/n/10 as.call[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 as.en vironment[][][] [][]is.array[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 is.ma trix[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 is.na[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 anyNA[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 is.nan [][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/n/10 is.finite[][][] [309] [310] [311] [312] [313] [314] Underfull \hbox (badness 1248) in paragraph at lines 20416--20419 []\T1/zi4/m/n/10 is.atomic []\T1/ptm/m/n/10 is true for the [][]atomic[][][] ty pes ([]\T1/zi4/m/n/10 "logical"[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 "integer"[]\ T1/ptm/m/n/10 , []\T1/zi4/m/n/10 "numeric"[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 " complex"[]\T1/ptm/m/n/10 , [315] [316] [317] [318] [319] Underfull \hbox (badness 4739) in paragraph at lines 20683--20685 []\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere d, see [320] [321] [322] [323] [324] Underfull \vbox (badness 10000) has occurred while \output is active [325] [326] [327] [328] [329] [330] [331] [332] [333] [334] [335] [336] [337] [338] Underfull \hbox (badness 2469) in paragraph at lines 21851--21856 []\T1/ptm/m/n/10 In late 2017 a []\T1/zi4/m/n/10 libcurl []\T1/ptm/m/n/10 in-st al-la-tion was seen di-vided into two li-braries, []\T1/zi4/m/n/10 libcurl []\T 1/ptm/m/n/10 and [339] Underfull \hbox (badness 1675) in paragraph at lines 21938--21947 []\T1/ptm/m/n/10 At startup, the li-brary search path is ini-tial-ized from the en-vi-ron-ment vari-ables []\T1/zi4/m/n/10 R_LIBS[]\T1/ptm/m/n/10 , Underfull \hbox (badness 3189) in paragraph at lines 21948--21961 []\T1/ptm/m/n/10 First, []\T1/zi4/m/n/10 .Library.site []\T1/ptm/m/n/10 is ini- tial-ized from []\T1/zi4/m/n/10 R_LIBS_SITE[]\T1/ptm/m/n/10 . If this is un-set or empty, the [340] Underfull \hbox (badness 10000) in paragraph at lines 21996--21999 []\T1/zi4/m/n/10 LOCALAPPDATA []\T1/ptm/m/n/10 (usu-ally []\T1/zi4/m/n/10 C:\Us ers\username\AppData\Local[]\T1/ptm/m/n/10 ) on Win-dows is a hid- Underfull \hbox (badness 4752) in paragraph at lines 21996--21999 \T1/ptm/m/n/10 den di-rec-tory and may not be viewed by some soft-ware. It may be opened by [341] [342] Underfull \hbox (badness 1014) in paragraph at lines 22130--22135 []\T1/ptm/m/n/10 Normally []\T1/zi4/m/n/10 library []\T1/ptm/m/n/10 re-turns (i n-vis-i-bly) the list of at-tached pack-ages, but []\T1/zi4/m/n/10 TRUE []\T1/p tm/m/n/10 or []\T1/zi4/m/n/10 FALSE []\T1/ptm/m/n/10 if [343] [344] [345] [346] [347] [348] [349] [350] [351] [352] [353] [354] [355] Underfull \hbox (badness 1264) in paragraph at lines 22977--22985 []\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways be sup-ported: Underfull \hbox (badness 4441) in paragraph at lines 23012--23015 []\T1/ptm/m/n/10 Note that set-ting cat-e-gory []\T1/zi4/m/n/10 "LC_ALL" []\T1/ ptm/m/n/10 sets only cat-e-gories []\T1/zi4/m/n/10 "LC_COLLATE"[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 "LC_CTYPE"[]\T1/ptm/m/n/10 , [356] [357] [358] [359] [360] [361] [362] [363] [364] [365] [366] [367] [368] Underfull \hbox (badness 5231) in paragraph at lines 23830--23832 []\T1/ptm/m/n/10 The al-go-rithm used by []\T1/zi4/m/n/10 make.unique []\T1/ptm /m/n/10 has the prop-erty that []\T1/zi4/m/n/10 make.unique(c(A, B)) == [369] [370] [371] [372] [373] [374] [375] [376] [377] [378] [379] [380] [381] [382] [383] [384] [385] Underfull \hbox (badness 6380) in paragraph at lines 24940--24946 [][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Data _ compress ion$[][] \T1/ptm/m/n/10 for back-ground on data com-pres- Underfull \hbox (badness 1472) in paragraph at lines 24940--24946 [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Bzip2$[][]\T1/ptm /m/n/10 , and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / XZ _ Utils$[][] [386] [387] [388] [389] [390] [391] [392] [393] [394] Underfull \hbox (badness 2790) in paragraph at lines 25453--25456 []\T1/zi4/m/n/10 packageStartupMessage []\T1/ptm/m/n/10 is a vari-ant whose mes -sages can be sup-pressed sep-a-rately by Underfull \hbox (badness 1571) in paragraph at lines 25453--25456 []\T1/zi4/m/n/10 suppressPackageStartupMessages[]\T1/ptm/m/n/10 . (They are sti ll mes-sages, so can be sup-pressed by [395] [396] [397] [398] [399] Underfull \hbox (badness 1194) in paragraph at lines 25781--25784 []\T1/ptm/m/n/10 The de-fault method for []\T1/zi4/m/n/10 anyNA []\T1/ptm/m/n/1 0 han-dles atomic vec-tors with-out a class and []\T1/zi4/m/n/10 NULL[]\T1/ptm/ m/n/10 . It calls [400] [401] [402] Underfull \hbox (badness 2368) in paragraph at lines 25988--25994 []\T1/ptm/m/n/10 For an [][][]\T1/zi4/m/n/10 environment[][][] env[]\T1/ptm/m/n /10 , []\T1/zi4/m/n/10 names(env) []\T1/ptm/m/n/10 gives the names of the cor-r e-spond-ing list, i.e., [403] [404] [405] [406] [407] [408] Underfull \hbox (badness 10000) in paragraph at lines 26378--26381 []\T1/ptm/m/n/10 optional [][][]\T1/zi4/m/n/10 logical[][][] []\T1/ptm/m/n/10 e ven-tu-ally to be passed to []\T1/zi4/m/n/10 print()[]\T1/ptm/m/n/10 , used by [409] [410] [411] [412] [413] [414] [415] [416] [417] [418] Underfull \hbox (badness 10000) in paragraph at lines 27006--27008 []\T1/zi4/m/n/10 isNamespaceLoaded(pkg) []\T1/ptm/m/n/10 is equiv-a-lent to but more ef-fi-cient than []\T1/zi4/m/n/10 pkg %in% [419] [420] [421] [422] [423] [424] [425] Underfull \hbox (badness 2443) in paragraph at lines 27497--27505 \T1/ptm/m/n/10 suit-able char-ac-ter vec-tors as above, or nu-meric ver-sion ob -jects. For [426] [427] [428] [429] [430] [431] [432] Underfull \hbox (badness 1881) in paragraph at lines 27927--27930 []\T1/ptm/m/n/10 integer value con-trol-ling the print-ing of lan-guage con-str ucts which are Underfull \hbox (badness 6220) in paragraph at lines 27952--27954 []\T1/ptm/m/n/10 Extra command-line ar-gu-ment(s) for non-default meth-ods: see [433] [434] Underfull \hbox (badness 2142) in paragraph at lines 28093--28097 []\T1/ptm/m/n/10 the de-fault pa-per for-mat used by [][][]\T1/zi4/m/n/10 posts cript[][][][]\T1/ptm/m/n/10 ; set by en-vi-ron-ment vari-able Underfull \hbox (badness 1968) in paragraph at lines 28150--28155 []\T1/ptm/m/n/10 the com-mand used by [][][]\T1/zi4/m/n/10 postscript[][][] []\ T1/ptm/m/n/10 for print-ing; set by en-vi-ron-ment vari-able [435] [436] [437] [438] Underfull \hbox (badness 10000) in paragraph at lines 28446--28452 []\T1/ptm/m/n/10 The URL of a Bio-con-duc-tor mir-ror for use by [][][]\T1/zi4/ m/n/10 setRepositories[][][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 28446--28452 \T1/ptm/m/n/10 e.g. the de-fault `[]\T1/zi4/m/n/10 "https://bioconductor.org"[] \T1/ptm/m/n/10 ' or the Eu-ro-pean mir-ror Underfull \hbox (badness 10000) in paragraph at lines 28446--28452 \T1/ptm/m/n/10 `[]\T1/zi4/m/n/10 "https://bioconductor.statistik.tu-dortmund.de "[]\T1/ptm/m/n/10 '. Can be set by Underfull \hbox (badness 5878) in paragraph at lines 28459--28462 []\T1/ptm/m/n/10 default Cc: ad-dress used by [][][]\T1/zi4/m/n/10 create.post[ ][][] []\T1/ptm/m/n/10 (and hence [][][]\T1/zi4/m/n/10 bug.report[][][] []\T1/p tm/m/n/10 and Underfull \hbox (badness 2689) in paragraph at lines 28485--28487 []\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na l HTTP server, see Underfull \hbox (badness 10000) in paragraph at lines 28531--28536 []\T1/ptm/m/n/10 Used by [][][]\T1/zi4/m/n/10 install.packages[][][] []\T1/ptm/ m/n/10 (and in-di-rectly [439] Underfull \hbox (badness 2529) in paragraph at lines 28537--28548 \T1/ptm/m/n/10 in-di-rectly [][][]\T1/zi4/m/n/10 update.packages[][][][]\T1/ptm /m/n/10 ) on plat-forms which sup-port bi-nary pack-ages. Pos-si- Underfull \hbox (badness 2512) in paragraph at lines 28537--28548 \T1/ptm/m/n/10 ble val-ues are []\T1/zi4/m/n/10 "never"[]\T1/ptm/m/n/10 , []\T1 /zi4/m/n/10 "interactive" []\T1/ptm/m/n/10 (which means ask in in-ter-ac-tive u se and Underfull \hbox (badness 7203) in paragraph at lines 28549--28552 []\T1/ptm/m/n/10 default email-ing method used by [][][]\T1/zi4/m/n/10 create.p ost[][][] []\T1/ptm/m/n/10 and hence [][][]\T1/zi4/m/n/10 bug.report[][][] []\T 1/ptm/m/n/10 and [440] [441] [442] [443] [444] Underfull \vbox (badness 10000) has occurred while \output is active [445] Underfull \hbox (badness 10000) in paragraph at lines 28967--28971 \T1/ptm/m/n/10 el-e-ment []\T1/zi4/m/n/10 A[c(arrayindex.x, arrayindex.y)] = FU N(X[arrayindex.x], Y[arrayindex.y], [446] [447] Underfull \hbox (badness 10000) in paragraph at lines 29114--29117 []\T1/zi4/m/n/10 str2expression(s) []\T1/ptm/m/n/10 and []\T1/zi4/m/n/10 str2la ng(s) []\T1/ptm/m/n/10 re-turn spe-cial ver-sions of []\T1/zi4/m/n/10 parse(tex t=s, [448] Underfull \hbox (badness 7925) in paragraph at lines 29195--29199 []\T1/ptm/m/n/10 for a [][][]\T1/zi4/m/n/10 character[][][] []\T1/ptm/m/n/10 ve c-tor []\T1/zi4/m/n/10 s[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 str2expression(s) [ ]\T1/ptm/m/n/10 cor-re-sponds to Underfull \hbox (badness 1253) in paragraph at lines 29195--29199 [][][]\T1/zi4/m/n/10 parse[][][](text = s, keep.source=FALSE)[]\T1/ptm/m/n/10 , which is al-ways of type ([][][]\T1/zi4/m/n/10 typeof[][][][]\T1/ptm/m/n/10 ) and [][][]\T1/zi4/m/n/10 class[][][] Underfull \hbox (badness 2521) in paragraph at lines 29200--29209 []\T1/ptm/m/n/10 for a [][][]\T1/zi4/m/n/10 character[][][] []\T1/ptm/m/n/10 st ring []\T1/zi4/m/n/10 s[]\T1/ptm/m/n/10 , []\T1/zi4/m/n/10 str2lang(s) []\T1/pt m/m/n/10 cor-re-sponds to [][][]\T1/zi4/m/n/10 parse[][][](text = s, [449] [450] [451] [452] [453] [454] [455] [456] [457] [458] [459] [460] [461] [462] [463] [464] Underfull \hbox (badness 2726) in paragraph at lines 30214--30217 []\T1/ptm/m/n/10 character string (or []\T1/zi4/m/n/10 NULL[]\T1/ptm/m/n/10 ) i n-di-cat-ing [][][]\T1/zi4/m/n/10 NA[][][] []\T1/ptm/m/n/10 val-ues in printed out-put, see [465] [466] [467] [468] [469] [470] [471] [472] [473] [474] [475] [476] [477] [478] [479] [480] [481] [482] [483] Underfull \vbox (badness 3803) has occurred while \output is active [484] [485] [486] [487] [488] [489] [490] [491] [492] Underfull \hbox (badness 1533) in paragraph at lines 32024--32027 []\T1/ptm/m/n/10 As with all com-piled code, mis-specifying these func-tions ca n crash \T1/phv/m/n/10 R\T1/ptm/m/n/10 . Do in-clude the [493] [494] [495] Underfull \hbox (badness 1163) in paragraph at lines 32195--32206 []\T1/ptm/m/n/10 If all com-po-nents are dif-fer-ent (and no []\T1/zi4/m/n/10 N A[]\T1/ptm/m/n/10 s), the ranks are well de-fined, with val-ues in [496] [497] [498] [499] [500] [501] [502] Underfull \vbox (badness 3803) has occurred while \output is active [503] [504] Underfull \hbox (badness 6300) in paragraph at lines 32741--32743 []\T1/ptm/m/n/10 The sec-tion `Pro-cess-ing doc-u-men-ta-tion files' in the `Wr it-ing R Ex-ten-sions' man-ual: [505] [506] [507] [508] [509] [510] [511] [512] [513] [514] [515] [516] [517] [518] [519] [520] [521] Underfull \hbox (badness 10000) in paragraph at lines 33864--33868 []\T1/zi4/m/n/10 regexpr []\T1/ptm/m/n/10 and []\T1/zi4/m/n/10 gregexpr []\T1/p tm/m/n/10 sup-port `named cap-ture'. If groups are named, e.g., Underfull \hbox (badness 1221) in paragraph at lines 33864--33868 []\T1/zi4/m/n/10 "(?[A-Z][a-z]+)" []\T1/ptm/m/n/10 then the po-si-tions of the matches are also re-turned by name. Underfull \hbox (badness 3557) in paragraph at lines 33885--33887 []\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/zi4/m/n/10 https : / / pubs . opengroup . org / onlinepubs / 9699919799 / Underfull \hbox (badness 1122) in paragraph at lines 33888--33892 []\T1/ptm/m/n/10 The []\T1/zi4/m/n/10 pcre2pattern []\T1/ptm/m/n/10 or []\T1/zi 4/m/n/10 pcrepattern man []\T1/ptm/m/n/10 page (found as part of [][]$\T1/zi4/m /n/10 https : / / www . pcre . org / [522] [523] Underfull \vbox (badness 10000) has occurred while \output is active [524] [525] [526] [527] [528] [529] [530] [531] Underfull \hbox (badness 1655) in paragraph at lines 34490--34492 []\T1/ptm/m/n/10 a vec-tor (atomic, not a list) for []\T1/zi4/m/n/10 rle()[]\T1 /ptm/m/n/10 ; an ob-ject of class []\T1/zi4/m/n/10 "rle" []\T1/ptm/m/n/10 for [532] [533] [534] [535] [536] [537] [538] [539] [540] [541] [542] [543] [544] [545] [546] [547] [548] [549] [550] Underfull \hbox (badness 2261) in paragraph at lines 35693--35698 []\T1/ptm/m/n/10 If []\T1/zi4/m/n/10 strip.white []\T1/ptm/m/n/10 is of length 1, it ap-plies to all fields; oth-er-wise, if [551] [552] [553] [554] [555] [556] [557] [558] [559] [560] [561] [562] [563] [564] [565] [566] Underfull \hbox (badness 3668) in paragraph at lines 36728--36732 []\T1/zi4/m/n/10 getAllConnections []\T1/ptm/m/n/10 re-turns a se-quence of in- te-ger con-nec-tion de-scrip-tors for use with [567] Underfull \hbox (badness 10000) in paragraph at lines 36819--36830 \T1/zi4/m/n/10 / / learn . microsoft . com / en-[]us / cpp / c-[]language / par sing-[]c-[]command-[]line-[]arguments ? [568] [569] [570] [571] [572] [573] [574] [575] [576] [577] [578] [579] [580] [581] [582] [583] [584] [585] [586] [587] [588] [589] [590] [591] [592] Underfull \hbox (badness 10000) in paragraph at lines 38451--38453 [][][]$\T1/zi4/m/n/10 https : / / pubs . opengroup . org / onlinepubs / 9699919 799 / functions / snprintf . html$[][] \T1/ptm/m/n/10 for [593] [594] [595] [596] [597] [598] [599] Underfull \hbox (badness 2913) in paragraph at lines 38869--38873 \T1/ptm/m/n/10 ber of nested \T1/phv/m/n/10 R \T1/ptm/m/n/10 ex-pres-sions cur- rently un-der eval-u-a-tion, ex-ceeds the limit set by [600] [601] [602] Underfull \hbox (badness 1072) in paragraph at lines 39115--39119 []\T1/ptm/m/n/10 On front-ends which sup-port it, the com-mands his-tory is rea d from the file spec-i-fied by [603] Underfull \hbox (badness 10000) in paragraph at lines 39120--39124 []\T1/ptm/m/n/10 The command-line op-tion `[]\T1/zi4/m/n/10 --vanilla[]\T1/ptm/ m/n/10 ' im-plies `[]\T1/zi4/m/n/10 --no-site-file[]\T1/ptm/m/n/10 ', `[]\T1/zi 4/m/n/10 --no-init-file[]\T1/ptm/m/n/10 ', Underfull \hbox (badness 10000) in paragraph at lines 39160--39166 []\T1/ptm/m/n/10 On sys-tems with sub-architectures (mainly Win-dows), the file s `\T1/zi4/m/n/10 Renviron.site\T1/ptm/m/n/10 ' Underfull \hbox (badness 10000) in paragraph at lines 39160--39166 \T1/ptm/m/n/10 and `\T1/zi4/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' are looked for first in architecture-specific di-rec-to-ries, Underfull \hbox (badness 1320) in paragraph at lines 39160--39166 \T1/ptm/m/n/10 e.g. `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/zi4/m/n/10 /etc/i386/R environ.site\T1/ptm/m/n/10 '. And e.g. `\T1/zi4/m/n/10 .Renviron.i386\T1/ptm/m/ n/10 ' will be used in Underfull \hbox (badness 3009) in paragraph at lines 39175--39182 []\T1/ptm/m/n/10 On Unix ver-sions of \T1/phv/m/n/10 R \T1/ptm/m/n/10 there is also a file `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/zi4/m/n/10 /etc/Renviron\T1/pt m/m/n/10 ' which is read Underfull \hbox (badness 1038) in paragraph at lines 39175--39182 \T1/ptm/m/n/10 very early in the start-up pro-cess-ing. It con-tains en-vi-ron- ment vari-ables set by \T1/phv/m/n/10 R \T1/ptm/m/n/10 in the Underfull \hbox (badness 2573) in paragraph at lines 39175--39182 \T1/ptm/m/n/10 con-fig-ure pro-cess. Val-ues in that file can be over-rid-den i n site or user en-vi-ron-ment Underfull \hbox (badness 1917) in paragraph at lines 39175--39182 \T1/ptm/m/n/10 files: do not change `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/zi4/m/ n/10 /etc/Renviron\T1/ptm/m/n/10 ' it-self. Note that this is dis-tinct from [604] [605] [606] [607] Underfull \hbox (badness 2644) in paragraph at lines 39410--39414 []\T1/ptm/m/n/10 alternative to []\T1/zi4/m/n/10 exprs []\T1/ptm/m/n/10 or []\T 1/zi4/m/n/10 ...[]\T1/ptm/m/n/10 : an `expression-like' ob-ject, typ-i-cally an [608] [609] [610] Underfull \hbox (badness 1389) in paragraph at lines 39573--39580 []\T1/ptm/m/n/10 a char-ac-ter string. The de-fault for the []\T1/zi4/m/n/10 fo rmat []\T1/ptm/m/n/10 meth-ods is []\T1/zi4/m/n/10 "%Y-%m-%d [611] [612] [613] [614] [615] [616] [617] [618] [619] [620] [621] [622] [623] [624] [625] [626] [627] [628] [629] [630] [631] Underfull \hbox (badness 1158) in paragraph at lines 40939--40941 []\T1/ptm/m/n/10 integer code used in []\T1/zi4/m/n/10 quantile(*, type=quantil e.type) []\T1/ptm/m/n/10 for the de-fault [632] [633] [634] [635] [636] [637] [638] [639] [640] [641] Underfull \hbox (badness 1137) in paragraph at lines 41539--41545 []\T1/ptm/m/n/10 This ex-pands tilde (see [][]tilde ex-pan-sion[][][]) and wild -cards in file paths. For pre-cise de-tails Underfull \hbox (badness 4967) in paragraph at lines 41557--41562 []\T1/ptm/m/n/10 If a file-name starts with []\T1/zi4/m/n/10 . []\T1/ptm/m/n/10 this may need to be matched ex-plic-itly: for ex-am-ple [642] [643] Underfull \hbox (badness 1616) in paragraph at lines 41677--41682 []\T1/zi4/m/n/10 system("id") []\T1/ptm/m/n/10 is much more portable on Unix-al ikes, pro-vided only the POSIX op-tions [644] [645] [646] [647] Underfull \vbox (badness 3803) has occurred while \output is active [648] [649] [650] [651] [652] Underfull \hbox (badness 1472) in paragraph at lines 42224--42227 []\T1/ptm/m/n/10 logical. If []\T1/zi4/m/n/10 TRUE[]\T1/ptm/m/n/10 , func-tions keep their source in-clud-ing com-ments, see [653] [654] [655] LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined (Font) using `T1/zi4/m/n' instead on input line 42436. [656] [657] [658] [659] [660] [661] [662] [663] [664] [665] [666] [667] Underfull \hbox (badness 10000) in paragraph at lines 43175--43179 []\T1/ptm/m/n/10 On 64-bit plat-forms []\T1/zi4/m/sl/10 bin []\T1/ptm/m/n/10 ca n have $\OT1/cmr/m/n/10 2[]$ \T1/ptm/m/n/10 or more el-e-ments (i.e., []\T1/zi4 /m/sl/10 length(bin) > [668] [669] [670] [671] [672] Underfull \hbox (badness 10000) in paragraph at lines 43534--43537 [][][]\T1/zi4/m/sl/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [][]$https : / / developer . r-[]project . org / [673] [674] [675] Underfull \hbox (badness 10000) in paragraph at lines 43718--43722 [][][]\T1/zi4/m/sl/10 addTaskCallback[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/s l/10 removeTaskCallback[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 taskCallb ackManager[][][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/sl/10 https : / / developer . [676] [677] [678] [679] [680] [681] [682] [683] [684] [685] Underfull \hbox (badness 10000) in paragraph at lines 44366--44369 [][][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / wiki / Time _ zone$[] [] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/sl/10 https : / / data . iana . org / time -[]zones / [686] [687] [688] [689] [690] [691] Underfull \vbox (badness 10000) has occurred while \output is active [692] [693] [694] [695] [696] [697] [698] [699] Underfull \hbox (badness 1990) in paragraph at lines 45282--45290 []\T1/zi4/m/sl/10 try []\T1/ptm/m/n/10 eval-u-ates an ex-pres-sion and traps an y er-rors that oc-cur dur-ing the eval-u-a-tion. If Underfull \hbox (badness 4846) in paragraph at lines 45282--45290 \T1/ptm/m/n/10 an er-ror oc-curs then the er-ror mes-sage is printed to the [][ ][]\T1/zi4/m/sl/10 stderr[][][] []\T1/ptm/m/n/10 con-nec-tion un-less [700] [701] [702] [703] [704] [705] [706] [707] [708] [709] [710] [711] [712] [713] [714] [715] [716] [717] [718] [719] [720] [721] Underfull \hbox (badness 1014) in paragraph at lines 46719--46722 []\T1/ptm/m/n/10 logical, in-di-cat-ing if the warn-ing should be out-put im-me -di-ately, even if [722] [723] Underfull \hbox (badness 2401) in paragraph at lines 46852--46856 []\T1/ptm/m/n/10 See the de-scrip-tion of [][][]\T1/zi4/m/sl/10 options[][][](" warn") []\T1/ptm/m/n/10 for the cir-cum-stances un-der which there is a [724] [725] Underfull \hbox (badness 3492) in paragraph at lines 46978--46980 []\T1/zi4/m/sl/10 weekdays []\T1/ptm/m/n/10 and []\T1/zi4/m/sl/10 months []\T1/ ptm/m/n/10 re-turn a char-ac-ter vec-tor of names in the lo-cale in use, i.e., [726] [727] Underfull \hbox (badness 2111) in paragraph at lines 47064--47069 \T1/ptm/m/n/10 If [][][]\T1/zi4/m/sl/10 names[][][](.dimnames) []\T1/ptm/m/n/10 is not empty, these are used as col-umn names. [728] [729] [730] Underfull \hbox (badness 4001) in paragraph at lines 47312--47314 []\T1/ptm/m/n/10 Thomas Lum-ley (2003) \T1/ptm/m/it/10 Stan-dard non-stan-dard eval-u-a-tion rules\T1/ptm/m/n/10 . [][]$\T1/zi4/m/sl/10 https : / / developer . [731] [732] [733] [734] [735] [736] [737] Underfull \hbox (badness 5417) in paragraph at lines 47713--47717 []\T1/zi4/m/sl/10 .packages() []\T1/ptm/m/n/10 re-turns the names of the cur-re ntly at-tached pack-ages \T1/ptm/m/it/10 in-vis-i-bly \T1/ptm/m/n/10 whereas [738] Underfull \hbox (badness 10000) in paragraph at lines 47774--47778 []\T1/zi4/m/sl/10 .standard_regexps []\T1/ptm/m/n/10 re-turns a list of `stan-d ard' reg-exps, in-clud-ing el-e-ments named [739]) (./compiler-pkg.tex [740] Chapter 2. [741] [742] [743] [744]) (./datasets-pkg.tex Chapter 3. [745] [746] [747] [748] [749] [750] [751] [752] [753] [754] [755] [756] [757] [758] [759] [760] [761] Underfull \hbox (badness 1097) in paragraph at lines 1034--1038 []\T1/ptm/m/n/10 MacDonell, W.R. (1902). On crim-i-nal an-thro-pom-e-try and th e iden-ti-fi-ca-tion of crim-i-nals. [762] [763] [764] [765] [766] [767] [768] [769] [770] [771] [772] [773] [774] [775] [776] [777] [778] [779] [780] [781] [782] [783] [784] [785] [786] [787] [788] [789] [790] [791] [792] [793] [794] [795] [796] [797] [798] [799] [800] [801] [802] [803] Overfull \hbox (2.27475pt too wide) in paragraph at lines 3524--3524 []\T1/zi4/m/n/9 ## From https://pubs.usgs.gov/gip/Elevations-Distances/elvadis t.html#Geographic%20Centers[] [804] [805] [806] [807] [808] [809] [810] [811] [812] [813] [814] [815] [816] [817] [818] [819] [820] [821] [822] [823] [824] [825] [826] [827]) (./graphics-pkg.tex [828] Chapter 4. [829] [830] [831] [832] [833] [834] [835] [836] [837] [838] [839] Underfull \vbox (badness 3803) has occurred while \output is active [840] [841] [842] [843] [844] [845] Overfull \hbox (12.71341pt too wide) in paragraph at lines 1037--1037 [] \T1/zi4/m/n/9 main = "barplot(Freq ~ Class + Survived, *)", ylab = " # {passengers}", legend.text = TRUE)[] [846] [847] [848] [849] [850] [851] Underfull \hbox (badness 4634) in paragraph at lines 1410--1413 [][][]\T1/zi4/m/sl/10 boxplot.default[][][] []\T1/ptm/m/n/10 which al-ready wor ks nowa-days with data.frames; [][][]\T1/zi4/m/sl/10 boxplot.formula[][][][]\T1 /ptm/m/n/10 , [852] [853] [854] [855] [856] [857] [858] [859] [860] [861] [862] [863] [864] [865] [866] [867] [868] Underfull \hbox (badness 1728) in paragraph at lines 2388--2390 []\T1/ptm/m/n/10 a string in-di-cat-ing the x-axis style; use []\T1/zi4/m/sl/10 "n" []\T1/ptm/m/n/10 to sup-press and see also [869] Underfull \hbox (badness 1009) in paragraph at lines 2481--2488 \T1/ptm/m/n/10 be in as-cend-ing or-der. (The rest of this de-scrip-tion does n ot ap-ply to [870] [871] [872] [873] [874] [875] [876] [877] [878] [879] [880] [881] [882] [883] [884] [885] [886] [887] [888] [889] [890] [891] [892] Underfull \vbox (badness 10000) has occurred while \output is active [893] Underfull \vbox (badness 10000) has occurred while \output is active [894] [895] [896] [897] [898] [899] Underfull \vbox (badness 3803) has occurred while \output is active [900] [901] [902] [903] [904] [905] [906] Underfull \hbox (badness 3229) in paragraph at lines 4733--4738 []\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing if log-a-rith-mic axes are to be used, see [907] [908] [909] [910] [911] Underfull \hbox (badness 1107) in paragraph at lines 5233--5239 []\T1/ptm/m/n/10 is []\T1/zi4/m/sl/10 par("cin")/par("pin") []\T1/ptm/m/n/10 sc aled to user co-or-di-nates. Note that []\T1/zi4/m/sl/10 c([][]strwidth[][][](c h), [912] [913] Underfull \hbox (badness 10000) in paragraph at lines 5362--5365 [914 ] Underfull \hbox (badness 10000) in paragraph at lines 5423--5425 [915 ] [916] [917] [918] [919] [920] [921] [922] [923] [924] [925] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.plot}) ha s been already used, duplicate ignored \relax l.6097 \aliasA{plot}{plot.default}{plot} [926] [927] [928] [929] [930] [931] [932] [933] [934] [935] [936] [937] [938] [939] Overfull \hbox (31.57222pt too wide) in paragraph at lines 6997--6998 [][] [940 ] [941] Underfull \vbox (badness 3803) has occurred while \output is active [942] [943] [944] [945] [946] [947] [948] [949] [950] [951] [952] [953] [954] [955] [956] [957] [958] [959] [960] [961] [962] [963] [964] [965] [966] [967] [968] [969] [970] [971] [972] [973] [974] Underfull \hbox (badness 4954) in paragraph at lines 9109--9111 []\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color []\T1/zi4/m /sl/10 par(c("font.sub", Underfull \hbox (badness 1019) in paragraph at lines 9111--9113 []\T1/ptm/m/n/10 X axis la-bel us-ing font, size and color []\T1/zi4/m/sl/10 pa r(c("font.lab", "cex.lab", [975] [976] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.units}) h as been already used, duplicate ignored \relax l.9191 \HeaderA{units}{Graphical Units}{units} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.units.1}) has been already used, duplicate ignored \relax l.9191 \HeaderA{units}{Graphical Units}{units} [977] [978] [979] [980]) (./grDevices-pkg.tex Chapter 5. [981] [982] [983] [984] [985] Underfull \hbox (badness 2221) in paragraph at lines 282--286 []\T1/ptm/m/n/10 numeric vec-tor of length 3, []\T1/zi4/m/sl/10 c(mi, ma, n.)[] \T1/ptm/m/n/10 , with iden-ti-cal mean-ing to Underfull \hbox (badness 10000) in paragraph at lines 297--302 []\T1/ptm/m/n/10 Apart from that, [][][]\T1/zi4/m/sl/10 axisTicks[][][]() []\T1 /ptm/m/n/10 just calls the C func-tion []\T1/zi4/m/sl/10 CreateAtVector() []\T1 /ptm/m/n/10 in [986] [987] [988] [989] [990] [991] [992] [993] [994] Underfull \hbox (badness 1424) in paragraph at lines 901--903 [][][]\T1/zi4/m/sl/10 NA[][][] []\T1/ptm/m/n/10 (as in-te-ger or char-ac-ter) a nd []\T1/zi4/m/sl/10 "NA" []\T1/ptm/m/n/10 mean trans-par-ent, which can also b e spec-i-fied as [995] [996] [997] [998] [999] [1000] Underfull \hbox (badness 5175) in paragraph at lines 1229--1231 []\T1/ptm/m/n/10 There is cur-rently no doc-u-men-ta-tion about the al-go-rithm . The source code is in [1001] [1002] Underfull \hbox (badness 2512) in paragraph at lines 1348--1350 []\T1/ptm/m/n/10 For the white points [][]$\T1/zi4/m/sl/10 https : / / web . ar chive . org / web / 20190613001950 / http : / / efg2 . com / [1003] [1004] [1005] [1006] [1007] Underfull \hbox (badness 1490) in paragraph at lines 1648--1653 \T1/ptm/m/n/10 by [][][]\T1/zi4/m/sl/10 rasterImage[][][] []\T1/ptm/m/n/10 and [][][]\T1/zi4/m/sl/10 grid.raster[][][][]\T1/ptm/m/n/10 ? Pos-si-ble val-ues [] \T1/zi4/m/sl/10 "no"[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 "yes" []\T1/ptm/m/n/10 and Underfull \hbox (badness 3302) in paragraph at lines 1661--1665 []\T1/ptm/m/n/10 character: Does the de-vice sup-port pat-tern fills? One or mo re of [1008] [1009] [1010] [1011] [1012] [1013] Underfull \hbox (badness 1325) in paragraph at lines 2076--2086 []\T1/zi4/m/sl/10 "png48"[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 "pngmono"[]\T1/pt m/m/n/10 , []\T1/zi4/m/sl/10 "pnggray"[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 "png alpha"[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 "bmp16"[]\T1/ptm/m/n/10 , []\T1/zi4/ m/sl/10 "bmp16m" "bmp256"[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 "bmp32b"[]\T1/ptm /m/n/10 , [1014] [1015] Underfull \hbox (badness 10000) in paragraph at lines 2188--2190 []\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the set-ting of [1016] [1017] [1018] Underfull \hbox (badness 6758) in paragraph at lines 2376--2379 []\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript doc-u-men-ta-tion) are [1019] [1020] [1021] [1022] [1023] [1024] [1025] [1026] [1027] [1028] [1029] [1030] Underfull \hbox (badness 10000) in paragraph at lines 3132--3133 [1031] [1032] [1033] [1034] [1035] [1036] [1037] [1038] [1039] [1040] [1041] [1042] Underfull \vbox (badness 3803) has occurred while \output is active [1043] [1044] [1045] [1046] Underfull \vbox (badness 10000) has occurred while \output is active [1047] [1048] [1049] [1050] Underfull \hbox (badness 1418) in paragraph at lines 4410--4417 \T1/ptm/m/n/10 it is one of []\T1/zi4/m/sl/10 "AvantGarde"[]\T1/ptm/m/n/10 , [] \T1/zi4/m/sl/10 "Bookman"[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 "Courier"[]\T1/pt m/m/n/10 , []\T1/zi4/m/sl/10 "Helvetica"[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 "H elvetica-Narrow"[]\T1/ptm/m/n/10 , [1051] [1052] [1053] [1054] [1055] [1056] [1057] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.symbol}) has been already used, duplicate ignored \relax l.4875 \aliasA{symbol}{plotmath}{symbol} [1058] [1059] [1060] [1061] Underfull \vbox (badness 3803) has occurred while \output is active [1062] [1063] Underfull \hbox (badness 1584) in paragraph at lines 5268--5270 []\T1/ptm/m/n/10 For type []\T1/zi4/m/sl/10 "cairo"[]\T1/ptm/m/n/10 , the []\T1 /zi4/m/sl/10 symbolfamily []\T1/ptm/m/n/10 ar-gu-ment can be sup-plied. See Underfull \hbox (badness 1067) in paragraph at lines 5272--5279 \T1/ptm/m/n/10 The lat-ter will only be avail-able if the sys-tem was com-piled with sup- [1064] [1065] [1066] [1067] Underfull \hbox (badness 1377) in paragraph at lines 5574--5579 []\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the color model: cur-rently al-lowed val-ues [1068] [1069] Underfull \hbox (badness 1377) in paragraph at lines 5678--5683 []\T1/ptm/m/n/10 Color mod-els pro-vided for back-wards com-pat-i-bil-ity are [ ]\T1/zi4/m/sl/10 "rgb" []\T1/ptm/m/n/10 (which is RGB+gray) and [1070] Underfull \hbox (badness 7344) in paragraph at lines 5747--5749 []\T1/ptm/m/n/10 Support for Com-puter Mod-ern fonts is based on a con-tri-bu-t ion by Brian D'Urso [1071] [1072] Underfull \hbox (badness 2035) in paragraph at lines 5886--5895 []\T1/ptm/m/n/10 Mappings for a num-ber of stan-dard Adobe fonts (and URW equiv -a-lents) are also pro- Underfull \hbox (badness 10000) in paragraph at lines 5886--5895 \T1/ptm/m/n/10 vided: []\T1/zi4/m/sl/10 "AvantGarde"[]\T1/ptm/m/n/10 , []\T1/zi 4/m/sl/10 "Bookman"[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 "Courier"[]\T1/ptm/m/n/ 10 , []\T1/zi4/m/sl/10 "Helvetica"[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 "Helveti ca-Narrow"[]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 5886--5895 []\T1/zi4/m/sl/10 "NewCenturySchoolbook"[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 "P alatino" []\T1/ptm/m/n/10 and []\T1/zi4/m/sl/10 "Times"[]\T1/ptm/m/n/10 ; []\T1 /zi4/m/sl/10 "URWGothic"[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 "URWBookman"[]\T1/ ptm/m/n/10 , [1073] Underfull \hbox (badness 10000) in paragraph at lines 5953--5958 []\T1/zi4/m/sl/10 BousungEG-Light-GB []\T1/ptm/m/n/10 can be found at [][]$\T1/ zi4/m/sl/10 https : / / ftp . gnu . org / pub / non-[]gnu / [1074] [1075] [1076] Underfull \hbox (badness 1546) in paragraph at lines 6093--6101 []\T1/ptm/m/n/10 arguments []\T1/zi4/m/sl/10 onefile[]\T1/ptm/m/n/10 , []\T1/zi 4/m/sl/10 family[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 title[]\T1/ptm/m/n/10 , [] \T1/zi4/m/sl/10 fonts[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 encoding[]\T1/ptm/m/n /10 , []\T1/zi4/m/sl/10 bg[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 fg[]\T1/ptm/m/n/ 10 , []\T1/zi4/m/sl/10 width[]\T1/ptm/m/n/10 , [1077] [1078] [1079] [1080] [1081] [1082] Underfull \hbox (badness 6625) in paragraph at lines 6537--6540 []\T1/ptm/m/n/10 Murrell, P., Ooms, J., Al-laire, J.J. (2015), "Record-ing and Re-play-ing the Graph- [1083] [1084] Underfull \hbox (badness 10000) in paragraph at lines 6641--6644 []\T1/zi4/m/sl/10 rgb2hsv []\T1/ptm/m/n/10 trans-forms col-ors from RGB space ( red/green/blue) into HSV space [1085] [1086] [1087] [1088] Overfull \hbox (9.73488pt too wide) in paragraph at lines 6878--6878 []\T1/zi4/m/n/9 ## but now, x in [-0.5, 20] -- "too far" ==> "wrap around" pro blem (without \TS1/zi4/m/n/9 '\T1/zi4/m/n/9 continuous=TRUE\TS1/zi4/m/n/9 '\T1/ zi4/m/n/9 ):[] [1089] [1090] [1091] [1092] [1093] [1094] [1095] [1096] [1097] [1098] Underfull \hbox (badness 1189) in paragraph at lines 7507--7509 []\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used . One of [1099] Underfull \hbox (badness 10000) in paragraph at lines 7612--7614 []\T1/zi4/m/sl/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" []\T1/ptm/m/n/10 for C JK lan-guages and [1100] [1101] [1102] [1103] [1104] Underfull \hbox (badness 3780) in paragraph at lines 7927--7933 []\T1/ptm/m/n/10 the font fam-ily to be used. This must be one of []\T1/zi4/m/s l/10 "AvantGarde"[]\T1/ptm/m/n/10 , [1105] [1106] [1107] [1108] [1109] [1110]) (./grid-pkg.tex Chapter 6. [1111] [1112] [1113] [1114] [1115] [1116] [1117] [1118] [1119] Underfull \hbox (badness 2680) in paragraph at lines 551--554 []\T1/ptm/m/n/10 Note that []\T1/zi4/m/sl/10 preDrawDetails []\T1/ptm/m/n/10 an d []\T1/zi4/m/sl/10 postDrawDetails []\T1/ptm/m/n/10 are also called in the cal -cu-la-tion of [1120] [1121] [1122] [1123] [1124] [1125] [1126] [1127] [1128] [1129] [1130] Underfull \hbox (badness 4279) in paragraph at lines 1188--1197 [][][]\T1/ptm/m/n/10 Grid[][][], [][][]\T1/zi4/m/sl/10 pushViewport[][][][]\T1/ ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 popViewport[][][][]\T1/ptm/m/n/10 , [][][]\T 1/zi4/m/sl/10 downViewport[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 seekVi ewport[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 upViewport[][][][]\T1/ptm/ m/n/10 , [][][]\T1/zi4/m/sl/10 unit[][][][]\T1/ptm/m/n/10 , [1131] [1132] [1133] [1134] [1135] [1136] [1137] [1138] [1139] [1140] [1141] [1142] [1143] [1144] [1145] [1146] [1147] [1148] [1149] [1150] [1151] [1152] [1153] [1154] [1155] [1156] [1157] [1158] [1159] [1160] [1161] [1162] Underfull \hbox (badness 10000) in paragraph at lines 3103--3105 []\T1/ptm/m/n/10 A func-tion that re-turns an affine trans-for-ma-tion ma-trix; see [1163] [1164] [1165] [1166] [1167] [1168] [1169] [1170] [1171] [1172] [1173] [1174] [1175] [1176] [1177] [1178] Underfull \vbox (badness 10000) has occurred while \output is active [1179] [1180] [1181] [1182] [1183] [1184] [1185] [1186] [1187] [1188] [1189] [1190] [1191] [1192] Underfull \hbox (badness 1067) in paragraph at lines 4842--4845 []\T1/ptm/m/n/10 Both func-tions cre-ate a seg-ments grob (a graph-i-cal ob-jec t de-scrib-ing seg-ments), but only [1193] [1194] [1195] [1196] [1197] [1198] Underfull \hbox (badness 7256) in paragraph at lines 5193--5195 []\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject s are co-erced by [1199] [1200] [1201] [1202] [1203] [1204] [1205] Underfull \hbox (badness 2142) in paragraph at lines 5647--5651 []\T1/ptm/m/n/10 ob-jects. For []\T1/zi4/m/sl/10 gridGTreeCoords []\T1/ptm/m/n/ 10 a list of ei-ther []\T1/zi4/m/sl/10 "GridGrobCoords" []\T1/ptm/m/n/10 or [1206] [1207] Underfull \hbox (badness 4699) in paragraph at lines 5729--5734 []\T1/ptm/m/n/10 Either a []\T1/zi4/m/sl/10 "GridGrobCoords" []\T1/ptm/m/n/10 o b-ject (a list of lists with com-po-nents []\T1/zi4/m/sl/10 x []\T1/ptm/m/n/10 and []\T1/zi4/m/sl/10 y[]\T1/ptm/m/n/10 ) or a [1208] [1209] [1210] [1211] [1212] [1213] [1214] [1215] [1216] [1217] [1218] [1219] [1220] [1221] [1222] [1223] [1224] [1225] [1226] [1227] [1228] [1229] [1230] [1231] [1232] [1233] [1234] [1235] [1236] [1237] [1238] [1239]) (./methods-pkg.tex [1240] Chapter 7. [1241] [1242] [1243] [1244] [1245] [1246] [1247] [1248] Underfull \vbox (badness 10000) has occurred while \output is active [1249] Underfull \vbox (badness 10000) has occurred while \output is active [1250] [1251] [1252] [1253] [1254] [1255] [1256] [1257] [1258] [1259] Underfull \hbox (badness 2237) in paragraph at lines 1384--1386 []\T1/ptm/m/n/10 The class []\T1/zi4/m/sl/10 "className" []\T1/ptm/m/n/10 ex-te nds []\T1/zi4/m/sl/10 "character" []\T1/ptm/m/n/10 and has a slot []\T1/zi4/m/s l/10 "package"[]\T1/ptm/m/n/10 , also of class [1260] [1261] [1262] [1263] [1264] [1265] [1266] [1267] [1268] Underfull \hbox (badness 10000) in paragraph at lines 1980--1985 []\T1/ptm/m/n/10 The ar-gu-ment to []\T1/zi4/m/sl/10 insertSource []\T1/ptm/m/n /10 can be an ob-ject of class Underfull \hbox (badness 1038) in paragraph at lines 1980--1985 \T1/ptm/m/n/10 file name is passed to []\T1/zi4/m/sl/10 insertSource []\T1/ptm/ m/n/10 it calls []\T1/zi4/m/sl/10 evalSource []\T1/ptm/m/n/10 to ob-tain the [1269] [1270] [1271] Underfull \hbox (badness 2213) in paragraph at lines 2212--2217 []\T1/ptm/m/n/10 To re-strict the search to classes in a par-tic-u-lar pack-age , use []\T1/zi4/m/sl/10 where = [1272] [1273] [1274] [1275] [1276] Underfull \hbox (badness 10000) in paragraph at lines 2572--2575 []\T1/ptm/m/n/10 As you might ex-pect [][][]\T1/zi4/m/sl/10 setGeneric[][][] [] \T1/ptm/m/n/10 and [][][]\T1/zi4/m/sl/10 setGroupGeneric[][][] []\T1/ptm/m/n/10 cre-ate ob-jects of class [1277] [1278] Underfull \hbox (badness 1132) in paragraph at lines 2712--2716 []\T1/ptm/m/n/10 In []\T1/zi4/m/sl/10 getGenerics[]\T1/ptm/m/n/10 , if []\T1/zi 4/m/sl/10 TRUE[]\T1/ptm/m/n/10 , the []\T1/zi4/m/sl/10 package []\T1/ptm/m/n/10 slot of the re-turned re-sult is in [1279] Underfull \hbox (badness 1033) in paragraph at lines 2748--2753 \T1/ptm/m/n/10 In ad-di-tion, []\T1/zi4/m/sl/10 removeGeneric []\T1/ptm/m/n/10 re-moves the func-tion it-self; []\T1/zi4/m/sl/10 removeMethods []\T1/ptm/m/n/1 0 re-stores the [1280] [1281] [1282] [1283] [1284] [1285] [1286] Underfull \hbox (badness 1102) in paragraph at lines 3305--3307 []\T1/zi4/m/sl/10 getPackageName []\T1/ptm/m/n/10 re-turns the character-string name of the pack-age (with-out the ex-tra-ne-ous [1287] [1288] [1289] [1290] [1291] Underfull \hbox (badness 10000) in paragraph at lines 3642--3651 []\T1/ptm/m/n/10 The [1292] [1293] Underfull \hbox (badness 10000) in paragraph at lines 3762--3763 [] \T1/zi4/m/sl/10 Pos <- setClass("Pos", slots = c(latitude = "numeric", longi tude = "numeric", [1294] Underfull \hbox (badness 10000) in paragraph at lines 3846--3847 []\T1/zi4/m/sl/10 Currency <- setClass("Currency", slots = c(unit = "character" ), contains = [1295] [1296] [1297] [1298] [1299] [1300] [1301] [1302] [1303] [1304] Underfull \hbox (badness 1769) in paragraph at lines 4477--4483 []\T1/ptm/m/n/10 class [][][]\T1/zi4/m/sl/10 MethodsList[][][] []\T1/ptm/m/n/10 for the ob-jects defin-ing sets of meth-ods as-so-ci-ated with a par-tic-u-lar Underfull \hbox (badness 1939) in paragraph at lines 4477--4483 []\T1/zi4/m/sl/10 MethodDefinition[]\T1/ptm/m/n/10 , or an ex-ten-sion. Class [ ][][]\T1/zi4/m/sl/10 MethodWithNext[][][] []\T1/ptm/m/n/10 for an ex-ten-sion u sed by [1305] [1306] [1307] [1308] [1309] [1310] [1311] [1312] [1313] [1314] Underfull \vbox (badness 10000) has occurred while \output is active [1315] [1316] [1317] Underfull \hbox (badness 4036) in paragraph at lines 5442--5445 []\T1/ptm/m/n/10 Object of class []\T1/zi4/m/sl/10 "PossibleMethod" []\T1/ptm/m /n/10 the method to use in re-sponse to a [1318] [1319] Underfull \hbox (badness 3803) in paragraph at lines 5517--5519 []\T1/ptm/m/n/10 arguments to spec-ify prop-er-ties of the new ob-ject, to be p assed to [1320] [1321] [1322] Underfull \hbox (badness 1087) in paragraph at lines 5748--5753 []\T1/ptm/m/n/10 In ad-di-tion, the cur-rently avail-able gener-ics with meth-o ds for this class are found (us-ing [1323] [1324] [1325] [1326] [1327] [1328] [1329] [1330] [1331] Underfull \hbox (badness 1675) in paragraph at lines 6455--6461 []\T1/ptm/m/n/10 can be con-verted ex-plic-itly as []\T1/zi4/m/sl/10 externalRe fMethod(f)[]\T1/ptm/m/n/10 , which re-turns an ob-ject of class [1332] [1333] [1334] [1335] Underfull \vbox (badness 10000) has occurred while \output is active [1336] [1337] [1338] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.S4}) has been already used, duplicate ignored \relax l.6976 \aliasA{S4}{S3Part}{S4} [1339] [1340] [1341] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Complex}) has been already used, duplicate ignored \relax l.7232 \aliasA{Complex}{S4groupGeneric}{Complex} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Logic}) h as been already used, duplicate ignored \relax l.7234 \aliasA{Logic}{S4groupGeneric}{Logic} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Math}) ha s been already used, duplicate ignored \relax l.7235 \aliasA{Math}{S4groupGeneric}{Math} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Ops}) has been already used, duplicate ignored \relax l.7237 \aliasA{Ops}{S4groupGeneric}{Ops} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Summary}) has been already used, duplicate ignored \relax l.7238 \aliasA{Summary}{S4groupGeneric}{Summary} [1342] Underfull \hbox (badness 2050) in paragraph at lines 7299--7303 []\T1/ptm/m/n/10 The mem-bers of the group de-fined by a par-tic-u-lar generic can be ob-tained by call-ing [1343] [1344] [1345] Underfull \hbox (badness 1286) in paragraph at lines 7487--7489 []\T1/ptm/m/n/10 for []\T1/zi4/m/sl/10 .selectSuperClasses() []\T1/ptm/m/n/10 o nly, a [][][]\T1/zi4/m/sl/10 list[][][] []\T1/ptm/m/n/10 of class ex-ten-sions, typ-i-cally [1346] [1347] [1348] [1349] [1350] [1351] [1352] [1353] [1354] [1355] [1356] [1357] [1358] [1359] [1360] [1361] [1362] [1363] [1364] [1365] [1366] [1367] [1368] [1369] [1370] [1371] [1372] Underfull \vbox (badness 10000) has occurred while \output is active [1373] [1374] [1375] [1376] [1377] [1378] [1379] [1380] [1381] [1382] [1383] [1384] [1385] [1386] Underfull \hbox (badness 1158) in paragraph at lines 10494--10497 []\T1/ptm/m/n/10 Chambers, John M. (2009) \T1/ptm/m/it/10 Class In-her-i-tance in R [][]$\T1/zi4/m/sl/10 https : / / johnmchambers . su . domains / [1387] Underfull \hbox (badness 1852) in paragraph at lines 10572--10576 []\T1/ptm/m/n/10 Each of the classes ex-tends the cor-re-spond-ing un-traced cl ass, from the data part; e.g., [1388] [1389] [1390] [1391]) (./parallel-pkg.tex [1392] Chapter 8. Underfull \hbox (badness 5490) in paragraph at lines 14--16 []\T1/ptm/m/n/10 There is sup-port for mul-ti-ple RNG streams with the `[]\T1/z i4/m/sl/10 "L\TS1/zi4/m/n/10 '\T1/zi4/m/sl/10 Ecuyer-CMRG"[]\T1/ptm/m/n/10 ' [] []RNG[][][]: see [1393] [1394] [1395] [1396] [1397] Underfull \hbox (badness 1320) in paragraph at lines 300--303 []\T1/ptm/m/n/10 It has meth-ods to do so for Linux, ma-cOS, FreeBSD, OpenBSD, So-laris and Win-dows. [1398] [1399] [1400] [1401] [1402] [1403] [1404] [1405] [1406] [1407] [1408] [1409] [1410] [1411] [1412] [1413] [1414] Underfull \hbox (badness 3386) in paragraph at lines 1400--1403 []\T1/ptm/m/n/10 An in-te-ger vec-tor of length 7 as given by []\T1/zi4/m/sl/10 .Random.seed []\T1/ptm/m/n/10 when the [1415] [1416]) (./splines-pkg.tex Chapter 9. Underfull \hbox (badness 10000) in paragraph at lines 22--24 []\T1/ptm/m/n/10 Douglas M. Bates \T1/zi4/m/sl/10 \T1/ptm /m/n/10 and William N. Ven-ables [1417] [1418] [1419] [1420] [1421] [1422] [1423] [1424] [1425] [1426] [1427] [1428] [1429] [1430] [1431] [1432]) (./stats-pkg.tex Chapter 10. [1433] [1434] [1435] [1436] [1437] [1438] [1439] [1440] [1441] [1442] [1443] [1444] [1445] [1446] Underfull \hbox (badness 1412) in paragraph at lines 901--903 []\T1/ptm/m/n/10 A fit-ted model ob-ject, for ex-am-ple from []\T1/zi4/m/sl/10 lm []\T1/ptm/m/n/10 or []\T1/zi4/m/sl/10 aov[]\T1/ptm/m/n/10 , or a for-mula fo r [1447] [1448] [1449] [1450] [1451] [1452] [1453] [1454] Underfull \hbox (badness 2503) in paragraph at lines 1389--1392 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of []\T1/zi4/m/sl/10 "two.sided"[]\T1/ptm/m/n/10 , [1455] [1456] [1457] [1458] [1459] [1460] [1461] [1462] [1463] [1464] [1465] [1466] [1467] [1468] [1469] [1470] [1471] [1472] [1473] [1474] [1475] [1476] [1477] [1478] [1479] [1480] [1481] [1482] [1483] [1484] [1485] [1486] [1487] [1488] Underfull \hbox (badness 2503) in paragraph at lines 3561--3564 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of []\T1/zi4/m/sl/10 "two.sided"[]\T1/ptm/m/n/10 , [1489] [1490] Package amsmath Warning: Foreign command \atopwithdelims; (amsmath) \frac or \genfrac should be used instead (amsmath) on input line 3674. [1491] [1492] [1493] [1494] [1495] [1496] [1497] [1498] [1499] [1500] [1501] [1502] [1503] [1504] [1505] [1506] [1507] [1508] Underfull \hbox (badness 3989) in paragraph at lines 4820--4827 []\T1/ptm/m/n/10 a nu-meric vec-tor of length 2, equal to say $\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 g[]; g[]\OT1/cmr/m/n/10 )$\T1/ptm/m/n/10 , where $\OML/cmm/m/ it/10 g[] \OT1/cmr/m/n/10 = [1509] [1510] [1511] [1512] [1513] [1514] [1515] [1516] [1517] [1518] Underfull \hbox (badness 2556) in paragraph at lines 5474--5477 []\T1/ptm/m/n/10 character; par-tially matched to []\T1/zi4/m/sl/10 "circular"[ ]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 "open"[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 "filter"[]\T1/ptm/m/n/10 . For [1519] [1520] [1521] [1522] [1523] [1524] [1525] Underfull \hbox (badness 2503) in paragraph at lines 5886--5890 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of []\T1/zi4/m/sl/10 "two.sided"[]\T1/ptm/m/n/10 , [1526] [1527] [1528] [1529] [1530] [1531] [1532] [1533] [1534] [1535] [1536] [1537] [1538] Underfull \hbox (badness 7081) in paragraph at lines 6678--6681 []\T1/ptm/m/n/10 Objects of class []\T1/zi4/m/sl/10 "hclust" []\T1/ptm/m/n/10 c an be con-verted to class []\T1/zi4/m/sl/10 "dendrogram" []\T1/ptm/m/n/10 us-in g method Underfull \hbox (badness 10000) in paragraph at lines 6682--6684 []\T1/zi4/m/sl/10 rev.dendrogram []\T1/ptm/m/n/10 sim-ply re-turns the den-dro- gram []\T1/zi4/m/sl/10 x []\T1/ptm/m/n/10 with re-versed nodes, see also [1539] [1540] [1541] [1542] [1543] [1544] Underfull \vbox (badness 10000) has occurred while \output is active [1545] [1546] [1547] Underfull \vbox (badness 10000) has occurred while \output is active [1548] [1549] [1550] [1551] [1552] Underfull \hbox (badness 10000) in paragraph at lines 7578--7581 []\T1/ptm/m/n/10 optionally, the dis-tance method used; re-sult-ing from [][][] \T1/zi4/m/sl/10 dist[][][]()[]\T1/ptm/m/n/10 , the [1553] [1554] [1555] [1556] [1557] [1558] Underfull \vbox (badness 3803) has occurred while \output is active [1559] [1560] [1561] [1562] [1563] [1564] [1565] [1566] [1567] [1568] [1569] [1570] [1571] [1572] [1573] [1574] Underfull \vbox (badness 3803) has occurred while \output is active [1575] [1576] [1577] [1578] [1579] [1580] Underfull \hbox (badness 2626) in paragraph at lines 9275--9278 []\T1/ptm/m/n/10 Either []\T1/zi4/m/sl/10 "convolution" []\T1/ptm/m/n/10 or []\ T1/zi4/m/sl/10 "recursive" []\T1/ptm/m/n/10 (and can be ab-bre-vi-ated). If [1581] Underfull \hbox (badness 2503) in paragraph at lines 9382--9386 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of []\T1/zi4/m/sl/10 "two.sided"[]\T1/ptm/m/n/10 , [1582] [1583] [1584] [1585] [1586] [1587] [1588] [1589] [1590] [1591] [1592] [1593] [1594] [1595] [1596] [1597] [1598] [1599] [1600] [1601] [1602] Underfull \hbox (badness 4518) in paragraph at lines 10730--10735 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1603] [1604] [1605] [1606] [1607] Underfull \hbox (badness 2142) in paragraph at lines 11092--11095 []\T1/ptm/m/n/10 positive con-ver-gence tol-er-ance $\OML/cmm/m/it/10 ^^O$\T1/p tm/m/n/10 ; the it-er-a-tions con-verge when $\OMS/cmsy/m/n/10 j\OML/cmm/m/it/1 0 dev \OMS/cmsy/m/n/10 ^^@ Underfull \hbox (badness 1253) in paragraph at lines 11111--11114 []\T1/ptm/m/n/10 When []\T1/zi4/m/sl/10 trace []\T1/ptm/m/n/10 is true, calls t o [][][]\T1/zi4/m/sl/10 cat[][][] []\T1/ptm/m/n/10 pro-duce the out-put for eac h IWLS it-er-a-tion. Hence, [1608] Underfull \hbox (badness 1708) in paragraph at lines 11173--11177 []\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter- na-tives are: [1609] [1610] [1611] [1612] [1613] [1614] Underfull \hbox (badness 1694) in paragraph at lines 11569--11572 []\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these de-fault to [1615] [1616] [1617] [1618] [1619] [1620] [1621] [1622] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.hat}) has been already used, duplicate ignored \relax l.12050 \aliasA{hat}{influence.measures}{hat} [1623] [1624] Underfull \hbox (badness 1484) in paragraph at lines 12195--12197 []\T1/ptm/m/n/10 The func-tion []\T1/zi4/m/sl/10 hat() []\T1/ptm/m/n/10 ex-ists mainly for S (ver-sion 2) com-pat-i-bil-ity; we rec-om-mend us-ing [1625] [1626] [1627] [1628] [1629] [1630] [1631] [1632] [1633] [1634] Underfull \hbox (badness 10000) in paragraph at lines 12782--12784 []\T1/ptm/m/n/10 tolerance even-tu-ally passed to [][][]\T1/zi4/m/sl/10 solve.d efault[][][] []\T1/ptm/m/n/10 when []\T1/zi4/m/sl/10 SSinit = [1635] [1636] [1637] [1638] [1639] Underfull \hbox (badness 2894) in paragraph at lines 13124--13128 []\T1/ptm/m/n/10 logical or in-te-ger num-ber, cur-rently only used in the de-f ault method [1640] [1641] [1642] [1643] [1644] [1645] [1646] Underfull \hbox (badness 1496) in paragraph at lines 13552--13558 []\T1/ptm/m/n/10 Gunar Schröer and Di-et-rich Tren-kler (1995). Ex-act and Ran- dom-iza-tion Dis-tri-bu-tions of [1647] [1648] [1649] [1650] [1651] [1652] Underfull \hbox (badness 4518) in paragraph at lines 13955--13960 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1653] [1654] [1655] [1656] [1657] [1658] [1659] [1660] [1661] [1662] Underfull \hbox (badness 4518) in paragraph at lines 14617--14622 []\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co -ercible by [1663] [1664] [1665] Underfull \hbox (badness 6412) in paragraph at lines 14757--14761 []\T1/ptm/m/n/10 Only for the (de-fault) case []\T1/zi4/m/sl/10 (surface = "int erpolate", statistics = Underfull \hbox (badness 1199) in paragraph at lines 14764--14766 []\T1/ptm/m/n/10 the num-ber of it-er-a-tions used in ro-bust fit-ting, i.e. on ly if []\T1/zi4/m/sl/10 family []\T1/ptm/m/n/10 is [1666] [1667] [1668] [1669] [1670] [1671] [1672] [1673] [1674] [1675] [1676] [1677] [1678] [1679] [1680] [1681] [1682] [1683] Underfull \hbox (badness 2503) in paragraph at lines 15841--15845 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of []\T1/zi4/m/sl/10 "two.sided"[]\T1/ptm/m/n/10 , [1684] [1685] [1686] [1687] [1688] [1689] [1690] [1691] Underfull \hbox (badness 10000) in paragraph at lines 16354--16360 []\T1/zi4/m/sl/10 model.extract(m, "offset") []\T1/ptm/m/n/10 and []\T1/zi4/m/s l/10 model.extract(m, "response") []\T1/ptm/m/n/10 are equiv-a-lent to Underfull \hbox (badness 1867) in paragraph at lines 16354--16360 []\T1/zi4/m/sl/10 model.offset(m) []\T1/ptm/m/n/10 and []\T1/zi4/m/sl/10 model. response(m) []\T1/ptm/m/n/10 re-spec-tively. []\T1/zi4/m/sl/10 model.offset []\ T1/ptm/m/n/10 sums any terms [1692] [1693] [1694] [1695] [1696] [1697] [1698] [1699] [1700] [1701] [1702] [1703] [1704] [1705] [1706] [1707] [1708] [1709] [1710] [1711] [1712] [1713] [1714] [1715] [1716] [1717] [1718] Underfull \hbox (badness 1158) in paragraph at lines 18012--18015 []\T1/ptm/m/n/10 the ex-pres-sion that was passed to []\T1/zi4/m/sl/10 nls []\T 1/ptm/m/n/10 as the data ar-gu-ment. The ac- [1719] [1720] Underfull \vbox (badness 10000) has occurred while \output is active [1721] Underfull \vbox (badness 10000) has occurred while \output is active [1722] [1723] [1724] [1725] [1726] [1727] [1728] [1729] [1730] [1731] [1732] [1733] [1734] [1735] Underfull \hbox (badness 1377) in paragraph at lines 19055--19060 []\T1/ptm/m/n/10 A vec-tor of scal-ing val-ues for the pa-ram-e-ters. Op-ti-miz a-tion is per-formed on Underfull \hbox (badness 1735) in paragraph at lines 19060--19063 []\T1/ptm/m/n/10 A vec-tor of step sizes for the finite-difference ap-prox-i-ma -tion to the gra-di-ent, on Underfull \hbox (badness 2343) in paragraph at lines 19073--19077 []\T1/ptm/m/n/10 Relative con-ver-gence tol-er-ance. The al-go-rithm stops if i t is un-able to re-duce Underfull \hbox (badness 3471) in paragraph at lines 19073--19077 \T1/ptm/m/n/10 the value by a fac-tor of []\T1/zi4/m/sl/10 reltol * (abs(val) + reltol) []\T1/ptm/m/n/10 at a step. De-faults to Underfull \hbox (badness 2662) in paragraph at lines 19081--19085 []\T1/ptm/m/n/10 The fre-quency of re-ports for the []\T1/zi4/m/sl/10 "BFGS"[]\ T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 "L-BFGS-B" []\T1/ptm/m/n/10 and []\T1/zi4/m/s l/10 "SANN" []\T1/ptm/m/n/10 meth-ods if [1736] [1737] [1738] Underfull \vbox (badness 10000) has occurred while \output is active [1739] Overfull \hbox (15.73795pt too wide) in paragraph at lines 19306--19306 []\T1/zi4/m/n/9 ## 1-D minimization: "Brent" or optimize() being preferred.. b ut NM may be ok and "unavoidable",[] Overfull \hbox (3.75941pt too wide) in paragraph at lines 19309--19309 []\T1/zi4/m/n/9 system.time(ro <- optim(1, function(x) (x-pi)^2, control=list( warn.1d.NelderMead = FALSE)))[] [1740] [1741] [1742] [1743] [1744] [1745] [1746] Underfull \hbox (badness 1337) in paragraph at lines 19771--19774 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1747] [1748] [1749] [1750] [1751] [1752] [1753] [1754] [1755] Underfull \hbox (badness 10000) in paragraph at lines 20240--20246 \T1/zi4/m/sl/10 legend = "Cook\TS1/zi4/m/n/10 '\T1/zi4/m/sl/10 s distance", lty = cook.lty, col = cook.col, text.col [1756] [1757] [1758] [1759] [1760] [1761] [1762] Underfull \hbox (badness 1194) in paragraph at lines 20667--20670 []\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting of the con-fi-dence [1763] [1764] [1765] [1766] [1767] [1768] Underfull \hbox (badness 2503) in paragraph at lines 21045--21048 []\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of []\T1/zi4/m/sl/10 "two.sided"[]\T1/ptm/m/n/10 , Underfull \hbox (badness 3919) in paragraph at lines 21072--21074 []\T1/ptm/m/n/10 the char-ac-ter string []\T1/zi4/m/sl/10 "Exact Poisson test" []\T1/ptm/m/n/10 or []\T1/zi4/m/sl/10 "Comparison of Poisson [1769] [1770] [1771] [1772] [1773] [1774] [1775] [1776] [1777] [1778] [1779] [1780] [1781] [1782] [1783] [1784] [1785] [1786] Underfull \hbox (badness 10000) in paragraph at lines 22150--22156 []\T1/ptm/m/n/10 For time-series pre-dic-tion, [][][]\T1/zi4/m/sl/10 predict.ar [][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 predict.Arima[][][][]\T1/ptm/m/n /10 , [][][]\T1/zi4/m/sl/10 predict.arima0[][][][]\T1/ptm/m/n/10 , [1787] [1788] [1789] [1790] [1791] [1792] [1793] [1794] [1795] [1796] [1797] [1798] [1799] [1800] [1801] [1802] [1803] [1804] [1805] [1806] [1807] [1808] [1809] [1810] [1811] Underfull \hbox (badness 1337) in paragraph at lines 23626--23632 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1812] [1813] [1814] [1815] [1816] [1817] [1818] [1819] Underfull \hbox (badness 1436) in paragraph at lines 24116--24119 \T1/ptm/m/n/10 per-cent-ages. In \T1/phv/m/n/10 R \T1/ptm/m/n/10 ver-sions up t o 4.0.x, this had been set to []\T1/zi4/m/sl/10 max(2, [1820] Underfull \hbox (badness 10000) in paragraph at lines 24254--24255 []\T1/ptm/m/n/10 Wikipedia: [][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . o rg / wiki / Quantile # Estimating _ quantiles _ from _ a _ [1821] [1822] [1823] [1824] [1825] [1826] [1827] [1828] [1829] [1830] [1831] [1832] [1833] [1834] [1835] [1836] Underfull \hbox (badness 1824) in paragraph at lines 25224--25230 []\T1/ptm/m/n/10 Here, all the NAs in []\T1/zi4/m/sl/10 x []\T1/ptm/m/n/10 are first re-placed by al-ter- Underfull \hbox (badness 1033) in paragraph at lines 25224--25230 \T1/ptm/m/n/10 nat-ing $\OMS/cmsy/m/n/10 ^^F\OML/cmm/m/it/10 B$ \T1/ptm/m/n/10 where $\OML/cmm/m/it/10 B$ \T1/ptm/m/n/10 is a ``Big'' num-ber (with $\OT1/cmr/ m/n/10 2\OML/cmm/m/it/10 B < M\OMS/cmsy/m/n/10 ^^C$\T1/ptm/m/n/10 , where [1837] Underfull \hbox (badness 10000) in paragraph at lines 25245--25248 []\T1/ptm/m/n/10 Apart from the end val-ues, the re-sult []\T1/zi4/m/sl/10 y = runmed(x, k) []\T1/ptm/m/n/10 sim-ply has []\T1/zi4/m/sl/10 y[j] = [1838] [1839] [1840] [1841] [1842] [1843] [1844] [1845] [1846] Underfull \hbox (badness 2165) in paragraph at lines 25820--25825 []\T1/ptm/m/n/10 Each of the fol-low-ing are []\T1/zi4/m/sl/10 "selfStart" []\T 1/ptm/m/n/10 mod-els (with ex-am-ples) [][][]\T1/zi4/m/sl/10 SSasymp[][][][]\T1 /ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 SSasympOff[][][][]\T1/ptm/m/n/10 , [1847] [1848] [1849] [1850] Underfull \hbox (badness 1867) in paragraph at lines 26030--26032 []\T1/ptm/m/n/10 potentially fur-ther ar-gu-ments passed to and from meth-ods. Passed to Underfull \hbox (badness 10000) in paragraph at lines 26046--26050 []\T1/ptm/m/n/10 where []\T1/zi4/m/sl/10 NN <- [][]nobs[][][](object, use.fallb ack = use.fallback) []\T1/ptm/m/n/10 and []\T1/zi4/m/sl/10 PP <- [1851] [1852] [1853] [1854] [1855] [1856] [1857] [1858] [1859] [1860] [1861] [1862] [1863] [1864] [1865] [1866] [1867] [1868] [1869] [1870] [1871] [1872] [1873] [1874] [1875] Underfull \vbox (badness 10000) has occurred while \output is active [1876] [1877] Underfull \hbox (badness 3514) in paragraph at lines 27698--27703 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/zi4/m/sl/10 inp ut[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1878] [1879] [1880] [1881] Overfull \hbox (2.23795pt too wide) in paragraph at lines 27932--27932 [] \T1/zi4/m/n/9 quote({f(t[0.5]) == frac(phi[1],2)}~{} %=>% {}~~{t[0.5] == frac(log(2), e^{phi[2]})}),[] Underfull \hbox (badness 3514) in paragraph at lines 27968--27974 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/zi4/m/sl/10 inp ut[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1882] Overfull \hbox (14.22568pt too wide) in paragraph at lines 28028--28028 [] \T1/zi4/m/n/9 control = list(scaleOffset=1, printEval=TRUE, tol= 1e-11, nDcentral=TRUE), trace=TRUE)[] [1883] [1884] [1885] [1886] Underfull \hbox (badness 3514) in paragraph at lines 28201--28206 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/zi4/m/sl/10 inp ut[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1887] Underfull \hbox (badness 3514) in paragraph at lines 28288--28293 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/zi4/m/sl/10 inp ut[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1888] Underfull \hbox (badness 3514) in paragraph at lines 28353--28358 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/zi4/m/sl/10 inp ut[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1889] [1890] Underfull \hbox (badness 3514) in paragraph at lines 28447--28452 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/zi4/m/sl/10 inp ut[]\T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1891] [1892] Underfull \hbox (badness 6691) in paragraph at lines 28539--28544 []\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as []\T1/zi4/m/sl/10 x[] \T1/ptm/m/n/10 . It is the value of the ex-pres-sion [1893] [1894] [1895] [1896] [1897] [1898] [1899] [1900] Underfull \hbox (badness 4024) in paragraph at lines 29026--29029 []\T1/ptm/m/n/10 the span (in lags) of the loess win-dow for trend ex-trac-tion , which [1901] [1902] [1903] [1904] [1905] [1906] [1907] [1908] [1909] [1910] Underfull \hbox (badness 5431) in paragraph at lines 29629--29631 []\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above []\T1 /zi4/m/sl/10 cov.unscaled[]\T1/ptm/m/n/10 , if [1911] [1912] [1913] Underfull \hbox (badness 5431) in paragraph at lines 29839--29842 []\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above []\T1 /zi4/m/sl/10 cov.unscaled[]\T1/ptm/m/n/10 , if [1914] [1915] [1916] [1917] [1918] [1919] Underfull \hbox (badness 1337) in paragraph at lines 30154--30158 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1920] [1921] Underfull \hbox (badness 1127) in paragraph at lines 30291--30294 []\T1/ptm/m/n/10 non-centrality pa-ram-e-ter $\OML/cmm/m/it/10 ^^N$\T1/ptm/m/n/ 10 ; cur-rently ex-cept for []\T1/zi4/m/sl/10 rt()[]\T1/ptm/m/n/10 , ac-cu-rate only for [1922] [1923] [1924] Underfull \hbox (badness 1616) in paragraph at lines 30497--30500 []\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial resid-u-als, when [1925] [1926] [1927] [1928] [1929] [1930] [1931] [1932] [1933] [1934] [1935] [1936] [1937] [1938] [1939] [1940] [1941] [1942] [1943] [1944] [1945] Underfull \hbox (badness 3557) in paragraph at lines 31724--31728 []\T1/ptm/m/n/10 Setting []\T1/zi4/m/sl/10 extendInt []\T1/ptm/m/n/10 to a non- []\T1/zi4/m/sl/10 "no" []\T1/ptm/m/n/10 string, means search-ing for the cor-re ct []\T1/zi4/m/sl/10 interval = [1946] [1947] [1948] Underfull \vbox (badness 10000) has occurred while \output is active [1949] [1950] [1951] Underfull \hbox (badness 1337) in paragraph at lines 32091--32095 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1952] [1953] [1954] [1955] [1956] [1957] [1958] [1959] [1960] Underfull \hbox (badness 1337) in paragraph at lines 32619--32623 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth- e-sis, must be one of [1961] [1962] [1963] Overfull \hbox (0.71648pt too wide) in paragraph at lines 32827--32827 []\T1/zi4/m/n/9 wilcox.test( 4:2, 3:1, paired=TRUE) # Warning: canno t compute exact p-value with ties[] [1964] [1965] [1966] Overfull \hbox (19.71954pt too wide) in paragraph at lines 32988--32988 [] \T1/zi4/m/sl/10 frequency = NULL, deltat = NULL, extend = FALSE, ts.ep s = getOption("ts.eps"), ...)[] [1967] [1968] [1969] [1970] [1971]) (./stats4-pkg.tex [1972] Chapter 11. [1973] [1974] [1975] Underfull \vbox (badness 10000) has occurred while \output is active [1976] Underfull \vbox (badness 10000) has occurred while \output is active [1977] [1978] [1979] [1980] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.show.Rdas h.methods}) has been already used, duplicate ignored \relax l.503 ...Package \pkg{stats4}}{show.Rdash.methods} [1981] [1982] [1983]) (./tcltk-pkg.tex [1984] Chapter 12. [1985] [1986] [1987] [1988] [1989] [1990] [1991] Underfull \vbox (badness 10000) has occurred while \output is active [1992] Underfull \vbox (badness 10000) has occurred while \output is active [1993] Underfull \hbox (badness 1546) in paragraph at lines 672--679 []\T1/zi4/m/sl/10 tcl []\T1/ptm/m/n/10 pro-vides a generic in-ter-face to call- ing any Tk or Tcl com-mand by sim-ply run-ning [1994] [1995] [1996] [1997] [1998] Underfull \vbox (badness 10000) has occurred while \output is active [1999] [2000] [2001] [2002] [2003] [2004] [2005] [2006]) (./tools-pkg.tex Chapter 13. [2007] LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined (Font) using `T1/zi4/m/n' instead on input line 72. [2008] Underfull \hbox (badness 3039) in paragraph at lines 167--170 []\T1/zi4/m/sl/10 assertWarning() []\T1/ptm/m/n/10 as-serts that a warn-ing wil l be sig-nalled, but \T1/ptm/m/it/10 not \T1/ptm/m/n/10 an er-ror, whereas [2009] [2010] Underfull \hbox (badness 1308) in paragraph at lines 288--301 []\T1/ptm/m/n/10 At a min-i-mum, the en-vi-ron-ment should con-tain rou-tines t o ren-der each of the 12 types Underfull \hbox (badness 4967) in paragraph at lines 288--301 \T1/ptm/m/n/10 of bib-li-o-graphic en-try sup-ported by [][][]\T1/zi4/m/sl/10 b ibentry[][][] []\T1/ptm/m/n/10 as well as sev-eral other rou-tines de- Underfull \hbox (badness 10000) in paragraph at lines 288--301 []\T1/zi4/m/sl/10 formatIncollection[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 format InProceedings[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 formatManual[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 formatMastersthesis[]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 288--301 []\T1/zi4/m/sl/10 formatMisc[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 formatPhdthesi s[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 formatProceedings[]\T1/ptm/m/n/10 , []\T1 /zi4/m/sl/10 formatTechreport []\T1/ptm/m/n/10 and [2011] [2012] Underfull \hbox (badness 3039) in paragraph at lines 392--394 []\T1/zi4/m/sl/10 NULL []\T1/ptm/m/n/10 or char-ac-ter; name of vi-gnette en-gi ne to use. Over-rides any [2013] Underfull \hbox (badness 1142) in paragraph at lines 464--468 \T1/ptm/m/n/10 If given, vi-gnette source files are by de-fault looked for in s ub-di-rec-tory [2014] [2015] [2016] [2017] [2018] [2019] [2020] [2021] [2022] [2023] [2024] [2025] [2026] Underfull \hbox (badness 1014) in paragraph at lines 1220--1222 []\T1/ptm/m/n/10 a log-i-cal in-di-cat-ing whether to also sum-ma-rize the re-v erse de-pen-den-cies Underfull \hbox (badness 7238) in paragraph at lines 1226--1228 []\T1/ptm/m/n/10 a char-ac-ter string giv-ing the path to the di-rec-tory of a pre-vi-ous [2027] Underfull \hbox (badness 10000) in paragraph at lines 1263--1266 []\T1/ptm/m/n/10 Results and tim-ings can con-ve-niently be sum-ma-rized us-ing Overfull \hbox (15.52087pt too wide) in paragraph at lines 1263--1266 []\T1/zi4/m/sl/10 summarize_check_packages_in_dir_results []\T1/ptm/m/n/10 and []\T1/zi4/m/sl/10 summarize_check_packages_in_dir_timings[]\T1/ptm/m/n/10 , [2028] [2029] [2030] [2031] [2032] [2033] Underfull \hbox (badness 10000) in paragraph at lines 1637--1640 []\T1/ptm/m/n/10 Internal func-tions []\T1/zi4/m/sl/10 CRAN_aliases_db[]\T1/ptm /m/n/10 , []\T1/zi4/m/sl/10 CRAN_archive_db[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 CRAN_current_db []\T1/ptm/m/n/10 and [2034] [2035] Underfull \hbox (badness 4096) in paragraph at lines 1756--1764 \T1/zi4/m/sl/10 "Imports", "LinkingTo", "Suggests", "Enhances")[]\T1/ptm/m/n/10 . Char-ac-ter string Underfull \hbox (badness 1082) in paragraph at lines 1766--1768 []\T1/ptm/m/n/10 a char-ac-ter vec-tor of \T1/phv/m/n/10 R \T1/ptm/m/n/10 li-br ary trees, or []\T1/zi4/m/sl/10 NULL []\T1/ptm/m/n/10 for all known trees (see [2036] [2037] [2038] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.GSC}) has been already used, duplicate ignored \relax l.1967 \aliasA{GSC}{find\_gs\_cmd}{GSC} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.R.Rul.GSC MD}) has been already used, duplicate ignored \relax l.1968 ...sA{R\_GSCMD}{find\_gs\_cmd}{R.Rul.GSCMD} [2039] [2040] [2041] [2042] [2043] [2044] [2045] [2046] Underfull \hbox (badness 3386) in paragraph at lines 2442--2445 []\T1/ptm/m/n/10 The de-fault method of []\T1/zi4/m/sl/10 as.Rconcordance []\T1 /ptm/m/n/10 searches for strings match-ing the pat-tern of [2047] [2048] Underfull \hbox (badness 4096) in paragraph at lines 2582--2590 \T1/zi4/m/sl/10 "Imports", "LinkingTo", "Suggests", "Enhances")[]\T1/ptm/m/n/10 . Char-ac-ter string [2049] [2050] [2051] [2052] [2053] [2054] [2055] [2056] [2057] [2058] [2059] [2060] [2061] [2062] [2063] Underfull \hbox (badness 1424) in paragraph at lines 3516--3518 []\T1/zi4/m/sl/10 NULL []\T1/ptm/m/n/10 or a named (by top-ics) char-ac-ter vec -tor of links, as re-turned by [2064] [2065] [2066] [2067] [2068] [2069] [2070] [2071] [2072] [2073] [2074] Underfull \hbox (badness 10000) in paragraph at lines 4232--4234 []\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run , [2075] [2076] [2077] Underfull \hbox (badness 10000) in paragraph at lines 4388--4391 []\T1/ptm/m/n/10 Where sup-ported ([]\T1/zi4/m/sl/10 texi2dvi []\T1/ptm/m/n/10 5.0 and later; []\T1/zi4/m/sl/10 texify.exe []\T1/ptm/m/n/10 from MiK-TeX), op- tion [2078] [2079] [2080] [2081] [2082] Underfull \hbox (badness 1796) in paragraph at lines 4745--4750 []\T1/ptm/m/n/10 Users should ex-pect sig-nif-i-cantly smaller speedups over [] \T1/zi4/m/sl/10 write_PACKAGES []\T1/ptm/m/n/10 in the []\T1/zi4/m/sl/10 type = = [2083] [2084] Underfull \hbox (badness 1838) in paragraph at lines 4831--4837 []\T1/ptm/m/n/10 The re-main-ing steps are done only if file `\T1/zi4/m/sl/10 p o/\T1/ptm/m/sl/10 pkgname\T1/zi4/m/sl/10 .pot\T1/ptm/m/n/10 ' al-ready ex-ists. The Underfull \hbox (badness 10000) in paragraph at lines 4831--4837 \T1/ptm/m/n/10 `\T1/zi4/m/sl/10 src/*.{c,cc,cpp,m,mm}\T1/ptm/m/n/10 ' files in the pack-age are ex-am-ined to cre-ate a file [2085] [2086] [2087] [2088] Underfull \hbox (badness 2197) in paragraph at lines 5112--5122 []\T1/ptm/m/n/10 The de-fault cor-re-sponds to the fields needed by [][][]\T1/z i4/m/sl/10 available.packages[][][][]\T1/ptm/m/n/10 : [2089] Underfull \hbox (badness 1571) in paragraph at lines 5178--5182 []\T1/ptm/m/n/10 For a re-mote repos-i-tory there is a trade-off be-tween down- load speed and time spent by [2090] [2091] [2092] [2093]) (./utils-pkg.tex [2094] Chapter 14. [2095] Underfull \hbox (badness 2556) in paragraph at lines 47--52 []\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `[] \T1/zi4/m/sl/10 insertions[]\T1/ptm/m/n/10 ', [2096] [2097] [2098] [2099] [2100] [2101] [2102] [2103] [2104] [2105] Underfull \hbox (badness 10000) in paragraph at lines 728--734 []\T1/ptm/m/n/10 Functions []\T1/zi4/m/sl/10 aspell_package_Rd_files[]\T1/ptm/m /n/10 , []\T1/zi4/m/sl/10 aspell_package_vignettes[]\T1/ptm/m/n/10 , Underfull \hbox (badness 3343) in paragraph at lines 728--734 []\T1/zi4/m/sl/10 aspell_package_R_files []\T1/ptm/m/n/10 and []\T1/zi4/m/sl/10 aspell_package_C_files []\T1/ptm/m/n/10 per-form spell check-ing on the [2106] [2107] [2108] Underfull \hbox (badness 3861) in paragraph at lines 934--939 []\T1/ptm/m/n/10 Where pro-vided by the repos-i-tory, fields []\T1/zi4/m/sl/10 "OS_type"[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 "License"[]\T1/ptm/m/n/10 , []\T1 /zi4/m/sl/10 "License_is_FOSS"[]\T1/ptm/m/n/10 , [2109] [2110] [2111] Underfull \hbox (badness 10000) in paragraph at lines 1139--1141 []\T1/ptm/m/n/10 logical in-di-cat-ing if biben-tries should be sorted, us-ing [2112] [2113] [2114] Underfull \vbox (badness 10000) has occurred while \output is active [2115] [2116] [2117] [2118] [2119] Underfull \hbox (badness 1371) in paragraph at lines 1666--1668 []\T1/ptm/m/n/10 additional named ar-gu-ments such as []\T1/zi4/m/sl/10 method []\T1/ptm/m/n/10 and []\T1/zi4/m/sl/10 ccaddress []\T1/ptm/m/n/10 to pass to [2120] [2121] [2122] [2123] [2124] [2125] [2126] [2127] [2128] [2129] [2130] [2131] Underfull \hbox (badness 2057) in paragraph at lines 2386--2388 []\T1/ptm/m/n/10 None for []\T1/zi4/m/sl/10 chooseCRANmirror()[]\T1/ptm/m/n/10 , this func-tion is in-voked for its side ef-fect of up-dat-ing [2132] Underfull \hbox (badness 2150) in paragraph at lines 2461--2468 []\T1/ptm/m/n/10 If the ob-ject re-turned by []\T1/zi4/m/sl/10 citation() []\T1 /ptm/m/n/10 con-tains only one ref-er-ence, the as-so-ci-ated print Underfull \hbox (badness 1400) in paragraph at lines 2461--2468 \T1/ptm/m/n/10 method shows both a text ver-sion and a Bib-TeX en-try for it. I f a pack-age has more [2133] [2134] [2135] Underfull \vbox (badness 3803) has occurred while \output is active [2136] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.clipboard }) has been already used, duplicate ignored \relax l.2738 ... the Clipboard in MS Windows}{clipboard} [2137] [2138] [2139] [2140] [2141] [2142] [2143] [2144] [2145] [2146] [2147] [2148] [2149] [2150] [2151] [2152] [2153] [2154] [2155] [2156] [2157] Underfull \hbox (badness 6842) in paragraph at lines 4048--4053 []\T1/ptm/m/n/10 Support for method []\T1/zi4/m/sl/10 "libcurl" []\T1/ptm/m/n/1 0 was op-tional on Win-dows prior to \T1/phv/m/n/10 R \T1/ptm/m/n/10 4.2.0: use [2158] Underfull \hbox (badness 1430) in paragraph at lines 4111--4115 []\T1/ptm/m/n/10 The level of de-tail pro-vided dur-ing trans-fer can be set by the []\T1/zi4/m/sl/10 quiet []\T1/ptm/m/n/10 ar-gu-ment and the [2159] Underfull \hbox (badness 1184) in paragraph at lines 4182--4198 []\T1/ptm/m/n/10 On Win-dows with []\T1/zi4/m/sl/10 method = "libcurl"[]\T1/ptm /m/n/10 , the CA root cer-tifi-cates are pro-vided by the OS Underfull \hbox (badness 1019) in paragraph at lines 4182--4198 \T1/ptm/m/n/10 con-tain-ing `[]\T1/zi4/m/sl/10 "Schannel"[]\T1/ptm/m/n/10 '. If it does not, for ver-i-fi-ca-tion to be on the en-vi-ron-ment vari- Underfull \hbox (badness 1668) in paragraph at lines 4182--4198 \T1/ptm/m/n/10 able []\T1/zi4/m/sl/10 CURL_CA_BUNDLE []\T1/ptm/m/n/10 must be s et to a path to a cer-tifi-cate bun-dle file, usu-ally named [2160] [2161] Underfull \hbox (badness 10000) in paragraph at lines 4332--4334 []\T1/ptm/m/n/10 additional ar-gu-ments to be passed to [][][]\T1/zi4/m/sl/10 d ownload.file[][][] []\T1/ptm/m/n/10 and [2162] [2163] [2164] [2165] [2166] [2167] [2168] [2169] [2170] [2171] [2172] [2173] [2174] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.format}) has been already used, duplicate ignored \relax l.5111 ...mat Unordered and Ordered Lists}{format} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.format.1} ) has been already used, duplicate ignored \relax l.5111 ...mat Unordered and Ordered Lists}{format} [2175] [2176] [2177] [2178] [2179] [2180] [2181] [2182] Underfull \hbox (badness 1622) in paragraph at lines 5634--5638 []\T1/ptm/m/n/10 This func-tion will search for Win-dows han-dles, for pass-ing to ex-ter-nal GUIs or to the [2183] [2184] [2185] [2186] [2187] [2188] Underfull \hbox (badness 1448) in paragraph at lines 6019--6024 []\T1/ptm/m/n/10 External pointer ob-jects are com-pared as ref-er-ence ob-ject s, cor-re-spond-ing to call-ing [2189] [2190] [2191] [2192] [2193] [2194] [2195] [2196] Underfull \hbox (badness 1371) in paragraph at lines 6567--6569 []\T1/ptm/m/n/10 additional named ar-gu-ments such as []\T1/zi4/m/sl/10 method []\T1/ptm/m/n/10 and []\T1/zi4/m/sl/10 ccaddress []\T1/ptm/m/n/10 to pass to [2197] [2198] Underfull \hbox (badness 1502) in paragraph at lines 6656--6662 []\T1/ptm/m/n/10 a char-ac-ter string to be matched in the help page `key-words '. `Key- Underfull \hbox (badness 2103) in paragraph at lines 6656--6662 \T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are listed in file [2199] [2200] Underfull \hbox (badness 10000) in paragraph at lines 6833--6842 []\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de x, Underfull \hbox (badness 3354) in paragraph at lines 6833--6842 \T1/ptm/m/n/10 `\T1/ptm/m/sl/10 R_DOC_DIR\T1/zi4/m/sl/10 /html/packages.html\T1 /ptm/m/n/10 ', which can be re-made by [][][]\T1/zi4/m/sl/10 make.packages.html [][][]()[]\T1/ptm/m/n/10 . [2201] Underfull \hbox (badness 2150) in paragraph at lines 6895--6898 []\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion to search. See [2202] [2203] Underfull \hbox (badness 3118) in paragraph at lines 7034--7036 []\T1/ptm/m/n/10 For de-tails of the lock-ing which is done, see the sec-tion ` Lock-ing' in the help for [2204] [2205] [2206] Underfull \hbox (badness 1325) in paragraph at lines 7213--7217 []\T1/ptm/m/n/10 a ma-trix as re-turned by [][][]\T1/zi4/m/sl/10 available.pack ages[][][] []\T1/ptm/m/n/10 list-ing pack-ages avail-able [2207] Underfull \hbox (badness 1424) in paragraph at lines 7306--7309 []\T1/ptm/m/n/10 logical: if true, re-duce the amount of out-put. This is \T1/p tm/m/it/10 not \T1/ptm/m/n/10 passed to [2208] Underfull \hbox (badness 3219) in paragraph at lines 7378--7385 []\T1/ptm/m/n/10 An al-ter-na-tive (and the cur-rent de-fault) is []\T1/zi4/m/s l/10 "both" []\T1/ptm/m/n/10 which means `use bi-nary if avail- Underfull \hbox (badness 5175) in paragraph at lines 7378--7385 \T1/ptm/m/n/10 able and cur-rent, oth-er-wise try source'. The ac-tion if there are source pack-ages Underfull \hbox (badness 1342) in paragraph at lines 7378--7385 \T1/ptm/m/n/10 which are pre-ferred but may con-tain code which needs to be com -piled is con-trolled by Underfull \hbox (badness 1596) in paragraph at lines 7378--7385 [][][]\T1/zi4/m/sl/10 getOption[][][]("install.packages.compile.from.source")[] \T1/ptm/m/n/10 . []\T1/zi4/m/sl/10 type = "both" []\T1/ptm/m/n/10 will be silen tly Underfull \hbox (badness 2932) in paragraph at lines 7386--7389 []\T1/ptm/m/n/10 Using pack-ages with []\T1/zi4/m/sl/10 type = "source" []\T1/p tm/m/n/10 al-ways works pro-vided the pack-age con-tains no [2209] [2210] Underfull \hbox (badness 1024) in paragraph at lines 7515--7518 []\T1/ptm/m/n/10 For other repos-i-to-ries, us-ing []\T1/zi4/m/sl/10 available. packages(filters = "OS_type")[\T1/ptm/m/sl/10 pkgname\T1/zi4/m/sl/10 , ] []\T1/ ptm/m/n/10 will Underfull \hbox (badness 10000) in paragraph at lines 7548--7553 [][][]\T1/zi4/m/sl/10 update.packages[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/s l/10 available.packages[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 download. packages[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 installed.packages[][][] []\T1/ptm/m/n/10 , [2211] Underfull \hbox (badness 5133) in paragraph at lines 7607--7611 []\T1/ptm/m/n/10 a char-ac-ter vec-tor giv-ing the fields to ex-tract from each pack-age's [2212] [2213] [2214] [2215] [2216] [2217] [2218] [2219] [2220] [2221] [2222] Underfull \hbox (badness 10000) in paragraph at lines 8271--8273 []\T1/ptm/m/n/10 typically the re-sult of []\T1/zi4/m/sl/10 methods(..)[]\T1/pt m/m/n/10 , an \T1/phv/m/n/10 R \T1/ptm/m/n/10 ob-ject of S3 class [2223] [2224] [2225] [2226] [2227] [2228] [2229] [2230] [2231] [2232] [2233] [2234] [2235] Underfull \hbox (badness 2310) in paragraph at lines 9058--9063 []\T1/ptm/m/n/10 If a `\T1/zi4/m/sl/10 DESCRIPTION\T1/ptm/m/n/10 ' file for the given pack-age is found and can suc-cess-fully be read, [2236] [2237] [2238] [2239] [2240] [2241] [2242] [2243] [2244] Underfull \hbox (badness 1248) in paragraph at lines 9629--9633 []\T1/zi4/m/sl/10 R CMD build []\T1/ptm/m/n/10 builds \T1/phv/m/n/10 R \T1/ptm/ m/n/10 source tar-balls. The name(s) of the pack-ages are taken from the [2245] Underfull \hbox (badness 1789) in paragraph at lines 9707--9709 []\T1/ptm/m/n/10 See `Writ-ing R Ex-ten-sions' and the `R for Win-dows FAQ' for more dis-cus-sion of the [2246] [2247] [2248] [2249] Underfull \hbox (badness 2600) in paragraph at lines 9931--9934 []\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the name of the help topic; de-faults to [2250] [2251] [2252] [2253] [2254] [2255] [2256] [2257] [2258] Underfull \hbox (badness 1097) in paragraph at lines 10568--10571 []\T1/ptm/m/n/10 The name []\T1/zi4/m/sl/10 "clipboard" []\T1/ptm/m/n/10 may al so be used on Win-dows, in which case [2259] [2260] Underfull \hbox (badness 3000) in paragraph at lines 10704--10709 [][][]\T1/zi4/m/sl/10 scan[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 type.c onvert[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 read.fwf[][][] []\T1/ptm/m /n/10 for read-ing \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ixed \T1/ptm/m/it/10 w\T1/pt m/m/n/10 idth \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ormatted in-put; [][][]\T1/zi4/m/ sl/10 read.table[][][][]\T1/ptm/m/n/10 ; [2261] [2262] [2263] [2264] [2265] [2266] [2267] [2268] [2269] Underfull \hbox (badness 2134) in paragraph at lines 11299--11304 [][][]\T1/zi4/m/sl/10 scan[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 type.c onvert[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 read.fwf[][][] []\T1/ptm/m /n/10 for read-ing \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ixed \T1/ptm/m/it/10 w\T1/pt m/m/n/10 idth \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ormatted in-put; [][][]\T1/zi4/m/ sl/10 write.table[][][][]\T1/ptm/m/n/10 ; [2270] Underfull \hbox (badness 10000) in paragraph at lines 11355--11360 []\T1/ptm/m/n/10 The `hive' con-tain-ing the key. The ab-bre-vi-a-tions are for Underfull \hbox (badness 10000) in paragraph at lines 11355--11360 []\T1/zi4/m/sl/10 HKEY_LOCAL_MACHINE[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 HKEY_C LASSES_ROOT[]\T1/ptm/m/n/10 . []\T1/zi4/m/sl/10 HKEY_CURRENT_USER[]\T1/ptm/m/n/ 10 , [2271] [2272] [2273] [2274] [2275] [2276] [2277] [2278] Underfull \hbox (badness 1824) in paragraph at lines 11853--11857 \T1/zi4/m/sl/10 / / en . wikipedia . org / w / index . php ? title = Roman _ nu merals & oldid = 1188781837$[][]\T1/ptm/m/n/10 . Ac-cessed [2279] [2280] [2281] [2282] [2283] [2284] [2285] Underfull \hbox (badness 4060) in paragraph at lines 12299--12302 []\T1/ptm/m/n/10 If `[]\T1/zi4/m/sl/10 --default-packages[]\T1/ptm/m/n/10 ' is not used, then []\T1/zi4/m/sl/10 Rscript []\T1/ptm/m/n/10 checks the en-vi-ron- ment vari-able Overfull \hbox (18.77168pt too wide) in paragraph at lines 12322--12322 []\T1/zi4/m/n/9 Rscript --default-packages=methods,datasets,utils,grDevices,gr aphics,stats -e \TS1/zi4/m/n/9 '\T1/zi4/m/n/9 sessionInfo()\TS1/zi4/m/n/9 '[] [2286] [2287] [2288] [2289] Underfull \hbox (badness 2150) in paragraph at lines 12577--12579 [][][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / wiki / Ctags$[][]\T1/ ptm/m/n/10 , [][]$\T1/zi4/m/sl/10 https : / / www . gnu . org / software / emac s / manual / [2290] [2291] [2292] [2293] Underfull \hbox (badness 10000) in paragraph at lines 12797--12801 []\T1/ptm/m/n/10 The de-fault for []\T1/zi4/m/sl/10 stylepath []\T1/ptm/m/n/10 is now taken from the en-vi-ron-ment vari-able Underfull \hbox (badness 10000) in paragraph at lines 12830--12836 []\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y ou can add a [2294] Underfull \hbox (badness 2762) in paragraph at lines 12845--12851 \T1/ptm/m/n/10 UTF-8 lo-cales (note that pdf-TeX as-sumes UTF-8 by de-fault sin ce 2018). Ei-ther set [2295] [2296] Underfull \hbox (badness 1009) in paragraph at lines 13020--13032 []\T1/ptm/m/n/10 Before each code chunk is eval-u-ated, zero or more hook func- tions can be ex-e-cuted. If Underfull \hbox (badness 4779) in paragraph at lines 13060--13062 []\T1/ptm/m/n/10 The file `\T1/zi4/m/sl/10 Rconsole\T1/ptm/m/n/10 ' con-fig-ure s the R GUI ([]\T1/zi4/m/sl/10 Rgui[]\T1/ptm/m/n/10 ) con-sole un-der MS Win-do ws and [2297] Underfull \hbox (badness 1077) in paragraph at lines 13090--13097 \T1/ptm/m/n/10 (strip-ping any trail-ing slash), oth-er-wise to the Win-dows `p er-sonal' di-rec-tory, oth-er-wise to [2298] [2299] [2300] [2301] [2302] [2303] Underfull \hbox (badness 3780) in paragraph at lines 13515--13521 []\T1/ptm/m/n/10 A Bio-con-duc-tor mir-ror can be se-lected by set-ting [][][]\ T1/zi4/m/sl/10 options[][][]("BioC_mirror")[]\T1/ptm/m/n/10 , e.g. via [2304] Underfull \hbox (badness 2635) in paragraph at lines 13533--13536 []\T1/ptm/m/n/10 Repository `[]\T1/zi4/m/sl/10 CRAN[]\T1/ptm/m/n/10 ' is treate d spe-cially: the value is taken from the cur-rent set-ting of [2305] [2306] [2307] Underfull \hbox (badness 2302) in paragraph at lines 13743--13745 []\T1/ptm/m/n/10 Convert file paths to the short form. This is an in-ter-face t o the Win-dows API call [2308] [2309] [2310] [2311] [2312] Underfull \hbox (badness 4441) in paragraph at lines 14042--14047 []\T1/ptm/m/n/10 logical; if []\T1/zi4/m/sl/10 TRUE []\T1/ptm/m/n/10 (de-fault) , [][][]\T1/zi4/m/sl/10 deparse[][][](control = \T1/ptm/m/sl/10 control\T1/zi4/ m/sl/10 ) []\T1/ptm/m/n/10 will not have Underfull \hbox (badness 5970) in paragraph at lines 14051--14054 []\T1/ptm/m/n/10 the page width to be used. The de-fault is the cur-rently ac-t ive [2313] [2314] [2315] [2316] [2317] [2318] [2319] Underfull \hbox (badness 2932) in paragraph at lines 14482--14489 []\T1/ptm/m/n/10 If []\T1/zi4/m/sl/10 syntax = NULL []\T1/ptm/m/n/10 (the de-fa ult) then the avail-able syn-tax ob-jects are con-sulted in turn, Underfull \hbox (badness 1688) in paragraph at lines 14482--14489 \T1/ptm/m/n/10 and se-lected if their []\T1/zi4/m/sl/10 extension []\T1/ptm/m/n /10 com-po-nent matches (as a reg-exp) the file name. Ob- [2320] [2321] [2322] [2323] Underfull \hbox (badness 6510) in paragraph at lines 14794--14798 []\T1/ptm/m/n/10 When ar-gu-ment []\T1/zi4/m/sl/10 tar []\T1/ptm/m/n/10 is set to the com-mand []\T1/zi4/m/sl/10 tar []\T1/ptm/m/n/10 on ma-cOS, en-vi-ron-men t vari-able [2324] Underfull \hbox (badness 10000) in paragraph at lines 14801--14804 [][][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / wiki / Tar _ (file _ format)$[][]\T1/ptm/m/n/10 , [][]$\T1/zi4/m/sl/10 https : / / pubs . opengroup . org / Underfull \hbox (badness 2245) in paragraph at lines 14801--14804 \T1/zi4/m/sl/10 onlinepubs / 9699919799 / utilities / pax . html # tag _ 20 _ 9 2 _ 13 _ 06$[][] \T1/ptm/m/n/10 for the way the POSIX [2325] [2326] [2327] [2328] [2329] [2330] [2331] [2332] [2333] [2334] Underfull \hbox (badness 10000) in paragraph at lines 15474--15479 []\T1/ptm/m/n/10 Arguments such as []\T1/zi4/m/sl/10 destdir []\T1/ptm/m/n/10 a nd []\T1/zi4/m/sl/10 dependencies []\T1/ptm/m/n/10 to be passed to Underfull \hbox (badness 3861) in paragraph at lines 15474--15479 [][][]\T1/zi4/m/sl/10 install.packages[][][] []\T1/ptm/m/n/10 and []\T1/zi4/m/s l/10 ignore_repo_cache[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 max_repo_cache_age [ ]\T1/ptm/m/n/10 and Underfull \hbox (badness 1052) in paragraph at lines 15480--15482 []\T1/ptm/m/n/10 character, in-di-cat-ing the type of pack-age to down-load and in-stall. See Underfull \hbox (badness 10000) in paragraph at lines 15539--15542 [][][]\T1/zi4/m/sl/10 install.packages[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/ sl/10 available.packages[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 download .packages[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 installed.packages[][][ ][]\T1/ptm/m/n/10 , [2335] [2336] [2337] [2338] [2339] [2340] [2341] [2342] [2343] [2344] [2345] [2346] [2347] [2348] [2349] [2350]) [2351] [2352] (./boot-pkg.tex Chapter 15. [2353] [2354] [2355] [2356] [2357] [2358] [2359] [2360] [2361] [2362] [2363] Underfull \hbox (badness 1297) in paragraph at lines 799--809 []\T1/ptm/m/n/10 Where random-number gen-er-a-tion is done in the worker pro-ce sses, the de-fault be-haviour Underfull \hbox (badness 1881) in paragraph at lines 826--828 []\T1/ptm/m/n/10 Davison, A.C., Hink-ley, D.V. and Schecht-man, E. (1986) Ef-fi -cient boot-strap sim-u-la-tion. [2364] [2365] Underfull \vbox (badness 10000) has occurred while \output is active [2366] [2367] [2368] Underfull \hbox (badness 2150) in paragraph at lines 1105--1111 []\T1/ptm/m/n/10 The ob-served value of the statis-tic of in-ter-est. The de-fa ult value is [2369] [2370] [2371] [2372] [2373] Underfull \hbox (badness 1571) in paragraph at lines 1445--1447 []\T1/ptm/m/n/10 Rawlings, J.O. (1988) \T1/ptm/m/it/10 Ap-plied Re-gres-sion An al-y-sis\T1/ptm/m/n/10 . Wadsworth and Brooks/Cole Statis- [2374] [2375] [2376] [2377] [2378] [2379] Underfull \hbox (badness 1005) in paragraph at lines 1800--1807 []\T1/ptm/m/n/10 The sim-u-la-tion type. Pos-si-ble types are []\T1/zi4/m/sl/10 "ordinary" []\T1/ptm/m/n/10 (case re-sam-pling), [2380] [2381] [2382] [2383] Underfull \hbox (badness 7379) in paragraph at lines 2084--2086 []\T1/ptm/m/n/10 The length of time (in months) that the res-i-dent spent at Ch an-ning House. [2384] [2385] [2386] [2387] Underfull \hbox (badness 1565) in paragraph at lines 2338--2343 []\T1/ptm/m/n/10 The ob-served value of the statis-tic of in-ter-est on the ori g-i-nal data set [2388] Underfull \hbox (badness 1881) in paragraph at lines 2432--2434 []\T1/ptm/m/n/10 Davison, A.C., Hink-ley, D.V. and Schecht-man, E. (1986) Ef-fi -cient boot-strap sim-u-la-tion. [2389] Underfull \hbox (badness 2970) in paragraph at lines 2536--2540 []\T1/ptm/m/n/10 The un-bi-ased es-ti-ma-tor uses a mul-ti-plier of []\T1/zi4/m /sl/10 n/((n-1)*(n-2)) []\T1/ptm/m/n/10 where []\T1/zi4/m/sl/10 n []\T1/ptm/m/n /10 is the sam-ple Underfull \hbox (badness 2310) in paragraph at lines 2536--2540 \T1/ptm/m/n/10 size, if []\T1/zi4/m/sl/10 unbiased []\T1/ptm/m/n/10 is []\T1/zi 4/m/sl/10 FALSE []\T1/ptm/m/n/10 then a mul-ti-plier of []\T1/zi4/m/sl/10 1/n [ ]\T1/ptm/m/n/10 is used. This is mul-ti-plied by [2390] [2391] [2392] [2393] [2394] [2395] [2396] [2397] [2398] [2399] [2400] [2401] [2402] [2403] [2404] [2405] [2406] [2407] [2408] [2409] [2410] [2411] [2412] [2413] [2414] [2415] [2416] [2417] [2418] [2419] [2420] [2421] [2422] [2423] [2424] [2425] [2426] [2427] Underfull \hbox (badness 3000) in paragraph at lines 4959--4962 []\T1/ptm/m/n/10 The in-dex of the statis-tic of in-ter-est within the out-put of a call to [2428] [2429] [2430] [2431] Underfull \hbox (badness 2293) in paragraph at lines 5238--5241 []\T1/ptm/m/n/10 An in-te-ger giv-ing the num-ber of classes to be used in the boot-strap Underfull \hbox (badness 1668) in paragraph at lines 5238--5241 \T1/ptm/m/n/10 his-togram. The de-fault is the in-te-ger be-tween 10 and 100 cl os-est to [2432] [2433] [2434] [2435] [2436] [2437] [2438] [2439] [2440] [2441] [2442] [2443] Underfull \hbox (badness 4954) in paragraph at lines 6021--6024 []\T1/ptm/m/n/10 The re-turned value is an ob-ject of class []\T1/zi4/m/sl/10 " saddle.distn"[]\T1/ptm/m/n/10 . See the help file for [2444] [2445] [2446] [2447] [2448] [2449] [2450] [2451] [2452] [2453] [2454] Underfull \hbox (badness 1596) in paragraph at lines 6742--6746 []\T1/ptm/m/n/10 A char-ac-ter string in-di-cat-ing the type of sec-ond ar-gu-m ent ex-pected by [2455] [2456] [2457] [2458] [2459] Underfull \vbox (badness 3803) has occurred while \output is active [2460] [2461] [2462] [2463] [2464]) (./class-pkg.tex Chapter 16. [2465] [2466] [2467] [2468] [2469] [2470] [2471] [2472] [2473] [2474] [2475] [2476] [2477] [2478] [2479] [2480] [2481]) (./cluster-pkg.tex [2482] Chapter 17. [2483] [2484] [2485] [2486] [2487] [2488] [2489] [2490] [2491] [2492] [2493] [2494] Underfull \hbox (badness 1412) in paragraph at lines 782--787 []\T1/ptm/m/n/10 Kaufman and Rousseeuw (see [][][]\T1/zi4/m/sl/10 agnes[][][][] \T1/ptm/m/n/10 ), orig-i-nally. Met-ric []\T1/zi4/m/sl/10 "jaccard"[]\T1/ptm/m/ n/10 : Kamil Ko-zlowski [2495] [2496] Underfull \hbox (badness 10000) in paragraph at lines 882--884 []\T1/ptm/m/n/10 list with sil-hou-ette width in-for-ma-tion for the best sam-p le, see [2497] [2498] Underfull \hbox (badness 10000) in paragraph at lines 992--994 []\T1/ptm/m/n/10 simply cor-re-sponds to the global max-i-mum, i.e., is Underfull \hbox (badness 1342) in paragraph at lines 1006--1010 []\T1/ptm/m/n/10 This, the de-fault, has been pro-posed by Mar-tin Maech-ler in 2012, [2499] [2500] Underfull \vbox (badness 3803) has occurred while \output is active [2501] [2502] [2503] [2504] [2505] Underfull \hbox (badness 10000) in paragraph at lines 1474--1477 [2506] [2507] Underfull \hbox (badness 2503) in paragraph at lines 1583--1586 []\T1/ptm/m/n/10 an ob-ject of class []\T1/zi4/m/sl/10 "hclust" []\T1/ptm/m/n/1 0 or []\T1/zi4/m/sl/10 "twins"[]\T1/ptm/m/n/10 , i.e., typ-i-cally the re-sult of [2508] Underfull \hbox (badness 4954) in paragraph at lines 1680--1682 []\T1/ptm/b/n/10 A\T1/ptm/m/n/10 symmetric bi-nary vari-able, aka []\T1/zi4/m/s l/10 "A" []\T1/ptm/m/n/10 in re-sult []\T1/zi4/m/sl/10 Types[]\T1/ptm/m/n/10 , see [2509] Underfull \hbox (badness 7667) in paragraph at lines 1694--1698 []\T1/ptm/b/n/10 I\T1/ptm/m/n/10 nterval scaled -- the \T1/ptm/b/n/10 de-fault \T1/ptm/m/n/10 for all nu-meric Underfull \hbox (badness 10000) in paragraph at lines 1694--1698 \T1/ptm/m/n/10 (incl []\T1/zi4/m/sl/10 integer[]\T1/ptm/m/n/10 ) columns of []\ T1/zi4/m/sl/10 x[]\T1/ptm/m/n/10 , aka []\T1/zi4/m/sl/10 "I" []\T1/ptm/m/n/10 i n re-sult []\T1/zi4/m/sl/10 Types[]\T1/ptm/m/n/10 , see [2510] [2511] Overfull \hbox (5.24408pt too wide) in paragraph at lines 1866--1866 []\T1/zi4/m/n/9 summary(dA123 <- daisy(flowerN)) # .. all 3 logicals treated * A*symmetric binary (w/ warning)[] Overfull \hbox (11.23795pt too wide) in paragraph at lines 1877--1877 []\T1/zi4/m/n/9 ## Still, using Euclidean/Manhattan distance for {0-1} *is* id entical to treating them as "N" :[] [2512] [2513] [2514] [2515] [2516] Underfull \hbox (badness 10000) in paragraph at lines 2212--2215 [2517] Underfull \hbox (badness 10000) in paragraph at lines 2223--2229 [][][]\T1/zi4/m/sl/10 predict.ellipsoid[][][] []\T1/ptm/m/n/10 which is also th e [][][]\T1/zi4/m/sl/10 predict[][][] []\T1/ptm/m/n/10 method for []\T1/zi4/m/s l/10 ellipsoid []\T1/ptm/m/n/10 ob-jects. [2518] [2519] [2520] Underfull \hbox (badness 6675) in paragraph at lines 2457--2459 []\T1/ptm/m/n/10 list with sil-hou-ette in-for-ma-tion of the near-est crisp cl us-ter-ing, see [2521] [2522] [2523] [2524] [2525] [2526] [2527] [2528] [2529] [2530] Underfull \hbox (badness 2980) in paragraph at lines 3059--3063 [][][]\T1/zi4/m/sl/10 agnes[][][] []\T1/ptm/m/n/10 for back-ground and ref-er-e nces; [][][]\T1/zi4/m/sl/10 pam.object[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/ sl/10 clara[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 daisy[][][][]\T1/ptm/ m/n/10 , [][][]\T1/zi4/m/sl/10 partition.object[][][][]\T1/ptm/m/n/10 , [2531] [2532] [2533] [2534] [2535] [2536] Underfull \hbox (badness 1142) in paragraph at lines 3406--3409 []\T1/ptm/m/n/10 graphical pa-ram-e-ters (see [][][]\T1/zi4/m/sl/10 par[][][][] \T1/ptm/m/n/10 ) may also be sup-plied and are passed to [2537] Underfull \hbox (badness 1142) in paragraph at lines 3525--3528 []\T1/ptm/m/n/10 graphical pa-ram-e-ters (see [][][]\T1/zi4/m/sl/10 par[][][][] \T1/ptm/m/n/10 ) may also be sup-plied and are passed to [2538] [2539] [2540] [2541] Underfull \hbox (badness 2582) in paragraph at lines 3748--3753 [][][]\T1/zi4/m/sl/10 partition.object[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/ sl/10 clusplot.partition[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 clusplot .default[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 pam[][][][]\T1/ptm/m/n/1 0 , [][][]\T1/zi4/m/sl/10 pam.object[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl /10 clara[][][][]\T1/ptm/m/n/10 , [2542] Underfull \hbox (badness 2698) in paragraph at lines 3810--3815 []\T1/ptm/m/n/10 Note that cur-rently the method func-tion sim-ply calls []\T1/ zi4/m/sl/10 plot([][]as.hclust[][][](x), ...)[]\T1/ptm/m/n/10 , which Underfull \hbox (badness 4792) in paragraph at lines 3810--3815 \T1/ptm/m/n/10 dis-patches to [][][]\T1/zi4/m/sl/10 plot.hclust[][][](..)[]\T1/ ptm/m/n/10 . If more flex-i-ble plots are needed, con-sider []\T1/zi4/m/sl/10 x x <- [2543] Underfull \hbox (badness 10000) in paragraph at lines 3883--3885 []\T1/ptm/m/n/10 Available as `\T1/zi4/m/sl/10 pluton.dat\T1/ptm/m/n/10 ' from the archive of the Uni-ver-sity of Antwer-pen, [2544] [2545] [2546] [2547] Underfull \hbox (badness 10000) in paragraph at lines 4097--4099 []\T1/ptm/m/n/10 a []\T1/zi4/m/sl/10 dissimilarity []\T1/ptm/m/n/10 ob-ject or a []\T1/zi4/m/sl/10 summary.dissimilarity []\T1/ptm/m/n/10 one for [2548] [2549] [2550] [2551] Underfull \hbox (badness 2626) in paragraph at lines 4326--4331 []\T1/ptm/m/n/10 arguments passed [][][]\T1/zi4/m/sl/10 barplot[][][]()[]\T1/pt m/m/n/10 ; note that the de-fault used to be []\T1/zi4/m/sl/10 col = [2552] Underfull \hbox (badness 1383) in paragraph at lines 4403--4408 []\T1/ptm/m/n/10 While []\T1/zi4/m/sl/10 silhouette() []\T1/ptm/m/n/10 is \T1/p tm/m/it/10 in-trin-sic \T1/ptm/m/n/10 to the [][][]\T1/zi4/m/sl/10 partition[][ ][] []\T1/ptm/m/n/10 clus-ter-ings, and hence has a (triv-ial) [2553] [2554] [2555] [2556] [2557] [2558] [2559] [2560] Underfull \hbox (badness 10000) in paragraph at lines 4844--4846 []\T1/ptm/m/n/10 Sample data set ac-com-pa-ny-ing the ref-er-ence be-low (file `\T1/zi4/m/sl/10 xclara.dat\T1/ptm/m/n/10 ' in side [2561]) (./codetools-pkg.tex [2562] Chapter 18. [2563] [2564] [2565] [2566] [2567]) (./foreign-pkg.tex [2568] Chapter 19. Underfull \hbox (badness 10000) in paragraph at lines 33--37 []\T1/ptm/m/n/10 SAS Tech-ni-cal Sup-port doc-u-ment TS-140: ``The Record Lay-o ut of Underfull \hbox (badness 10000) in paragraph at lines 33--37 \T1/ptm/m/n/10 a Data Set in SAS Trans-port (XPORT) For-mat'' avail-able as [][ ]$\T1/zi4/m/sl/10 https : Underfull \hbox (badness 10000) in paragraph at lines 33--37 \T1/zi4/m/sl/10 / / support . sas . com / content / dam / SAS / support / en / technical-[]papers / Underfull \hbox (badness 10000) in paragraph at lines 33--37 \T1/zi4/m/sl/10 record-[]layout-[]of-[]a-[]sas-[]version-[]5-[]or-[]6-[]data-[] set-[]in-[]sas-[]transport-[]xport-[]format . [2569] Underfull \hbox (badness 10000) in paragraph at lines 78--80 []\T1/ptm/m/n/10 Attribute-Relation File For-mat [][]$\T1/zi4/m/sl/10 https : / / waikato . github . io / weka-[]wiki / formats _ and _ [2570] [2571] [2572] [2573] [2574] [2575] [2576] [2577] Underfull \hbox (badness 2846) in paragraph at lines 502--511 []\T1/ptm/m/n/10 character: what to do with du-pli-cated value la-bels for dif- fer-ent lev- Underfull \hbox (badness 5417) in paragraph at lines 502--511 \T1/ptm/m/n/10 els. For []\T1/zi4/m/sl/10 "append" []\T1/ptm/m/n/10 (the de-fau lt), the first orig-i-nal value la-bel is Underfull \hbox (badness 6001) in paragraph at lines 502--511 \T1/ptm/m/n/10 kept while fur-ther du-pli-cated la-bels are re-named to []\T1/z i4/m/sl/10 paste0(label, [2578] Overfull \hbox (6.73795pt too wide) in paragraph at lines 620--620 []\T1/zi4/m/n/9 ### Expect lots of warnings as value labels (corresponding to R factor labels) are uncomplete,[] [2579] [2580] [2581] [2582] Underfull \hbox (badness 10000) in paragraph at lines 808--809 [2583] Underfull \hbox (badness 10000) in paragraph at lines 865--869 []\T1/ptm/m/n/10 SAS Tech-ni-cal Sup-port doc-u-ment TS-140: ``The Record Lay-o ut of Underfull \hbox (badness 10000) in paragraph at lines 865--869 \T1/ptm/m/n/10 a Data Set in SAS Trans-port (XPORT) For-mat'' avail-able at [][ ]$\T1/zi4/m/sl/10 https : Underfull \hbox (badness 10000) in paragraph at lines 865--869 \T1/zi4/m/sl/10 / / support . sas . com / content / dam / SAS / support / en / technical-[]papers / Underfull \hbox (badness 10000) in paragraph at lines 865--869 \T1/zi4/m/sl/10 record-[]layout-[]of-[]a-[]sas-[]version-[]5-[]or-[]6-[]data-[] set-[]in-[]sas-[]transport-[]xport-[]format . [2584] [2585] Underfull \hbox (badness 10000) in paragraph at lines 986--988 []\T1/ptm/m/n/10 Attribute-Relation File For-mat [][]$\T1/zi4/m/sl/10 https : / / waikato . github . io / weka-[]wiki / formats _ and _ [2586] [2587] [2588] [2589] Underfull \hbox (badness 10000) in paragraph at lines 1265--1271 []\T1/ptm/m/n/10 The work for this func-tion is done by []\T1/zi4/m/sl/10 forei gn:::writeForeignStata[]\T1/ptm/m/n/10 , [2590] [2591]) (./KernSmooth-pkg.tex [2592] Chapter 20. [2593] [2594] [2595] [2596] [2597] [2598] [2599] [2600] [2601] [2602] [2603]) (./lattice-pkg.tex [2604] Chapter 21. [2605] Underfull \hbox (badness 1484) in paragraph at lines 114--118 []\T1/ptm/m/n/10 Bell Lab's Trel-lis Page con-tains sev-eral doc-u-ments out-li n-ing the use of Trel-lis graph-ics; Underfull \hbox (badness 10000) in paragraph at lines 114--118 \T1/zi4/m/sl/10 20081020164041 / http : / / cm . bell-[]labs . com / cm / ms / departments / sia / project / trellis / [2606] [2607] [2608] Underfull \vbox (badness 10000) has occurred while \output is active [2609] [2610] [2611] [2612] [2613] [2614] [2615] [2616] [2617] [2618] [2619] [2620] [2621] [2622] Underfull \hbox (badness 1062) in paragraph at lines 1395--1399 \T1/ptm/m/n/10 no-ta-tion for the x and y axes re-spec-tively. See doc-u-men-ta -tion for [2623] [2624] Underfull \hbox (badness 1803) in paragraph at lines 1563--1580 [][][]\T1/zi4/m/sl/10 Lattice[][][] []\T1/ptm/m/n/10 for an overview of the pac k-age, as well as [][][]\T1/zi4/m/sl/10 barchart.table[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 print.trellis[][][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1563--1580 [][][]\T1/zi4/m/sl/10 panel.stripplot[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/s l/10 panel.superpose[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 panel.loess[ ][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 panel.average[][][][]\T1/ptm/m/n/ 10 , [][][]\T1/zi4/m/sl/10 strip.default[][][][]\T1/ptm/m/n/10 , [2625] [2626] [2627] Underfull \hbox (badness 3009) in paragraph at lines 1705--1707 []\T1/ptm/m/n/10 additional ar-gu-ments passed to [][][]\T1/zi4/m/sl/10 xyplot[ ][][][]\T1/ptm/m/n/10 , which may pass them on to Underfull \hbox (badness 6808) in paragraph at lines 1735--1739 []\T1/ptm/m/n/10 graphical ar-gu-ments, which are pro-cessed and even-tu-ally p assed to [2628] [2629] [2630] [2631] [2632] [2633] Underfull \hbox (badness 10000) in paragraph at lines 2137--2140 []\T1/ptm/m/n/10 When []\T1/zi4/m/sl/10 breaks []\T1/ptm/m/n/10 is un-spec-i-fi ed, the value of [2634] [2635] [2636] [2637] [2638] [2639] [2640] [2641] [2642] Underfull \vbox (badness 10000) has occurred while \output is active [2643] [2644] Underfull \hbox (badness 2781) in paragraph at lines 2871--2873 []\T1/ptm/m/n/10 A color ramp spec-i-fi-ca-tion, as in the []\T1/zi4/m/sl/10 co l.regions []\T1/ptm/m/n/10 ar-gu-ment in [2645] [2646] Underfull \hbox (badness 2486) in paragraph at lines 3021--3025 []\T1/ptm/m/n/10 Other use-ful ar-gu-ments are men-tioned in the help page for the de-fault panel func-tion [2647] [2648] [2649] [2650] [2651] [2652] [2653] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.parallel} ) has been already used, duplicate ignored \relax l.3506 \aliasA{parallel}{B\_08\_splom}{parallel} [2654] [2655] Underfull \hbox (badness 2368) in paragraph at lines 3644--3644 []\T1/zi4/m/sl/10 auto.key[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 prepanel[]\T1/pt m/m/n/10 , []\T1/zi4/m/sl/10 scales[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 strip[] \T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 groups[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 x lab[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 xlim[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/1 0 ylab[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 ylim[]\T1/ptm/m/n/10 , [2656] [2657] [2658] [2659] [2660] Underfull \hbox (badness 5696) in paragraph at lines 3992--3996 []\T1/ptm/m/n/10 A pos-si-ble use of this ar-gu-ment is to change the de-fault set-tings Underfull \hbox (badness 10000) in paragraph at lines 3992--3996 \T1/ptm/m/n/10 by spec-i-fy-ing []\T1/zi4/m/sl/10 lattice.options(default.theme = "col.whitebg")[]\T1/ptm/m/n/10 . Underfull \hbox (badness 2435) in paragraph at lines 3992--3996 \T1/ptm/m/n/10 For back-compatibility, this is ini-tially (when lat-tice is loa ded) set to [2661] [2662] [2663] Underfull \hbox (badness 1389) in paragraph at lines 4175--4183 \T1/ptm/m/n/10 based on HCL palettes, but cus-tomiza-tion of the palettes is al -lowed. Ear-lier be-haviour [2664] Underfull \hbox (badness 1173) in paragraph at lines 4251--4255 []\T1/ptm/m/n/10 A char-ac-ter string giv-ing the name of a com-po-nent. If un- spec-i-fied in Underfull \hbox (badness 3219) in paragraph at lines 4278--4280 []\T1/ptm/m/n/10 A log-i-cal flag, in-di-cat-ing whether a warn-ing should be i s-sued when [2665] [2666] [2667] Underfull \hbox (badness 3492) in paragraph at lines 4478--4488 []\T1/ptm/m/n/10 A color spec-i-fi-ca-tion. []\T1/zi4/m/sl/10 col []\T1/ptm/m/n /10 is used for com-po-nents []\T1/zi4/m/sl/10 "plot.symbol"[]\T1/ptm/m/n/10 , [2668] Underfull \hbox (badness 10000) in paragraph at lines 4503--4506 []\T1/ptm/m/n/10 fill color, ap-pli-ca-ble for com-po-nents []\T1/zi4/m/sl/10 p lot.symbol[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 plot.polygon[]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4506--4508 []\T1/ptm/m/n/10 border color, ap-pli-ca-ble for com-po-nents []\T1/zi4/m/sl/10 plot.polygon []\T1/ptm/m/n/10 and [2669] [2670] [2671] [2672] [2673] [2674] [2675] [2676] [2677] [2678] Underfull \hbox (badness 6157) in paragraph at lines 5232--5235 []\T1/zi4/m/sl/10 plot.shingle []\T1/ptm/m/n/10 dis-plays the ranges of shin-gl es via rect-an-gles. []\T1/zi4/m/sl/10 print.shingle []\T1/ptm/m/n/10 and [2679] [2680] [2681] [2682] [2683] [2684] [2685] [2686] Underfull \hbox (badness 10000) in paragraph at lines 5684--5687 []\T1/ptm/m/n/10 logical, spec-i-fy-ing whether the la-bels etc should be hor-i -zon-tal. Underfull \hbox (badness 5592) in paragraph at lines 5684--5687 []\T1/zi4/m/sl/10 horizontal=FALSE []\T1/ptm/m/n/10 is use-ful for strips on th e left of pan-els us-ing [2687] [2688] [2689] [2690] [2691] Underfull \hbox (badness 4805) in paragraph at lines 6045--6049 []\T1/ptm/m/n/10 logical, whether the view-port be-ing as-signed fo-cus should be high- Underfull \hbox (badness 10000) in paragraph at lines 6056--6063 []\T1/ptm/m/n/10 For []\T1/zi4/m/sl/10 panel.identify.qqmath[]\T1/ptm/m/n/10 , ex-tra pa-ram-e-ters are passed on to Underfull \hbox (badness 1226) in paragraph at lines 6056--6063 []\T1/zi4/m/sl/10 panel.identify[]\T1/ptm/m/n/10 . For []\T1/zi4/m/sl/10 panel. identify[]\T1/ptm/m/n/10 , ex-tra ar-gu-ments are treated as Underfull \hbox (badness 2418) in paragraph at lines 6056--6063 \T1/ptm/m/n/10 graph-i-cal pa-ram-e-ters and are used for la-belling. For []\T1 /zi4/m/sl/10 trellis.focus Underfull \hbox (badness 10000) in paragraph at lines 6056--6063 []\T1/ptm/m/n/10 and []\T1/zi4/m/sl/10 trellis.switchFocus[]\T1/ptm/m/n/10 , th ese are used (in com-bi-na-tion with Underfull \hbox (badness 1259) in paragraph at lines 6056--6063 [][][]\T1/zi4/m/sl/10 lattice.options[][][][]\T1/ptm/m/n/10 ) for high-light-in g the cho-sen view-port if so re-quested. [2692] [2693] [2694] [2695] Underfull \hbox (badness 4242) in paragraph at lines 6356--6361 []\T1/ptm/m/n/10 Graphical pa-ram-e-ters for the bars. By de-fault, the trel-li s pa-ram-e- Underfull \hbox (badness 2529) in paragraph at lines 6356--6361 \T1/ptm/m/n/10 ter []\T1/zi4/m/sl/10 plot.polygon []\T1/ptm/m/n/10 is used if t here is no group-ing vari-able, oth-er-wise [2696] [2697] Underfull \hbox (badness 2310) in paragraph at lines 6472--6477 []\T1/ptm/m/n/10 Creates Box and Whisker plot of []\T1/zi4/m/sl/10 x []\T1/ptm/ m/n/10 for ev-ery level of []\T1/zi4/m/sl/10 y []\T1/ptm/m/n/10 (or the other w ay round if [2698] [2699] [2700] [2701] [2702] [2703] [2704] [2705] [2706] [2707] [2708] [2709] [2710] Underfull \hbox (badness 3168) in paragraph at lines 7330--7334 []\T1/ptm/m/n/10 to know what ar-gu-ments this func-tion is passed when called. Use [2711] [2712] [2713] [2714] Underfull \hbox (badness 2012) in paragraph at lines 7601--7604 []\T1/ptm/m/n/10 Further ar-gu-ments, of-ten graph-i-cal pa-ram-e-ters, even-tu -ally passed on to [2715] [2716] [2717] [2718] Underfull \hbox (badness 3333) in paragraph at lines 7808--7810 []\T1/ptm/m/n/10 default colours are ob-tained from []\T1/zi4/m/sl/10 plot.symb ol []\T1/ptm/m/n/10 and []\T1/zi4/m/sl/10 plot.line []\T1/ptm/m/n/10 us-ing Underfull \hbox (badness 2318) in paragraph at lines 7836--7844 []\T1/zi4/m/sl/10 "spline" []\T1/ptm/m/n/10 adds a cu-bic smooth-ing spline fit (same as [][][]\T1/zi4/m/sl/10 panel.spline[][][][]\T1/ptm/m/n/10 ). [2719] [2720] [2721] Underfull \vbox (badness 10000) has occurred while \output is active [2722] [2723] [2724] [2725] Underfull \hbox (badness 1436) in paragraph at lines 8309--8315 []\T1/ptm/m/n/10 A log-i-cal flag de-ter-min-ing whether the de-fault graph-i-c al pa-ram-e-ters for [2726] [2727] [2728] [2729] [2730] [2731] [2732] [2733] Underfull \hbox (badness 10000) in paragraph at lines 8878--8881 []\T1/ptm/m/n/10 Extra ar-gu-ments. Passed down to []\T1/zi4/m/sl/10 panel.supe rpose []\T1/ptm/m/n/10 from [2734] Underfull \hbox (badness 1092) in paragraph at lines 8924--8926 []\T1/ptm/m/n/10 Deepayan Sarkar \T1/zi4/m/sl/10 \T1/ptm/m/n/10 ([]\T1/zi4/m/sl/10 panel.superpose.2 []\T1/ptm/m/n/10 orig-i-n ally con- [2735] [2736] [2737] Underfull \hbox (badness 3895) in paragraph at lines 9085--9088 []\T1/ptm/m/n/10 details of his-togram cal-cu-la-tions. []\T1/zi4/m/sl/10 type []\T1/ptm/m/n/10 has a dif-fer-ent mean-ing in Underfull \hbox (badness 6625) in paragraph at lines 9095--9095 []\T1/zi4/m/sl/10 perspective[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 distance[]\T1 /ptm/m/n/10 , []\T1/zi4/m/sl/10 xlim[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 ylim[] \T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 zlim[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 scr een[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 R.mat[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/ 10 aspect[]\T1/ptm/m/n/10 , [2738] Underfull \hbox (badness 1515) in paragraph at lines 9160--9164 []\T1/ptm/m/n/10 numeric vec-tor of length two, rep-re-sent-ing prob-a-bil-i-ti es. If used with [2739] [2740] Underfull \hbox (badness 6316) in paragraph at lines 9266--9271 []\T1/ptm/m/n/10 which packet (counted ac-cord-ing to the packet or-der, de-scr ibed in Underfull \hbox (badness 5908) in paragraph at lines 9283--9286 []\T1/ptm/m/n/10 list, sim-i-lar to those pro-duced by []\T1/zi4/m/sl/10 xscale .components.default []\T1/ptm/m/n/10 and [2741] [2742] Underfull \vbox (badness 10000) has occurred while \output is active [2743] [2744] [2745] Underfull \hbox (badness 2418) in paragraph at lines 9574--9578 []\T1/ptm/m/n/10 returns a list with sev-eral com-po-nents, in-clud-ing []\T1/z i4/m/sl/10 left, right, left.name, right.name, [2746] [2747] [2748] [2749] [2750] [2751] Underfull \hbox (badness 2310) in paragraph at lines 10018--10022 []\T1/ptm/m/n/10 Factor with lev-els []\T1/zi4/m/sl/10 "Svansota"[]\T1/ptm/m/n/ 10 , []\T1/zi4/m/sl/10 "No. 462"[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 "Manchuria "[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 "No. 475"[]\T1/ptm/m/n/10 , []\T1/zi4/m/s l/10 "Velvet"[]\T1/ptm/m/n/10 , Underfull \hbox (badness 3701) in paragraph at lines 10023--10026 []\T1/ptm/m/n/10 Factor with 6 lev-els: []\T1/zi4/m/sl/10 "Grand Rapids"[]\T1/p tm/m/n/10 , []\T1/zi4/m/sl/10 "Duluth"[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 "Uni versity Farm"[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 "Morris"[]\T1/ptm/m/n/10 , [2752] [2753] [2754] [2755] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.melanoma} ) has been already used, duplicate ignored \relax l.10249 \aliasA{melanoma}{H\_melanoma}{melanoma} [2756] [2757] [2758] [2759] Underfull \hbox (badness 4144) in paragraph at lines 10473--10476 []\T1/ptm/m/n/10 Rural Health Re-form Pol-icy Re-search Cen-ter. _Ex-plor-ing R u-ral and Ur-ban Mor-tal- Underfull \hbox (badness 1509) in paragraph at lines 10473--10476 \T1/ptm/m/n/10 ity Dif-fer-ences_, Au-gust 2015 Bethesda, MD. [][]$\T1/zi4/m/sl /10 https : / / ruralhealth . und . edu / projects / [2760]) (./MASS-pkg.tex Chapter 22. [2761] [2762] [2763] [2764] [2765] [2766] [2767] [2768] [2769] [2770] [2771] [2772] [2773] [2774] [2775] [2776] [2777] [2778] [2779] [2780] [2781] [2782] [2783] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.confint.g lm}) has been already used, duplicate ignored \relax l.1477 ...{confint.glm}{confint-MASS}{confint.glm} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.confint.n ls}) has been already used, duplicate ignored \relax l.1478 ...{confint.nls}{confint-MASS}{confint.nls} [2784] [2785] [2786] [2787] [2788] [2789] [2790] [2791] [2792] [2793] [2794] [2795] [2796] [2797] [2798] [2799] [2800] [2801] [2802] Underfull \hbox (badness 10000) in paragraph at lines 2785--2790 []\T1/zi4/m/sl/10 "geometric"[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 "log-normal"[ ]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 "lognormal"[]\T1/ptm/m/n/10 , []\T1/zi4/m/s l/10 "logistic"[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 "negative [2803] [2804] [2805] Underfull \hbox (badness 4686) in paragraph at lines 2957--2959 []\T1/ptm/m/n/10 An early ter-mi-na-tion cri-te-rion. If any par-tial de-nom-i- na-tor ex-ceeds [2806] [2807] [2808] [2809] [2810] [2811] [2812] [2813] [2814] [2815] [2816] [2817] [2818] [2819] [2820] [2821] [2822] [2823] [2824] [2825] [2826] [2827] [2828] [2829] [2830] [2831] [2832] Underfull \hbox (badness 1117) in paragraph at lines 4732--4735 []\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo rm []\T1/zi4/m/sl/10 response ~ [2833] Underfull \hbox (badness 1117) in paragraph at lines 4811--4814 []\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo rm []\T1/zi4/m/sl/10 response ~ [2834] [2835] [2836] [2837] [2838] [2839] [2840] [2841] [2842] [2843] [2844] [2845] [2846] [2847] [2848] [2849] [2850] [2851] [2852] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.npk}) has been already used, duplicate ignored \relax l.6080 ...sical N, P, K Factorial Experiment}{npk} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.npk.1}) h as been already used, duplicate ignored \relax l.6080 ...sical N, P, K Factorial Experiment}{npk} [2853] [2854] [2855] [2856] [2857] [2858] Underfull \vbox (badness 10000) has occurred while \output is active [2859] [2860] [2861] [2862] [2863] [2864] [2865] [2866] Underfull \hbox (badness 1117) in paragraph at lines 6981--6988 []\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo rm []\T1/zi4/m/sl/10 response ~ [2867] Underfull \hbox (badness 3138) in paragraph at lines 7052--7058 []\T1/ptm/m/n/10 The log-log and com-ple-men-tary log-log links are the in-crea s-ing func-tions $\OML/cmm/m/it/10 F[]\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 p\OT1/c mr/m/n/10 ) = [2868] [2869] [2870] Underfull \hbox (badness 1910) in paragraph at lines 7231--7234 []\T1/ptm/m/n/10 the di-men-sion of the space to be used. If this is less than []\T1/zi4/m/sl/10 min(p, [2871] [2872] [2873] [2874] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.profile.g lm}) has been already used, duplicate ignored \relax l.7508 ... for Profiling glm Objects}{profile.glm} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.profile.g lm.1}) has been already used, duplicate ignored \relax l.7508 ... for Profiling glm Objects}{profile.glm} [2875] [2876] [2877] [2878] Underfull \hbox (badness 4686) in paragraph at lines 7803--7805 []\T1/ptm/m/n/10 An early ter-mi-na-tion cri-te-rion. If any par-tial de-nom-i- na-tor ex-ceeds [2879] [2880] [2881] [2882] [2883] [2884] [2885] [2886] [2887] [2888] [2889] [2890] [2891] [2892] [2893] [2894] [2895] [2896] [2897] [2898] [2899] [2900] [2901] [2902] [2903] [2904] [2905] [2906] [2907] [2908] [2909] [2910] [2911] [2912] [2913] [2914] [2915] [2916] [2917] [2918]) (./Matrix-pkg.tex Chapter 23. Underfull \hbox (badness 10000) in paragraph at lines 35--38 []\T1/ptm/m/n/10 Note that the cur-rent im-ple-men-ta-tion de-tails are sub-jec t to change, and if you Underfull \hbox (badness 10000) in paragraph at lines 35--38 \T1/ptm/m/n/10 con-sider work-ing with these classes, please con-tact the pack- age main-tain-ers [2919] Underfull \hbox (badness 1769) in paragraph at lines 89--92 []\T1/ptm/m/n/10 This is cur-rently ex-per-i-men-tal and not yet used for our o wn code. Please con-tact us [2920] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.all.equal }) has been already used, duplicate ignored \relax l.182 ...{all.equal}{all.equal-methods}{all.equal} [2921] Underfull \hbox (badness 3098) in paragraph at lines 264--266 []\T1/ptm/m/n/10 optional ar-gu-ments passed to the de-fault method for generic func-tion [2922] [2923] [2924] [2925] Underfull \hbox (badness 5119) in paragraph at lines 492--496 []\T1/ptm/m/n/10 logical; if true the re-sult will be sym-met-ric (in-her-it-in g from class [2926] Underfull \hbox (badness 2035) in paragraph at lines 590--593 []\T1/ptm/m/n/10 The value of []\T1/zi4/m/sl/10 bdiag() []\T1/ptm/m/n/10 in-her -its from class [][][]\T1/zi4/m/sl/10 CsparseMatrix[][][][]\T1/ptm/m/n/10 , whe reas []\T1/zi4/m/sl/10 .bdiag() []\T1/ptm/m/n/10 re-turns a [2927] [2928] [2929] [2930] Underfull \hbox (badness 5817) in paragraph at lines 913--916 []\T1/ptm/m/n/10 Class [][][]\T1/zi4/m/sl/10 BunchKaufmanFactorization[][][][]\ T1/ptm/m/n/10 , di-rectly. Class [][][]\T1/zi4/m/sl/10 MatrixFactorization[][][ ][]\T1/ptm/m/n/10 , by class Underfull \hbox (badness 6758) in paragraph at lines 919--924 []\T1/ptm/m/n/10 Objects can be gen-er-ated di-rectly by calls of the form []\T 1/zi4/m/sl/10 new("BunchKaufman", ...) Underfull \hbox (badness 2961) in paragraph at lines 919--924 []\T1/ptm/m/n/10 or []\T1/zi4/m/sl/10 new("pBunchKaufman", ...)[]\T1/ptm/m/n/10 , but they are more typ-i-cally ob-tained as the value of [2931] [2932] Underfull \hbox (badness 10000) in paragraph at lines 1081--1086 []\T1/ptm/m/n/10 An ob-ject rep-re-sent-ing the fac-tor-iza-tion, in-her-it-ing from vir-tual class [2933] [2934] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.cbind2.Rd ash.methods}) has been already used, duplicate ignored \relax l.1185 ... on cbind2/rbind2}{cbind2.Rdash.methods} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.cbind2}) has been already used, duplicate ignored \relax l.1186 \aliasA{cbind2}{cbind2-methods}{cbind2} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.rbind2}) has been already used, duplicate ignored \relax l.1195 \aliasA{rbind2}{cbind2-methods}{rbind2} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.rbind2.Rd ash.methods}) has been already used, duplicate ignored \relax l.1204 ...s}{cbind2-methods}{rbind2.Rdash.methods} [2935] Underfull \hbox (badness 10000) in paragraph at lines 1322--1329 []\T1/ptm/m/n/10 The im-ple-men-ta-tion of class []\T1/zi4/m/sl/10 CHMfactor [] \T1/ptm/m/n/10 is based on CHOLMOD's C-level [2936] [2937] [2938] [2939] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.chol}) ha s been already used, duplicate ignored \relax l.1625 \aliasA{chol}{chol-methods}{chol} [2940] Underfull \hbox (badness 6220) in paragraph at lines 1656--1658 []\T1/ptm/m/n/10 Methods for [][][]\T1/zi4/m/sl/10 sparseMatrix[][][] []\T1/ptm /m/n/10 are built on CHOLMOD rou-tines []\T1/zi4/m/sl/10 cholmod_analyze []\T1/ ptm/m/n/10 and [2941] Underfull \hbox (badness 2334) in paragraph at lines 1730--1734 []\T1/ptm/m/n/10 The LA-PACK source code, in-clud-ing doc-u-men-ta-tion; see [] []$\T1/zi4/m/sl/10 https : / / netlib . org / lapack / Underfull \hbox (badness 1616) in paragraph at lines 1730--1734 \T1/zi4/m/sl/10 double / dpstrf . f$[][]\T1/ptm/m/n/10 , [][]$\T1/zi4/m/sl/10 h ttps : / / netlib . org / lapack / double / dpotrf . f$[][]\T1/ptm/m/n/10 , and [][]$\T1/zi4/m/sl/10 https : / / netlib . [2942] Underfull \vbox (badness 10000) has occurred while \output is active [2943] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.chol2inv} ) has been already used, duplicate ignored \relax l.1854 ...sA{chol2inv}{chol2inv-methods}{chol2inv} [2944] [2945] Underfull \hbox (badness 10000) in paragraph at lines 2005--2008 []\T1/ptm/m/n/10 Class [][][]\T1/zi4/m/sl/10 CholeskyFactorization[][][][]\T1/p tm/m/n/10 , di-rectly. Class [][][]\T1/zi4/m/sl/10 MatrixFactorization[][][][]\ T1/ptm/m/n/10 , by class Underfull \hbox (badness 7722) in paragraph at lines 2011--2019 []\T1/ptm/m/n/10 Objects can be gen-er-ated di-rectly by calls of the form []\T 1/zi4/m/sl/10 new("Cholesky", ...) []\T1/ptm/m/n/10 or Underfull \hbox (badness 1990) in paragraph at lines 2051--2060 []\T1/ptm/m/n/10 In \T1/ptm/b/n/10 Ma-trix []\T1/zi4/m/sl/10 < 1.6-0[]\T1/ptm/m /n/10 , class []\T1/zi4/m/sl/10 Cholesky []\T1/ptm/m/n/10 ex-tended [][][]\T1/z i4/m/sl/10 dtrMatrix[][][] []\T1/ptm/m/n/10 and class []\T1/zi4/m/sl/10 pCholes ky []\T1/ptm/m/n/10 ex-tended Underfull \hbox (badness 2334) in paragraph at lines 2066--2070 []\T1/ptm/m/n/10 The LA-PACK source code, in-clud-ing doc-u-men-ta-tion; see [] []$\T1/zi4/m/sl/10 https : / / netlib . org / lapack / Underfull \hbox (badness 1616) in paragraph at lines 2066--2070 \T1/zi4/m/sl/10 double / dpstrf . f$[][]\T1/ptm/m/n/10 , [][]$\T1/zi4/m/sl/10 h ttps : / / netlib . org / lapack / double / dpotrf . f$[][]\T1/ptm/m/n/10 , and [][]$\T1/zi4/m/sl/10 https : / / netlib . [2946] [2947] Underfull \hbox (badness 6220) in paragraph at lines 2185--2187 []\T1/ptm/m/n/10 Methods for [][][]\T1/zi4/m/sl/10 sparseMatrix[][][] []\T1/ptm /m/n/10 are built on CHOLMOD rou-tines []\T1/zi4/m/sl/10 cholmod_analyze []\T1/ ptm/m/n/10 and [2948] [2949] Underfull \hbox (badness 2334) in paragraph at lines 2315--2319 []\T1/ptm/m/n/10 The LA-PACK source code, in-clud-ing doc-u-men-ta-tion; see [] []$\T1/zi4/m/sl/10 https : / / netlib . org / lapack / Underfull \hbox (badness 1616) in paragraph at lines 2315--2319 \T1/zi4/m/sl/10 double / dpstrf . f$[][]\T1/ptm/m/n/10 , [][]$\T1/zi4/m/sl/10 h ttps : / / netlib . org / lapack / double / dpotrf . f$[][]\T1/ptm/m/n/10 , and [][]$\T1/zi4/m/sl/10 https : / / netlib . [2950] Underfull \vbox (badness 10000) has occurred while \output is active [2951] Underfull \vbox (badness 10000) has occurred while \output is active [2952] Underfull \vbox (badness 10000) has occurred while \output is active [2953] [2954] [2955] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.colMeans} ) has been already used, duplicate ignored \relax l.2696 ...asA{colMeans}{colSums-methods}{colMeans} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.colSums}) has been already used, duplicate ignored \relax l.2704 \aliasA{colSums}{colSums-methods}{colSums} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.rowMeans} ) has been already used, duplicate ignored \relax l.2711 ...asA{rowMeans}{colSums-methods}{rowMeans} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.rowSums}) has been already used, duplicate ignored \relax l.2719 \aliasA{rowSums}{colSums-methods}{rowSums} [2956] [2957] Underfull \hbox (badness 3547) in paragraph at lines 2888--2891 []\T1/ptm/m/n/10 a num-ber $\OML/cmm/m/it/10 > \OT1/cmr/m/n/10 0$\T1/ptm/m/n/10 , the es-ti-mated (1-norm) con-di-tion num-ber $[]$; when [2958] [2959] [2960] [2961] [2962] [2963] [2964] Underfull \hbox (badness 1983) in paragraph at lines 3390--3398 []\T1/ptm/m/n/10 and [][][]\T1/zi4/m/sl/10 unpackedMatrix[][][][]\T1/ptm/m/n/10 . Al-ter-na-tively into the (cur-rently) three sub-classes [][][]\T1/zi4/m/sl/ 10 ddenseMatrix[][][][]\T1/ptm/m/n/10 , [2965] [2966] [2967] [2968] Underfull \hbox (badness 2717) in paragraph at lines 3712--3716 []\T1/ptm/m/n/10 However this means that a ma-trix typ-i-cally can be stored in more than one pos-si-ble [2969] [2970] Underfull \hbox (badness 3417) in paragraph at lines 3828--3830 []\T1/zi4/m/sl/10 .sparseDiagonal() []\T1/ptm/m/n/10 ex-ists pri-mar-ily to lev er-age ef-fi-cient C-level meth-ods avail-able for [2971] Underfull \hbox (badness 8019) in paragraph at lines 3933--3935 []\T1/zi4/m/sl/10 signature(x = "nMatrix")[]\T1/ptm/m/n/10 , se-man-ti-cally eq uiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion [][][]\T1/zi4/m/sl/1 0 which[][][](x, Underfull \hbox (badness 10000) in paragraph at lines 3936--3940 []\T1/zi4/m/sl/10 signature(x = "diagonalMatrix")[]\T1/ptm/m/n/10 : all these g roup meth-ods re-turn a [2972] [2973] [2974] [2975] [2976] Underfull \hbox (badness 1902) in paragraph at lines 4263--4265 [][][]\T1/zi4/m/sl/10 drop0[][][](x, tol=1e-10) []\T1/ptm/m/n/10 is some-times prefer-able to (and more ef-fi-cient than) []\T1/zi4/m/sl/10 zapsmall(x, Underfull \hbox (badness 2020) in paragraph at lines 4300--4303 []\T1/ptm/m/n/10 a typ-i-cally sparse ma-trix; in-ter-nally co-erced to ei-ther []\T1/zi4/m/sl/10 "[][]dgCMatrix[][][]" []\T1/ptm/m/n/10 or [2977] [2978] [2979] Underfull \hbox (badness 4378) in paragraph at lines 4503--4512 []\T1/ptm/m/n/10 or [][][]\T1/zi4/m/sl/10 chol[][][]() []\T1/ptm/m/n/10 is typ- i-cally used, e.g., see []\T1/zi4/m/sl/10 selectMethod("coerce", c(from="dsyMat rix", [2980] [2981] [2982] [2983] [2984] Underfull \hbox (badness 10000) in paragraph at lines 4834--4837 []\T1/ptm/m/n/10 Class []\T1/zi4/m/sl/10 "dMatrix"[]\T1/ptm/m/n/10 , by class [ ]\T1/zi4/m/sl/10 "dsparseMatrix"[]\T1/ptm/m/n/10 ; class []\T1/zi4/m/sl/10 "spa rseMatrix"[]\T1/ptm/m/n/10 , by classes [2985] Underfull \hbox (badness 4518) in paragraph at lines 4929--4932 []\T1/zi4/m/sl/10 signature(x = "dspMatrix", type = "character")[]\T1/ptm/m/n/1 0 , or []\T1/zi4/m/sl/10 x = "dsyMatrix" []\T1/ptm/m/n/10 or []\T1/zi4/m/sl/10 type = Underfull \hbox (badness 3690) in paragraph at lines 4932--4935 []\T1/zi4/m/sl/10 signature(x = "dspMatrix", type = "character")[]\T1/ptm/m/n/1 0 , or []\T1/zi4/m/sl/10 x = "dsyMatrix" []\T1/ptm/m/n/10 or []\T1/zi4/m/sl/10 type = [2986] [2987] Underfull \hbox (badness 2318) in paragraph at lines 5035--5039 []\T1/ptm/m/n/10 Class []\T1/zi4/m/sl/10 "dgCMatrix"[]\T1/ptm/m/n/10 , di-rectl y. Class []\T1/zi4/m/sl/10 "triangularMatrix"[]\T1/ptm/m/n/10 , di-rectly. Clas s []\T1/zi4/m/sl/10 "dMatrix"[]\T1/ptm/m/n/10 , [2988] [2989] Underfull \hbox (badness 3240) in paragraph at lines 5151--5155 []\T1/zi4/m/sl/10 signature(x = "dtpMatrix", logarithm = "logical")[]\T1/ptm/m/ n/10 : the [][][]\T1/zi4/m/sl/10 determinant[][][](x) [2990] [2991] [2992] Underfull \hbox (badness 10000) in paragraph at lines 5399--5401 []\T1/ptm/m/n/10 a ma-trix fac-tor-iza-tion, typ-i-cally in-her-it-ing from vir -tual class [2993] [2994] Underfull \hbox (badness 10000) in paragraph at lines 5522--5529 []\T1/zi4/m/sl/10 signature(x = "CHMfactor")[]\T1/ptm/m/n/10 : as []\T1/zi4/m/s l/10 expand2[]\T1/ptm/m/n/10 , but re-turn-ing []\T1/zi4/m/sl/10 list(P, L)[]\T 1/ptm/m/n/10 . Underfull \hbox (badness 1776) in paragraph at lines 5522--5529 []\T1/zi4/m/sl/10 expand(x)[["P"]] []\T1/ptm/m/n/10 and []\T1/zi4/m/sl/10 expan d2(x)[["P1"]] []\T1/ptm/m/n/10 rep-re-sent the same per-mu-ta-tion ma-trix Underfull \hbox (badness 10000) in paragraph at lines 5529--5544 []\T1/zi4/m/sl/10 signature(x = "sparseLU")[]\T1/ptm/m/n/10 : as []\T1/zi4/m/sl /10 expand2[]\T1/ptm/m/n/10 , but re-turn-ing []\T1/zi4/m/sl/10 list(P, L, U, Q )[]\T1/ptm/m/n/10 . Underfull \hbox (badness 10000) in paragraph at lines 5544--5549 []\T1/zi4/m/sl/10 signature(x = "denseLU")[]\T1/ptm/m/n/10 : as []\T1/zi4/m/sl/ 10 expand2[]\T1/ptm/m/n/10 , but re-turn-ing []\T1/zi4/m/sl/10 list(L, U, P)[]\ T1/ptm/m/n/10 . Underfull \hbox (badness 1142) in paragraph at lines 5544--5549 []\T1/zi4/m/sl/10 expand(x)[["P"]] []\T1/ptm/m/n/10 and []\T1/zi4/m/sl/10 expan d2(x)[["P1."]] []\T1/ptm/m/n/10 are iden-ti-cal mod-ulo []\T1/zi4/m/sl/10 Dimna mes[]\T1/ptm/m/n/10 . The [2995] [2996] [2997] [2998] [2999] [3000] [3001] Underfull \hbox (badness 1087) in paragraph at lines 5987--5993 []\T1/ptm/m/n/10 a string whose first three char-ac-ters spec-ify the class of the re-sult. It Underfull \hbox (badness 10000) in paragraph at lines 6000--6002 []\T1/ptm/m/n/10 a string in []\T1/zi4/m/sl/10 c("trace", "sumLog", "prod", "mi n", "max", "range", [3002] [3003] [3004] [3005] Underfull \hbox (badness 1931) in paragraph at lines 6262--6264 []\T1/ptm/m/n/10 a string spec-i-fy-ing how the []\T1/zi4/m/sl/10 zero.print [] \T1/ptm/m/n/10 codes should be aligned, see [3006] [3007] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.image}) h as been already used, duplicate ignored \relax l.6399 \aliasA{image}{image-methods}{image} [3008] Underfull \hbox (badness 1005) in paragraph at lines 6476--6481 []\T1/ptm/m/n/10 color for the bor-der of each rect-an-gle. []\T1/zi4/m/sl/10 N A []\T1/ptm/m/n/10 means no bor-der is drawn. Underfull \hbox (badness 1189) in paragraph at lines 6476--6481 \T1/ptm/m/n/10 When []\T1/zi4/m/sl/10 NULL []\T1/ptm/m/n/10 as by de-fault, []\ T1/zi4/m/sl/10 border.col <- if(lwd < .01) NA else NULL []\T1/ptm/m/n/10 is Underfull \hbox (badness 5862) in paragraph at lines 6495--6498 []\T1/ptm/m/n/10 All meth-ods cur-rently end up call-ing the method for the [][ ][]\T1/zi4/m/sl/10 dgTMatrix[][][] []\T1/ptm/m/n/10 class. Use [3009] Overfull \hbox (42.75635pt too wide) in paragraph at lines 6545--6545 []\T1/zi4/m/n/9 image(USCounties, c(1,100), c(1,100), useAbs=FALSE, lwd=3, bor der.col = adjustcolor("skyblue", 1/2))[] [3010] [3011] [3012] [3013] Underfull \hbox (badness 1509) in paragraph at lines 6810--6812 []\T1/ptm/m/n/10 an in-te-ger off-set, in-di-cat-ing that the re-sult should be a per-mu-ta-tion of [3014] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.anyNA}) h as been already used, duplicate ignored \relax l.6888 \aliasA{anyNA}{is.na-methods}{anyNA} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.is.finite }) has been already used, duplicate ignored \relax l.6895 ...asA{is.finite}{is.na-methods}{is.finite} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.is.infini te}) has been already used, duplicate ignored \relax l.6903 ...is.infinite}{is.na-methods}{is.infinite} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.is.na}) h as been already used, duplicate ignored \relax l.6911 \aliasA{is.na}{is.na-methods}{is.na} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.is.nan}) has been already used, duplicate ignored \relax l.6918 \aliasA{is.nan}{is.na-methods}{is.nan} [3015] [3016] [3017] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.isSymmetr ic}) has been already used, duplicate ignored \relax l.7077 ...etric}{isSymmetric-methods}{isSymmetric} Overfull \hbox (26.39984pt too wide) in paragraph at lines 7124--7124 []\T1/zi4/m/sl/10 isSymmetric(object, checkDN = TRUE, tol = 100 * .Machine$dou ble.eps, tol1 = 8 * tol, ...)[] [3018] [3019] [3020] [3021] [3022] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.kronecker }) has been already used, duplicate ignored \relax l.7453 ...kronecker}{kronecker-methods}{kronecker} [3023] [3024] [3025 pdfTeX warning (ext4): destination with the same identifier (name{Rfn.*,ndiMatr ix,Matrix.Rdash.method}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.7718 \end{Description} ] Underfull \hbox (badness 2478) in paragraph at lines 7736--7741 []\T1/ptm/m/n/10 Class []\T1/zi4/m/sl/10 "ldenseMatrix"[]\T1/ptm/m/n/10 , di-re ctly. Class []\T1/zi4/m/sl/10 "lMatrix"[]\T1/ptm/m/n/10 , by class []\T1/zi4/m/ sl/10 "ldenseMatrix"[]\T1/ptm/m/n/10 . Class Underfull \hbox (badness 10000) in paragraph at lines 7744--7747 []\T1/ptm/m/n/10 Currently, mainly [][][]\T1/zi4/m/sl/10 t[][][]() []\T1/ptm/m/ n/10 and co-er-cion meth-ods (for [][][]\T1/zi4/m/sl/10 as[][][](.)[]\T1/ptm/m/ n/10 ); use, e.g., [3026] [3027] [3028] Underfull \hbox (badness 10000) in paragraph at lines 7968--7971 []\T1/ptm/m/n/10 Currently, mainly [][][]\T1/zi4/m/sl/10 t[][][]() []\T1/ptm/m/ n/10 and co-er-cion meth-ods (for [][][]\T1/zi4/m/sl/10 as[][][](.)[]\T1/ptm/m/ n/10 ; use, e.g., [3029] Underfull \hbox (badness 10000) in paragraph at lines 8029--8032 []\T1/ptm/m/n/10 Currently, mainly [][][]\T1/zi4/m/sl/10 t[][][]() []\T1/ptm/m/ n/10 and co-er-cion meth-ods (for [][][]\T1/zi4/m/sl/10 as[][][](.)[]\T1/ptm/m/ n/10 ; use, e.g., [3030] [3031] [3032] [3033] pdfTeX warning (ext4): destination with the same identifier (name{Rfn..Rpcent.* .Rpcent.}) has been already used, duplicate ignored \relax l.8310 ...*\%}{matmult-methods}{.Rpcent.*.Rpcent.} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.crossprod }) has been already used, duplicate ignored \relax l.8384 ...A{crossprod}{matmult-methods}{crossprod} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.tcrosspro d}) has been already used, duplicate ignored \relax l.8460 ...tcrossprod}{matmult-methods}{tcrossprod} [3034] Underfull \hbox (badness 10000) in paragraph at lines 8618--8623 []\T1/zi4/m/sl/10 signature(x = "dtrMatrix", y = "matrix") []\T1/ptm/m/n/10 and other sig-na-tures (use Underfull \hbox (badness 5359) in paragraph at lines 8618--8623 []\T1/zi4/m/sl/10 showMethods("%*%", class="dtrMatrix")[]\T1/ptm/m/n/10 ): ma-t rix mul-ti-pli-ca-tion. Mul-ti-pli-ca-tion Underfull \hbox (badness 10000) in paragraph at lines 8627--8629 []\T1/zi4/m/sl/10 signature(x = "CsparseMatrix", y = "missing") []\T1/ptm/m/n/1 0 re-turns []\T1/zi4/m/sl/10 t(x) %*% x []\T1/ptm/m/n/10 as an Underfull \hbox (badness 10000) in paragraph at lines 8629--8631 []\T1/zi4/m/sl/10 signature(x = "TsparseMatrix", y = "missing") []\T1/ptm/m/n/1 0 re-turns []\T1/zi4/m/sl/10 t(x) %*% x []\T1/ptm/m/n/10 as an [3035] [3036] [3037] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.det}) has been already used, duplicate ignored \relax l.8856 \aliasA{det}{Matrix-class}{det} [3038] Underfull \hbox (badness 1527) in paragraph at lines 8933--8935 []\T1/zi4/m/sl/10 signature(x = "Matrix")[]\T1/ptm/m/n/10 : sim-ply de-fined as []\T1/zi4/m/sl/10 prod(dim(x)) []\T1/ptm/m/n/10 (and hence of mode Underfull \hbox (badness 4846) in paragraph at lines 8941--8944 []\T1/zi4/m/sl/10 signature(object = "Matrix")[]\T1/ptm/m/n/10 : draws an [][][ ]\T1/zi4/m/sl/10 image[][][] []\T1/ptm/m/n/10 of the ma-trix en-tries, us-ing Underfull \hbox (badness 10000) in paragraph at lines 8946--8949 [3039] [3040] [3041] Underfull \hbox (badness 10000) in paragraph at lines 9148--9150 []\T1/zi4/m/sl/10 signature(x = "MatrixFactorization", logarithm = "missing")[] \T1/ptm/m/n/10 : sets Underfull \hbox (badness 10000) in paragraph at lines 9154--9156 []\T1/zi4/m/sl/10 signature(x = "MatrixFactorization", value = "NULL")[]\T1/ptm /m/n/10 : re-turns []\T1/zi4/m/sl/10 x []\T1/ptm/m/n/10 with Underfull \hbox (badness 10000) in paragraph at lines 9156--9158 []\T1/zi4/m/sl/10 signature(x = "MatrixFactorization", value = "list")[]\T1/ptm /m/n/10 : re-turns []\T1/zi4/m/sl/10 x []\T1/ptm/m/n/10 with [3042] Underfull \hbox (badness 10000) in paragraph at lines 9193--9196 []\T1/ptm/m/n/10 Generic func-tions [][][]\T1/zi4/m/sl/10 expand1[][][] []\T1/p tm/m/n/10 and [][][]\T1/zi4/m/sl/10 expand2[][][] []\T1/ptm/m/n/10 for con-stru ct-ing ma-trix fac-tors from [3043] Underfull \hbox (badness 10000) in paragraph at lines 9311--9313 []\T1/ptm/m/n/10 logical in-di-cat-ing if []\T1/zi4/m/sl/10 X <- (X + t(X))/2 [ ]\T1/ptm/m/n/10 should be done, af-ter []\T1/zi4/m/sl/10 X <- [3044] [3045] [3046] Underfull \hbox (badness 2478) in paragraph at lines 9507--9512 []\T1/ptm/m/n/10 Class []\T1/zi4/m/sl/10 "ndenseMatrix"[]\T1/ptm/m/n/10 , di-re ctly. Class []\T1/zi4/m/sl/10 "lMatrix"[]\T1/ptm/m/n/10 , by class []\T1/zi4/m/ sl/10 "ndenseMatrix"[]\T1/ptm/m/n/10 . Class [3047] Underfull \hbox (badness 10000) in paragraph at lines 9515--9518 []\T1/ptm/m/n/10 Currently, mainly [][][]\T1/zi4/m/sl/10 t[][][]() []\T1/ptm/m/ n/10 and co-er-cion meth-ods (for [][][]\T1/zi4/m/sl/10 as[][][](.)[]\T1/ptm/m/ n/10 ); use, e.g., [3048] [3049] Underfull \hbox (badness 5924) in paragraph at lines 9696--9698 []\T1/ptm/m/n/10 fast sim-ple meth-ods pdfTeX warning (ext4): destination with the same identifier (name{Rfn.norm}) ha s been already used, duplicate ignored \relax l.9738 \aliasA{norm}{norm-methods}{norm} [3050] [3051] [3052] [3053] Underfull \hbox (badness 10000) in paragraph at lines 10031--10034 []\T1/ptm/m/n/10 Currently, mainly [][][]\T1/zi4/m/sl/10 t[][][]() []\T1/ptm/m/ n/10 and co-er-cion meth-ods (for [][][]\T1/zi4/m/sl/10 as[][][](.)[]\T1/ptm/m/ n/10 ; use, e.g., [3054] Underfull \hbox (badness 10000) in paragraph at lines 10095--10098 []\T1/ptm/m/n/10 Currently, mainly [][][]\T1/zi4/m/sl/10 t[][][]() []\T1/ptm/m/ n/10 and co-er-cion meth-ods (for [][][]\T1/zi4/m/sl/10 as[][][](.)[]\T1/ptm/m/ n/10 ; use, e.g., [3055] [3056] [3057] Underfull \hbox (badness 4242) in paragraph at lines 10295--10298 [][][]\T1/zi4/m/sl/10 pack[][][] []\T1/ptm/m/n/10 and [][][]\T1/zi4/m/sl/10 unp ack[][][][]\T1/ptm/m/n/10 ; its vir-tual "com-ple-ment" []\T1/zi4/m/sl/10 "[][] unpackedMatrix[][][]"[]\T1/ptm/m/n/10 ; its proper sub-classes [3058] Underfull \hbox (badness 3547) in paragraph at lines 10383--10386 []\T1/zi4/m/sl/10 signature(x = "pMatrix", y = "Matrix") []\T1/ptm/m/n/10 and o th-ers listed by []\T1/zi4/m/sl/10 showMethods("%*%", [3059] [3060] [3061] [3062] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.qr}) has been already used, duplicate ignored \relax l.10601 \aliasA{qr}{qr-methods}{qr} [3063] [3064] Underfull \vbox (badness 10000) has occurred while \output is active [3065] [3066] Underfull \hbox (badness 7186) in paragraph at lines 10845--10851 []\T1/ptm/m/n/10 for a dense ma-trix, this is the rank of [][][]\T1/zi4/m/sl/10 qr[][][](x, tol, [3067] [3068] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.rcond}) h as been already used, duplicate ignored \relax l.11002 \aliasA{rcond}{rcond-methods}{rcond} [3069] [3070] [3071] [3072] Underfull \hbox (badness 2351) in paragraph at lines 11284--11292 []\T1/ptm/m/n/10 The al-go-rithm first sam-ples ``en-coded'' $\OT1/cmr/m/n/10 ( \OML/cmm/m/it/10 i; j\OT1/cmr/m/n/10 )$\T1/ptm/m/n/10 s with-out re-place-ment, via one di-men-sional Underfull \hbox (badness 1509) in paragraph at lines 11284--11292 \T1/ptm/m/n/10 in-dices, if not []\T1/zi4/m/sl/10 symmetric [][]sample.int[][][ ](nrow*ncol, nnz)[]\T1/ptm/m/n/10 , then---if []\T1/zi4/m/sl/10 rand.x []\T1/pt m/m/n/10 is not []\T1/zi4/m/sl/10 NULL[]\T1/ptm/m/n/10 --- [3073] [3074] Underfull \hbox (badness 10000) in paragraph at lines 11441--11444 []\T1/ptm/m/n/10 Class [][][]\T1/zi4/m/sl/10 SchurFactorization[][][][]\T1/ptm/ m/n/10 , di-rectly. Class [][][]\T1/zi4/m/sl/10 MatrixFactorization[][][][]\T1/ ptm/m/n/10 , by class [3075] [3076] [3077] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.solve}) h as been already used, duplicate ignored \relax l.11630 \aliasA{solve}{solve-methods}{solve} [3078] [3079] Underfull \hbox (badness 5316) in paragraph at lines 11816--11821 []\T1/ptm/m/n/10 Methods for dense []\T1/zi4/m/sl/10 a []\T1/ptm/m/n/10 are bui lt on 14 LA-PACK rou-tines: class []\T1/zi4/m/sl/10 d..Matrix[]\T1/ptm/m/n/10 , where [3080] Underfull \hbox (badness 10000) in paragraph at lines 11916--11919 []\T1/ptm/m/n/10 Construct a sparse model or ``de-sign'' ma-trix, from a for-mu la and data frame [3081] Underfull \hbox (badness 10000) in paragraph at lines 11952--11955 []\T1/ptm/m/n/10 character string or []\T1/zi4/m/sl/10 NULL []\T1/ptm/m/n/10 or (co-er-ca-ble to) Underfull \hbox (badness 10000) in paragraph at lines 11963--11967 []\T1/ptm/m/n/10 should fac-tors have un-used lev-els dropped? The de-fault for [3082] [3083] [3084] [3085] [3086] [3087] [3088] [3089] Underfull \hbox (badness 10000) in paragraph at lines 12500--12508 []\T1/zi4/m/sl/10 (object = "sparseMatrix", uniqT=FALSE)[]\T1/ptm/m/n/10 : Re-t urns an ob-ject of S3 class Underfull \hbox (badness 1796) in paragraph at lines 12500--12508 []\T1/zi4/m/sl/10 "sparseSummary" []\T1/ptm/m/n/10 which is ba-si-cally a [][][ ]\T1/zi4/m/sl/10 data.frame[][][] []\T1/ptm/m/n/10 with columns []\T1/zi4/m/sl/ 10 (i,j,x) []\T1/ptm/m/n/10 (or just Underfull \hbox (badness 10000) in paragraph at lines 12525--12533 []\T1/zi4/m/sl/10 signature(from = "factor", to = "sparseMatrix")[]\T1/ptm/m/n/ 10 : Co-er-cion of a fac-tor to Underfull \hbox (badness 1112) in paragraph at lines 12525--12533 []\T1/zi4/m/sl/10 "sparseMatrix" []\T1/ptm/m/n/10 pro-duces the ma-trix of in-d i-ca-tor \T1/ptm/b/n/10 rows \T1/ptm/m/n/10 stored as an ob-ject of class [3090] [3091] [3092] [3093] [3094] Underfull \hbox (badness 5036) in paragraph at lines 12918--12920 []\T1/ptm/m/n/10 vector of the non zero en-tries; may be miss-ing in which case a [3095] [3096] Underfull \hbox (badness 2828) in paragraph at lines 13084--13087 []\T1/zi4/m/sl/10 signature(x = "sparseVector", mode = "character") []\T1/ptm/m /n/10 co-erces sparse vec-tors to Underfull \hbox (badness 2486) in paragraph at lines 13106--13109 []\T1/zi4/m/sl/10 signature(x = "sparseVector") []\T1/ptm/m/n/10 re-peat []\T1/ zi4/m/sl/10 x[]\T1/ptm/m/n/10 , with the same ar-gu-ment list []\T1/zi4/m/sl/10 (x, times, [3097] [3098] [3099] [3100] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.[<.Rdash. }) has been already used, duplicate ignored \relax l.13311 ...\Rdash{}}{subassign-methods}{[<.Rdash.} Underfull \hbox (badness 6910) in paragraph at lines 13398--13400 []\T1/ptm/m/n/10 is cur-rently a sim-ple fall-back [3101] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.[}) has b een already used, duplicate ignored \relax l.13445 \aliasA{[}{subscript-methods}{[} [3102] [3103] Underfull \hbox (badness 2057) in paragraph at lines 13656--13658 []\T1/ptm/m/n/10 These are generic func-tions with sev-eral meth-ods for dif-fe r-ent ma-trix classes, use e.g., Underfull \hbox (badness 10000) in paragraph at lines 13670--13675 []\T1/zi4/m/sl/10 skewpart(x) []\T1/ptm/m/n/10 re-turns a skew-symmetric ma-tri x, in-her-it-ing from [][][]\T1/zi4/m/sl/10 generalMatrix[][][][]\T1/ptm/m/n/10 , [3104] [3105] [3106] Underfull \hbox (badness 10000) in paragraph at lines 13826--13831 []\T1/ptm/m/n/10 Note that all []\T1/zi4/m/sl/10 new(.)[]\T1/ptm/m/n/10 , [][][ ]\T1/zi4/m/sl/10 spMatrix[][][] []\T1/ptm/m/n/10 and [][][]\T1/zi4/m/sl/10 spar seMatrix[][][](*, repr="T") []\T1/ptm/m/n/10 con-struc-tors for Underfull \hbox (badness 1831) in paragraph at lines 13832--13838 []\T1/ptm/m/n/10 For con-ve-nience, meth-ods for some op-er-a-tions such as []\ T1/zi4/m/sl/10 %*% []\T1/ptm/m/n/10 and []\T1/zi4/m/sl/10 crossprod []\T1/ptm/m /n/10 are de-fined [3107] [3108] [3109] Overfull \hbox (21.75807pt too wide) in paragraph at lines 14021--14027 []\T1/ptm/m/n/10 GAL lat-tice file `\T1/zi4/m/sl/10 usc_q.GAL\T1/ptm/m/n/10 ' ( re-trieved in 2008 from `\T1/zi4/m/sl/10 http://sal.uiuc.edu/weights/zips/usc.z ip\T1/ptm/m/n/10 ' [3110] [3111] [3112]) (./mgcv-pkg.tex Chapter 24. [3113] [3114] [3115] Underfull \hbox (badness 1142) in paragraph at lines 185--189 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from Underfull \hbox (badness 1043) in paragraph at lines 210--215 \T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known scale. [3116] [3117] [3118] [3119] [3120] Underfull \hbox (badness 10000) in paragraph at lines 379--386 [][][]\T1/zi4/m/sl/10 mgcv.parallel[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/ 10 mgcv-package[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 gamObject[][][][] \T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 gam.models[][][][]\T1/ptm/m/n/10 , [][][ ]\T1/zi4/m/sl/10 smooth.terms[][][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 7168) in paragraph at lines 379--386 [][][]\T1/zi4/m/sl/10 linear.functional.terms[][][][]\T1/ptm/m/n/10 , [][][]\T1 /zi4/m/sl/10 s[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 te[][][] [][]predi ct.gam[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 plot.gam[][][][]\T1/ptm/m/ n/10 , [][][]\T1/zi4/m/sl/10 summary.gam[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/ m/sl/10 gam.side[][][][]\T1/ptm/m/n/10 , [3121] [3122] [3123] [3124] [3125] [3126] Underfull \hbox (badness 1406) in paragraph at lines 704--705 []\T1/ptm/m/n/10 The MKL BLAS is mut-lithreaded by de-fault. Un-der linux set-t ing en-vi-ron-ment vari-able [3127] [3128] Underfull \hbox (badness 1158) in paragraph at lines 814--816 []\T1/ptm/m/n/10 Choosing the ba-sis di-men-sion, and check-ing the choice, whe n us-ing pe-nal-ized re-gres-sion [3129] Underfull \hbox (badness 1259) in paragraph at lines 877--878 []\T1/ptm/m/n/10 Wood, S.N. (2017) Gen-er-al-ized Ad-di-tive Mod-els: An In-tro -duc-tion with R (2nd edi-tion). [3130] Underfull \vbox (badness 10000) has occurred while \output is active [3131] [3132] [3133] [3134] [3135] [3136] [3137] Underfull \hbox (badness 1281) in paragraph at lines 1272--1273 []\T1/zi4/m/sl/10 deviance[]\T1/ptm/m/n/10 ,[]\T1/zi4/m/sl/10 martingale[]\T1/p tm/m/n/10 ,[]\T1/zi4/m/sl/10 score[]\T1/ptm/m/n/10 , or []\T1/zi4/m/sl/10 schoe nfeld []\T1/ptm/m/n/10 resid-u-als can be ex-tracted. See Klein amd [3138] [3139] Underfull \vbox (badness 10000) has occurred while \output is active [3140] [3141] [3142] Underfull \vbox (badness 10000) has occurred while \output is active [3143] [3144] [3145] [3146] [3147] [3148] [3149] [3150] [3151] [3152] [3153] [3154] [3155] [3156] [3157] Underfull \vbox (badness 2302) has occurred while \output is active [3158] [3159] [3160] [3161] [3162] Underfull \hbox (badness 1142) in paragraph at lines 2604--2608 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from Underfull \hbox (badness 1043) in paragraph at lines 2630--2636 \T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known scale. [3163] [3164] [3165] [3166] [3167] [3168] [3169] Underfull \vbox (badness 10000) has occurred while \output is active [3170] Underfull \vbox (badness 10000) has occurred while \output is active [3171] [3172] [3173] [3174] [3175] [3176] [3177] [3178] [3179] [3180] [3181] [3182] [3183] [3184] [3185] [3186] [3187] [3188] Underfull \hbox (badness 10000) in paragraph at lines 4071--4075 []\T1/ptm/m/n/10 Random ef-fects can be added to []\T1/zi4/m/sl/10 gam []\T1/pt m/m/n/10 mod-els us-ing []\T1/zi4/m/sl/10 s(...,bs="re") []\T1/ptm/m/n/10 terms (see [3189] [3190] Underfull \vbox (badness 10000) has occurred while \output is active [3191] Underfull \vbox (badness 10000) has occurred while \output is active [3192] [3193] Underfull \hbox (badness 1184) in paragraph at lines 4358--4362 []\T1/ptm/m/n/10 list of the square root penal-ties: last en-try is root of fix ed penalty, if [3194] [3195] [3196] [3197] [3198] [3199] [3200] [3201] [3202] [3203] [3204] [3205] [3206] Underfull \hbox (badness 1142) in paragraph at lines 5081--5085 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from [3207] [3208] Underfull \hbox (badness 1231) in paragraph at lines 5185--5187 []\T1/zi4/m/sl/10 gamm []\T1/ptm/m/n/10 per-forms poorly with bi-nary data, sin ce it uses PQL. It is bet-ter to use []\T1/zi4/m/sl/10 gam []\T1/ptm/m/n/10 wit h [3209] [3210] Underfull \vbox (badness 10000) has occurred while \output is active [3211] Underfull \vbox (badness 10000) has occurred while \output is active [3212] [3213] [3214] [3215] Underfull \hbox (badness 2181) in paragraph at lines 5626--5627 []\T1/ptm/m/n/10 one sided for-mula con-tain-ing vari-ables needed for pre-dic- tion, used by [3216] [3217] [3218] [3219] [3220] [3221] [3222] [3223] [3224] Underfull \vbox (badness 3803) has occurred while \output is active [3225] Underfull \hbox (badness 10000) in paragraph at lines 6130--6131 []\T1/ptm/m/n/10 A pre-fit gam ob-ject, as pro-duced by []\T1/zi4/m/sl/10 gam(. ..,fit=FALSE) []\T1/ptm/m/n/10 or [3226] [3227] [3228] [3229] [3230] [3231] [3232] [3233] [3234] [3235] [3236] Underfull \hbox (badness 1142) in paragraph at lines 6715--6719 \T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t aken from [3237] [3238] [3239] [3240] Underfull \vbox (badness 3803) has occurred while \output is active [3241] [3242] [3243] [3244] Underfull \hbox (badness 1087) in paragraph at lines 7087--7088 []\T1/ptm/m/n/10 If []\T1/zi4/m/sl/10 rho []\T1/ptm/m/n/10 and []\T1/zi4/m/sl/1 0 theta []\T1/ptm/m/n/10 were sup-plied then deriva-tives are w.r.t. these. In this case, and if [3245] [3246] [3247] Underfull \vbox (badness 10000) has occurred while \output is active [3248] Underfull \vbox (badness 10000) has occurred while \output is active [3249] [3250] [3251] [3252] [3253] [3254] [3255] [3256] [3257] [3258] [3259] Underfull \vbox (badness 4805) has occurred while \output is active [3260] [3261] [3262] Underfull \hbox (badness 1242) in paragraph at lines 8046--8047 []\T1/ptm/m/n/10 Development of mgcv ver-sion 1.8 was part funded by EP-SRC gra nts EP/K005251/1 and Underfull \hbox (badness 1122) in paragraph at lines 8072--8073 []\T1/ptm/m/n/10 When us-ing [][][]\T1/zi4/m/sl/10 NCV[][][] []\T1/ptm/m/n/10 w ith [][][]\T1/zi4/m/sl/10 gam[][][] []\T1/ptm/m/n/10 worth-while per-for-mance im-prove-ments are avail-able by set-ting [3263] [3264] [3265] [3266] [3267] [3268] [3269] [3270] [3271] [3272] [3273] [3274] [3275] [3276] [3277] Underfull \hbox (badness 6001) in paragraph at lines 8785--8787 []\T1/ptm/m/n/10 Simon N. Wood \T1/zi4/m/sl/10 \T1/p tm/m/n/10 mod-i-fied from Ven-ables and Rip-ley's [3278] [3279] [3280] [3281] [3282] [3283] [3284] [3285] [3286] [3287] [3288] Underfull \vbox (badness 10000) has occurred while \output is active [3289] [3290] Underfull \hbox (badness 1038) in paragraph at lines 9533--9536 []\T1/ptm/m/n/10 The fol-low-ing func-tions are pro-vided: []\T1/zi4/m/sl/10 Di m.pdIndot[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 coef.pdIdnot[]\T1/ptm/m/n/10 , [] \T1/zi4/m/sl/10 corMatrix.pdIdnot[]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 9533--9536 []\T1/zi4/m/sl/10 logDet.pdIdnot[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 pdConstruc t.pdIdnot[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 pdFactor.pdIdnot[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 pdMatrix.pdIdnot[]\T1/ptm/m/n/10 , [3291] Underfull \hbox (badness 10000) in paragraph at lines 9589--9592 []\T1/ptm/m/n/10 These func-tions ([]\T1/zi4/m/sl/10 pdTens[]\T1/ptm/m/n/10 , [ ]\T1/zi4/m/sl/10 pdConstruct.pdTens[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 pdFacto r.pdTens[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 pdMatrix.pdTens[]\T1/ptm/m/n/10 , [3292] [3293] [3294] [3295] [3296] [3297] [3298] [3299] [3300] [3301] [3302] [3303] Underfull \hbox (badness 1852) in paragraph at lines 10261--10264 []\T1/ptm/m/n/10 To fa-cil-i-tate plot-ting with [][][]\T1/zi4/m/sl/10 termplot [][][][]\T1/ptm/m/n/10 , if []\T1/zi4/m/sl/10 object []\T1/ptm/m/n/10 pos-sesse s an at-tribute []\T1/zi4/m/sl/10 "para.only" []\T1/ptm/m/n/10 and [3304] [3305] [3306] Underfull \hbox (badness 1852) in paragraph at lines 10430--10433 []\T1/ptm/m/n/10 To fa-cil-i-tate plot-ting with [][][]\T1/zi4/m/sl/10 termplot [][][][]\T1/ptm/m/n/10 , if []\T1/zi4/m/sl/10 object []\T1/ptm/m/n/10 pos-sesse s an at-tribute []\T1/zi4/m/sl/10 "para.only" []\T1/ptm/m/n/10 and [3307] [3308] Underfull \vbox (badness 10000) has occurred while \output is active [3309] Underfull \vbox (badness 10000) has occurred while \output is active [3310] Underfull \hbox (badness 1205) in paragraph at lines 10670--10671 []\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a tes at which Underfull \hbox (badness 2689) in paragraph at lines 10670--10671 \T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are as for Underfull \hbox (badness 1975) in paragraph at lines 10676--10681 []\T1/ptm/m/n/10 Smooth terms in a GAM for-mula are turned into smooth spec-i-f i-ca-tion ob-jects of class [3311] [3312] Underfull \hbox (badness 1205) in paragraph at lines 10760--10761 []\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a tes at which Underfull \hbox (badness 2689) in paragraph at lines 10760--10761 \T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are as for [3313] [3314] Underfull \vbox (badness 3803) has occurred while \output is active [3315] Underfull \hbox (badness 1253) in paragraph at lines 10959--10961 []\T1/ptm/m/n/10 Note that the op-ti-mized smooth-ing pa-ram-e-ter se-lec-tion cri-te-rion re-ported is one of GCV, [3316] [3317] [3318] [3319] [3320] [3321] Underfull \hbox (badness 4792) in paragraph at lines 11220--11223 []\T1/ptm/m/n/10 Alternatively, but less straight-for-wardly, the []\T1/zi4/m/s l/10 paraPen []\T1/ptm/m/n/10 ar-gu-ment to [][][]\T1/zi4/m/sl/10 gam[][][] []\ T1/ptm/m/n/10 can be used: Underfull \hbox (badness 10000) in paragraph at lines 11220--11223 \T1/ptm/m/n/10 see [][][]\T1/zi4/m/sl/10 gam.models[][][][]\T1/ptm/m/n/10 . If smooth-ing pa-ram-e-ter es-ti-ma-tion is by ML or REML (e.g. [3322] [3323] Underfull \hbox (badness 10000) in paragraph at lines 11327--11330 []\T1/ptm/m/n/10 the type of resid-u-als wanted. Usu-ally one of []\T1/zi4/m/sl /10 "deviance"[]\T1/ptm/m/n/10 , [3324] [3325] [3326] [3327] [3328] [3329] [3330] [3331] [3332] [3333] [3334] [3335] Underfull \vbox (badness 10000) has occurred while \output is active [3336] [3337] Underfull \hbox (badness 3861) in paragraph at lines 12118--12121 []\T1/ptm/m/n/10 INTERNAL rou-tine to ap-ply ini-tial Sl re-parameterization to model ma-trix X, or, if [3338] [3339] [3340] Underfull \hbox (badness 1320) in paragraph at lines 12233--12238 \T1/ptm/m/n/10 and []\T1/zi4/m/sl/10 b.orig = D*b.repara []\T1/ptm/m/n/10 (wher e []\T1/zi4/m/sl/10 b.orig []\T1/ptm/m/n/10 is the orig-i-nal pa-ram-e-ter vec- tor). If ma- [3341] [3342] Underfull \hbox (badness 1975) in paragraph at lines 12339--12344 []\T1/ptm/m/n/10 Smooth terms in a GAM for-mula are turned into smooth spec-i-f i-ca-tion ob-jects of class [3343] Underfull \hbox (badness 1762) in paragraph at lines 12428--12440 \T1/ptm/m/n/10 plate re-gres-sion splines: see [][][]\T1/zi4/m/sl/10 tprs[][][] []\T1/ptm/m/n/10 ); []\T1/zi4/m/sl/10 ts.smooth.spec []\T1/ptm/m/n/10 (thin pla te re-gres-sion splines with [3344] [3345] [3346] Underfull \vbox (badness 3803) has occurred while \output is active [3347] Underfull \hbox (badness 7667) in paragraph at lines 12640--12646 [][][]\T1/zi4/m/sl/10 gam[][][] []\T1/ptm/m/n/10 can use adap-tive smooths of o ne or two vari-ables, spec-i-fied via terms like [3348] Underfull \hbox (badness 10000) in paragraph at lines 12681--12682 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3349] [3350] [3351] [3352] Underfull \vbox (badness 3803) has occurred while \output is active [3353] Underfull \hbox (badness 10000) in paragraph at lines 12958--12960 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3354] [3355] [3356] Underfull \hbox (badness 10000) in paragraph at lines 13088--13089 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3357] [3358] Underfull \hbox (badness 1436) in paragraph at lines 13224--13231 \T1/ptm/m/n/10 nest-ing of the smooth within the fac-tor. Note how-ever that: i ) []\T1/zi4/m/sl/10 gamm []\T1/ptm/m/n/10 only al-lows one [3359] [3360] Underfull \hbox (badness 10000) in paragraph at lines 13323--13324 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3361] [3362] [3363] [3364] [3365] [3366] [3367] [3368] Underfull \vbox (badness 10000) has occurred while \output is active [3369] [3370] [3371] [3372] Underfull \hbox (badness 10000) in paragraph at lines 13924--13930 []\T1/ptm/m/n/10 A smooth spec-i-fi-ca-tion ob-ject as pro-duced by a Underfull \hbox (badness 1292) in paragraph at lines 13924--13930 []\T1/zi4/m/sl/10 s(...,bs="so",xt=list(bnd=bnd,...)) []\T1/ptm/m/n/10 term in a []\T1/zi4/m/sl/10 gam []\T1/ptm/m/n/10 for-mula. Note [3373] [3374] [3375] Underfull \vbox (badness 10000) has occurred while \output is active [3376] Underfull \vbox (badness 10000) has occurred while \output is active [3377] [3378] Underfull \hbox (badness 10000) in paragraph at lines 14268--14269 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3379] [3380] [3381] [3382] Overfull \hbox (35.26862pt too wide) in paragraph at lines 14480--14480 []\T1/zi4/m/n/9 b <- gam(y ~ s(x)+s(f1,x,bs="sz")+s(f2,x,bs="sz")+s(f1,f2,x,bs ="sz",id=1),data=dat,method="REML")[] [3383] [3384] Underfull \hbox (badness 3895) in paragraph at lines 14626--14629 [][][]\T1/zi4/m/sl/10 gam[][][] []\T1/ptm/m/n/10 can use isotropic smooths of a ny num-ber of vari-ables, spec-i-fied via terms like [3385] Underfull \hbox (badness 10000) in paragraph at lines 14671--14673 []\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a term [3386] [3387] [3388] [3389] [3390] [3391] Underfull \hbox (badness 1371) in paragraph at lines 14951--14957 []\T1/zi4/m/sl/10 bs="ad" []\T1/ptm/m/n/10 Uni-vari-ate and bi-vari-ate adap-ti ve smooths are avail-able (see Underfull \hbox (badness 10000) in paragraph at lines 14962--14964 []\T1/zi4/m/sl/10 bs="fs" []\T1/ptm/m/n/10 A spe-cial smoother class (see Underfull \hbox (badness 1132) in paragraph at lines 14962--14964 [][][]\T1/zi4/m/sl/10 smooth.construct.fs.smooth.spec[][][][]\T1/ptm/m/n/10 ) i s avail-able for the case in which a smooth is [3392] Underfull \hbox (badness 6461) in paragraph at lines 14996--15000 [][][]\T1/zi4/m/sl/10 s[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 te[][][][ ]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 t2[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi 4/m/sl/10 tprs[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 Duchon.spline[][][ ][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 cubic.regression.spline[][][][]\T1/pt m/m/n/10 , [][][]\T1/zi4/m/sl/10 p.spline[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4 /m/sl/10 d.spline[][][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 14996--15000 [][][]\T1/zi4/m/sl/10 mrf[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 soap[][ ][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 Spherical.Spline[][][][]\T1/ptm/m/n /10 , [][][]\T1/zi4/m/sl/10 adaptive.smooth[][][][]\T1/ptm/m/n/10 , [][][]\T1/z i4/m/sl/10 user.defined.smooth[][][][]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 14996--15000 [][][]\T1/zi4/m/sl/10 smooth.construct.re.smooth.spec[][][][]\T1/ptm/m/n/10 , [ ][][]\T1/zi4/m/sl/10 smooth.construct.gp.smooth.spec[][][][]\T1/ptm/m/n/10 , [3393] [3394] [3395] [3396] Underfull \hbox (badness 2326) in paragraph at lines 15200--15207 []\T1/ptm/m/n/10 These wrap-per func-tions ex-ist to al-low smooths spec-i-fied us-ing [][][]\T1/zi4/m/sl/10 smooth.construct[][][] []\T1/ptm/m/n/10 and [3397] Underfull \hbox (badness 2158) in paragraph at lines 15285--15285 []\T1/ptm/m/it/10 Extract smooth-ing pa-ram-e-ter es-ti-ma-tor co-vari-ance ma- trix from [3398] [3399] [3400] [3401] [3402] [3403] [3404] [3405] [3406] [3407] [3408] [3409] [3410] [3411] [3412] [3413] [3414] [3415] [3416] [3417] [3418] [3419] [3420] [3421] [3422] [3423] [3424] Overfull \hbox (21.42029pt too wide) in paragraph at lines 16847--16847 []\T1/zi4/m/sl/10 vcov(object, sandwich=FALSE, freq = FALSE, dispersion = NULL ,unconditional=FALSE, ...)[] [3425] [3426] [3427] Underfull \hbox (badness 1796) in paragraph at lines 16960--16963 []\T1/ptm/m/n/10 other op-tions to pass on to [][][]\T1/zi4/m/sl/10 persp[][][] []\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 image[][][] []\T1/ptm/m/n/10 or [][][] \T1/zi4/m/sl/10 contour[][][][]\T1/ptm/m/n/10 . In par-tic-u-lar [3428] [3429] [3430] [3431] [3432] [3433] Underfull \vbox (badness 3803) has occurred while \output is active [3434] [3435] [3436]) (./nlme-pkg.tex Chapter 25. [3437] [3438] [3439] [3440] [3441] [3442] [3443] [3444] [3445] [3446] [3447] [3448] [3449] [3450] [3451] [3452] [3453] [3454] [3455] [3456] [3457] [3458] [3459] [3460] [3461] [3462] [3463] [3464] [3465] [3466] [3467] [3468] [3469] [3470] [3471] [3472] [3473] Underfull \hbox (badness 10000) in paragraph at lines 2238--2244 [][][]\T1/zi4/m/sl/10 ACF.lme[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 cor ARMA[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 corClasses[][][][]\T1/ptm/m/ n/10 , [][][]\T1/zi4/m/sl/10 Dim.corSpatial[][][][]\T1/ptm/m/n/10 , [][][]\T1/z i4/m/sl/10 Initialize.corStruct[][][][]\T1/ptm/m/n/10 , [3474] [3475] [3476] [3477] [3478] [3479] [3480] [3481] [3482] [3483] [3484] [3485] [3486] [3487] [3488] [3489] [3490] [3491] [3492] [3493] [3494] [3495] [3496] [3497] [3498] [3499] [3500] [3501] [3502] [3503] [3504] [3505] [3506] [3507] [3508] [3509] Underfull \hbox (badness 1067) in paragraph at lines 4372--4377 \T1/ptm/m/n/10 ma-trix), []\T1/zi4/m/sl/10 fitted []\T1/ptm/m/n/10 (fit-ted val -ues), and []\T1/zi4/m/sl/10 residuals []\T1/ptm/m/n/10 (resid-u-als). De-fault s to [3510] [3511] [3512] [3513] [3514] [3515] [3516] [3517] [3518] [3519] [3520] [3521] [3522] Underfull \hbox (badness 10000) in paragraph at lines 5116--5120 [][][]\T1/zi4/m/sl/10 getCovariate.corStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/ zi4/m/sl/10 getCovariate.data.frame[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/ 10 getCovariate.varFunc[][][][]\T1/ptm/m/n/10 , [3523] [3524] [3525] [3526] [3527] [3528] [3529] [3530] Underfull \hbox (badness 10000) in paragraph at lines 5540--5543 [][][]\T1/zi4/m/sl/10 getGroups.corStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4 /m/sl/10 getGroups.data.frame[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 get Groups.gls[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 getGroups.lmList[][][] []\T1/ptm/m/n/10 , [3531] [3532] [3533] [3534] [3535] [3536] [3537] Underfull \hbox (badness 10000) in paragraph at lines 5915--5920 [][][]\T1/zi4/m/sl/10 getGroupsFormula.gls[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi 4/m/sl/10 getGroupsFormula.lmList[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 getGroupsFormula.lme[][][][]\T1/ptm/m/n/10 , [3538] [3539] [3540] [3541] [3542] Underfull \hbox (badness 1490) in paragraph at lines 6194--6205 [][][]\T1/zi4/m/sl/10 corClasses[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 glsControl[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 glsObject[][][][]\T1/p tm/m/n/10 , [][][]\T1/zi4/m/sl/10 glsStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/z i4/m/sl/10 plot.gls[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 predict.gls[] [][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 qqnorm.gls[][][][]\T1/ptm/m/n/10 , [3543] Underfull \hbox (badness 10000) in paragraph at lines 6258--6260 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is [3544] [3545] [3546] [3547] [3548] [3549] [3550] Underfull \hbox (badness 10000) in paragraph at lines 6667--6669 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is [3551] [3552] [3553] [3554] Underfull \hbox (badness 10000) in paragraph at lines 6936--6943 [][][]\T1/zi4/m/sl/10 formula[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 gap ply[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 gsummary[][][][]\T1/ptm/m/n/1 0 , [][][]\T1/zi4/m/sl/10 lme[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 plo t.nffGroupedData[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 plot.nfnGroupedD ata[][][][]\T1/ptm/m/n/10 , [3555] [3556] [3557] [3558] Underfull \hbox (badness 10000) in paragraph at lines 7196--7202 [][][]\T1/zi4/m/sl/10 Initialize.corStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi 4/m/sl/10 Initialize.glsStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 In itialize.lmeStruct[][][][]\T1/ptm/m/n/10 , [3559] [3560] [3561] [3562] [3563] [3564] [3565] [3566] [3567] [3568] [3569] [3570] [3571] [3572] [3573] [3574] [3575] [3576] [3577] [3578] [3579] Underfull \hbox (badness 10000) in paragraph at lines 8466--8468 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is [3580] [3581] [3582] [3583] [3584] Underfull \hbox (badness 10000) in paragraph at lines 8751--8758 [][][]\T1/zi4/m/sl/10 lm[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 lme.lmLi st[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 plot.lmList[][][][]\T1/ptm/m/n /10 , [][][]\T1/zi4/m/sl/10 pooledSD[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl /10 predict.lmList[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 residuals.lmLi st[][][][]\T1/ptm/m/n/10 , [3585] [3586] [3587] [3588] [3589] [3590] [3591] [3592] [3593] Underfull \hbox (badness 10000) in paragraph at lines 9266--9273 [][][]\T1/zi4/m/sl/10 lme[][][][]\T1/ptm/m/n/10 ,[][][]\T1/zi4/m/sl/10 gls[][][ ][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 logLik.corStruct[][][][]\T1/ptm/m/n/1 0 , [][][]\T1/zi4/m/sl/10 logLik.glsStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi 4/m/sl/10 logLik.lmeStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 logLik .lmList[][][][]\T1/ptm/m/n/10 , [3594] [3595] [3596] [3597] [3598] [3599] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Matrix}) has been already used, duplicate ignored \relax l.9628 ...rA{Matrix}{Assign Matrix Values}{Matrix} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.Matrix.1} ) has been already used, duplicate ignored \relax l.9628 ...rA{Matrix}{Assign Matrix Values}{Matrix} [3600] [3601] [3602] [3603] [3604] [3605] [3606] [3607] [3608] [3609] [3610] [3611] [3612] Underfull \hbox (badness 1596) in paragraph at lines 10395--10421 []\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a two-sided for-mula o f the form [3613] [3614] Underfull \hbox (badness 1490) in paragraph at lines 10511--10517 [][][]\T1/zi4/m/sl/10 nlmeControl[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 nlme.nlsList[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 nlmeObject[][][][]\ T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 nlsList[][][][]\T1/ptm/m/n/10 , [][][]\T1 /zi4/m/sl/10 nlmeStruct[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 pdClasses [][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 reStruct[][][][]\T1/ptm/m/n/10 , [3615] [3616] [3617] [3618] Underfull \hbox (badness 10000) in paragraph at lines 10752--10754 []\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D e-fault is [3619] [3620] [3621] [3622] [3623] [3624] [3625] [3626] [3627] [3628] [3629] [3630] [3631] [3632] [3633] [3634] [3635] [3636] [3637] [3638] [3639] [3640] [3641] [3642] [3643] [3644] [3645] [3646] [3647] [3648] [3649] [3650] [3651] [3652] [3653] [3654] [3655] [3656] [3657] [3658] [3659] [3660] [3661] [3662] [3663] [3664] [3665] Underfull \hbox (badness 1286) in paragraph at lines 13655--13662 []\T1/ptm/m/n/10 an op-tional log-i-cal func-tion or func-tion. If []\T1/zi4/m/ sl/10 TRUE []\T1/ptm/m/n/10 and ei-ther []\T1/zi4/m/sl/10 inner []\T1/ptm/m/n/1 0 or [3666] [3667] [3668] [3669] [3670] [3671] [3672] [3673] [3674] [3675] [3676] [3677] [3678] [3679] [3680] [3681] [3682] [3683] [3684] [3685] [3686] [3687] [3688] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.random.ef fects}) has been already used, duplicate ignored \relax l.15098 ...Extract Random Effects}{random.effects} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.random.ef fects.1}) has been already used, duplicate ignored \relax l.15098 ...Extract Random Effects}{random.effects} [3689] [3690] [3691] [3692] [3693] [3694] [3695] [3696] [3697] [3698] [3699] [3700] [3701] Underfull \hbox (badness 1067) in paragraph at lines 15840--15845 \T1/ptm/m/n/10 ma-trix), []\T1/zi4/m/sl/10 fitted []\T1/ptm/m/n/10 (fit-ted val -ues), and []\T1/zi4/m/sl/10 residuals []\T1/ptm/m/n/10 (resid-u-als). De-fault s to [3702] [3703] [3704] [3705] Underfull \hbox (badness 1448) in paragraph at lines 16083--16092 \T1/ptm/m/n/10 Op-tions in-clude []\T1/zi4/m/sl/10 "response" []\T1/ptm/m/n/10 for the "raw" resid-u-als (ob-served - fit-ted), [3706] [3707] [3708] [3709] [3710] [3711] [3712] [3713] [3714] [3715] [3716] Underfull \hbox (badness 1728) in paragraph at lines 16786--16789 []\T1/ptm/m/n/10 an op-tional log-i-cal value used to con-trol the amount of ou t-put in the [3717] [3718] [3719] [3720] [3721] Underfull \hbox (badness 8056) in paragraph at lines 17120--17129 \T1/zi4/m/sl/10 Symmetry" []\T1/ptm/m/n/10 for []\T1/zi4/m/sl/10 pdCompSymm[]\T 1/ptm/m/n/10 , []\T1/zi4/m/sl/10 "Diagonal" []\T1/ptm/m/n/10 for []\T1/zi4/m/sl /10 pdDiag[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 "Multiple of Underfull \hbox (badness 10000) in paragraph at lines 17120--17129 \T1/zi4/m/sl/10 an Identity" []\T1/ptm/m/n/10 for []\T1/zi4/m/sl/10 pdIdent[]\T 1/ptm/m/n/10 , []\T1/zi4/m/sl/10 "General Positive-Definite, Natural Underfull \hbox (badness 5756) in paragraph at lines 17120--17129 \T1/zi4/m/sl/10 Parametrization" []\T1/ptm/m/n/10 for []\T1/zi4/m/sl/10 pdNatur al[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 "General Positive-Definite" []\T1/ptm/m/ n/10 for [3722] [3723] [3724] [3725] [3726] Underfull \hbox (badness 10000) in paragraph at lines 17441--17449 [][][]\T1/zi4/m/sl/10 varComb[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 var ConstPower[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 varConstProp[][][][]\T 1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 varExp[][][][]\T1/ptm/m/n/10 , [][][]\T1/z i4/m/sl/10 varFixed[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 varIdent[][][ ][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 varPower[][][][]\T1/ptm/m/n/10 , [3727] [3728] [3729] [3730] [3731] [3732] [3733] [3734] [3735] [3736] [3737] [3738] Underfull \hbox (badness 10000) in paragraph at lines 18153--18163 [][][]\T1/zi4/m/sl/10 Variogram.corExp[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/ sl/10 Variogram.corGaus[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 Variogram .corLin[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 Variogram.corRatio[][][][ ]\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 18153--18163 [][][]\T1/zi4/m/sl/10 Variogram.corSpatial[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi 4/m/sl/10 Variogram.corSpher[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 Vari ogram.default[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 Variogram.gls[][][] []\T1/ptm/m/n/10 , [3739] [3740] [3741] [3742] [3743] [3744] Underfull \hbox (badness 5036) in paragraph at lines 18471--18480 [][][]\T1/zi4/m/sl/10 corSpatial[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 Variogram[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 Variogram.default[][][] []\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 Variogram.corExp[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 Variogram.corGaus[][][][]\T1/ptm/m/n/10 , [3745] [3746] [3747] [3748] [3749] [3750] [3751] [3752] [3753] [3754] [3755] [3756] [3757] [3758]) (./nnet-pkg.tex Chapter 26. [3759] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.multinom} ) has been already used, duplicate ignored \relax l.47 ...t Multinomial Log-linear Models}{multinom} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.multinom. 1}) has been already used, duplicate ignored \relax l.47 ...t Multinomial Log-linear Models}{multinom} Underfull \hbox (badness 1117) in paragraph at lines 79--88 []\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo rm []\T1/zi4/m/sl/10 response ~ [3760] [3761] [3762] [3763] [3764] [3765] [3766] [3767]) (./rpart-pkg.tex [3768] Chapter 27. [3769] [3770] [3771] [3772] [3773] [3774] [3775] [3776] [3777] [3778] [3779] Underfull \hbox (badness 10000) in paragraph at lines 771--775 []\T1/ptm/m/n/10 Logical. If []\T1/zi4/m/sl/10 TRUE []\T1/ptm/m/n/10 (de-fault) , adds to the la-bel Underfull \hbox (badness 1348) in paragraph at lines 771--775 \T1/zi4/m/sl/10 #events level1/ #events level2/ \T1/ptm/m/n/10 etc. for method []\T1/zi4/m/sl/10 class[]\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 n \T1/ptm/m/n/10 for [3780] [3781] [3782] [3783] [3784] [3785] [3786] [3787] [3788] [3789] [3790] [3791] [3792] [3793] [3794] [3795] [3796] [3797] [3798] [3799]) (./spatial-pkg.tex [3800] Chapter 28. [3801] [3802] [3803] [3804] [3805] [3806] Underfull \hbox (badness 10000) in paragraph at lines 423--427 [3807] [3808] [3809] [3810] [3811] [3812] [3813] [3814] [3815] [3816] [3817] [3818] [3819] [3820] [3821]) (./survival-pkg.tex [3822] Chapter 29. [3823] [3824] [3825] [3826] Underfull \hbox (badness 6412) in paragraph at lines 284--286 []\T1/ptm/m/n/10 an op-tional list or vec-tor of group-ing el-e-ments, each as long as [3827] [3828] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.aml}) has been already used, duplicate ignored \relax l.384 ... Myelogenous Leukemia survival data}{aml} pdfTeX warning (ext4): destination with the same identifier (name{Rfn.aml.1}) h as been already used, duplicate ignored \relax l.384 ... Myelogenous Leukemia survival data}{aml} [3829] [3830] [3831] [3832] [3833] [3834] [3835] [3836] [3837] [3838] [3839] [3840] [3841] Underfull \hbox (badness 1097) in paragraph at lines 1205--1207 []\T1/ptm/m/n/10 F.J. Anscombe (1949). Trans-for-ma-tions of Pois-son, bi-no-mi al and negative-binomial data. [3842] [3843] [3844] [3845] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.colon}) h as been already used, duplicate ignored \relax l.1407 ...erapy for Stage B/C colon cancer}{colon} [3846] Underfull \hbox (badness 3679) in paragraph at lines 1455--1459 []\T1/ptm/m/n/10 Peter Hig-gins has pointed out a data in-con-sis-tency, re-vea led by []\T1/zi4/m/sl/10 table(colon$nodes, [3847] [3848] [3849] [3850] [3851] [3852] [3853] [3854] [3855] Underfull \hbox (badness 3250) in paragraph at lines 2145--2150 \T1/ptm/m/n/10 ing guides and prepend []\T1/zi4/m/sl/10 survival:: []\T1/ptm/m/ n/10 onto ev-er-thing, in-clud-ing the spe-cial terms, e.g., Underfull \hbox (badness 10000) in paragraph at lines 2145--2150 []\T1/zi4/m/sl/10 survival::coxph(survival:Surv(time, status) ~ age + survival: :strata(inst), [3856] [3857] [3858] [3859] [3860] [3861] [3862] [3863] [3864] [3865] [3866] [3867] [3868] [3869] [3870] [3871] [3872] [3873] [3874] [3875] [3876] [3877] [3878] [3879] Underfull \hbox (badness 1389) in paragraph at lines 3683--3685 []\T1/ptm/m/n/10 Often used to add the ex-pected sur-vival curve(s) to a Kaplan -Meier plot gen-er-ated with [3880] [3881] [3882] [3883] [3884] Overfull \hbox (467.89665pt too wide) in alignment at lines 3976--3976 [] [] [3885] [3886] [3887] [3888] [3889] [3890] [3891] [3892] [3893] [3894] [3895] [3896] [3897] [3898] [3899] [3900] [3901] [3902] [3903] [3904] [3905] [3906] [3907] [3908] [3909] [3910] [3911] [3912] [3913] Underfull \hbox (badness 5274) in paragraph at lines 5766--5768 []\T1/ptm/m/n/10 an ob-ject of class []\T1/zi4/m/sl/10 "summary.survfit"[]\T1/p tm/m/n/10 , which is the re-sult of the [3914] [3915] [3916] [3917] [3918] [3919] [3920] [3921] [3922] [3923] [3924] [3925] [3926] [3927] [3928] [3929] [3930] [3931] [3932] [3933] [3934] Underfull \hbox (badness 1281) in paragraph at lines 7046--7049 []\T1/ptm/m/n/10 type of resid-u-als, with choices of []\T1/zi4/m/sl/10 "respon se"[]\T1/ptm/m/n/10 , []\T1/zi4/m/sl/10 "deviance"[]\T1/ptm/m/n/10 , []\T1/zi4/ m/sl/10 "dfbeta"[]\T1/ptm/m/n/10 , [3935] [3936] [3937] [3938] [3939] [3940] [3941] [3942] [3943] pdfTeX warning (ext4): destination with the same identifier (name{Rfn.solder}) has been already used, duplicate ignored \relax l.7635 ...ata from a soldering experiment}{solder} [3944] [3945] [3946] [3947] [3948] [3949] [3950] [3951] [3952] [3953] [3954] [3955] [3956] [3957] [3958] [3959] [3960] [3961] [3962] [3963] [3964] [3965] [3966] [3967] [3968] Underfull \hbox (badness 1038) in paragraph at lines 9294--9300 []\T1/ptm/m/n/10 op-tion does not cre-ate a curve, rather it re-trieves the pre -dicted sur-vival [3969] [3970] [3971] [3972] [3973] Underfull \hbox (badness 10000) in paragraph at lines 9652--9657 [][][]\T1/zi4/m/sl/10 survfit.formula[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/s l/10 survfit.coxph[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 survfit.object [][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 print.survfit[][][][]\T1/ptm/m/n /10 , [][][]\T1/zi4/m/sl/10 plot.survfit[][][][]\T1/ptm/m/n/10 , [3974] [3975] [3976] [3977] [3978] Underfull \hbox (badness 4441) in paragraph at lines 10042--10052 []\T1/ptm/m/n/10 by de-fault, the surv-fit rou-tines only re-turn in-for-ma-tio n at the [3979] [3980] [3981] Underfull \hbox (badness 1490) in paragraph at lines 10217--10226 [][][]\T1/zi4/m/sl/10 survfit.coxph[][][] []\T1/ptm/m/n/10 for sur-vival curves from Cox mod-els, [][][]\T1/zi4/m/sl/10 survfit.object[][][] []\T1/ptm/m/n/10 for a de-scrip-tion Underfull \hbox (badness 2213) in paragraph at lines 10217--10226 \T1/ptm/m/n/10 of the com-po-nents of a surv-fit ob-ject, [][][]\T1/zi4/m/sl/10 print.survfit[][][][]\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 plot.survfit[][][] []\T1/ptm/m/n/10 , [][][]\T1/zi4/m/sl/10 lines.survfit[][][][]\T1/ptm/m/n/10 , [3982] [3983] [3984] [3985] [3986] [3987] [3988] Underfull \hbox (badness 1354) in paragraph at lines 10715--10719 []\T1/ptm/m/n/10 survival times, for time de-pen-dent pre-dic-tion. It gives th e time range [3989] [3990] [3991] [3992] [3993] [3994] [3995] [3996] [3997] [3998] [3999] [4000] [4001] [4002] [4003] [4004] [4005] [4006] [4007] [4008] [4009] [4010] [4011] [4012] [4013] [4014]) (./fullrefman.ind [4015] [4016] [4017] [4018] [4019] [4020] [4021] [4022] [4023] [4024] [4025] [4026] [4027] [4028] [4029] [4030] [4031] [4032] [4033] [4034] [4035] [4036] [4037] [4038] [4039] [4040] [4041] [4042] [4043] [4044] Overfull \hbox (8.3567pt too wide) in paragraph at lines 2898--2900 []| \T1/zi4/m/it/10 smooth.construct.tensor.smooth.spec\T1/ptm/m/n/10 , [4045] [4046] [4047] [4048] [4049] [4050] [4051] Overfull \hbox (8.3567pt too wide) in paragraph at lines 3550--3552 []| \T1/zi4/m/it/10 smooth.construct.tensor.smooth.spec\T1/ptm/m/n/10 , [4052] [4053] [4054] [4055] [4056] [4057] [4058] [4059] [4060] [4061] [4062] Overfull \hbox (5.8567pt too wide) in paragraph at lines 4962--4964 []\T1/zi4/m/it/10 [,Matrix,lMatrix,missing,missing-method Overfull \hbox (0.8567pt too 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5502--5504 []\T1/zi4/m/it/10 %&%,RsparseMatrix,CsparseMatrix-method Overfull \hbox (0.8567pt too wide) in paragraph at lines 5504--5506 []\T1/zi4/m/it/10 %&%,RsparseMatrix,RsparseMatrix-method Overfull \hbox (0.8567pt too wide) in paragraph at lines 5506--5508 []\T1/zi4/m/it/10 %&%,RsparseMatrix,TsparseMatrix-method Overfull \hbox (5.8567pt too wide) in paragraph at lines 5510--5512 []\T1/zi4/m/it/10 %&%,RsparseMatrix,diagonalMatrix-method Overfull \hbox (0.8567pt too wide) in paragraph at lines 5516--5518 []\T1/zi4/m/it/10 %&%,TsparseMatrix,CsparseMatrix-method Overfull \hbox (0.8567pt too wide) in paragraph at lines 5518--5520 []\T1/zi4/m/it/10 %&%,TsparseMatrix,RsparseMatrix-method Overfull \hbox (0.8567pt too wide) in paragraph at lines 5520--5522 []\T1/zi4/m/it/10 %&%,TsparseMatrix,TsparseMatrix-method Overfull \hbox (5.8567pt too wide) in paragraph at lines 5524--5526 []\T1/zi4/m/it/10 %&%,TsparseMatrix,diagonalMatrix-method [4068] Overfull \hbox (5.8567pt too wide) in paragraph at lines 5544--5546 []\T1/zi4/m/it/10 %&%,diagonalMatrix,CsparseMatrix-method Overfull \hbox (5.8567pt too wide) in paragraph at lines 5546--5548 []\T1/zi4/m/it/10 %&%,diagonalMatrix,RsparseMatrix-method Overfull \hbox (5.8567pt too wide) in paragraph at lines 5548--5550 []\T1/zi4/m/it/10 %&%,diagonalMatrix,TsparseMatrix-method Overfull \hbox (10.8567pt too wide) in paragraph at lines 5552--5554 []\T1/zi4/m/it/10 %&%,diagonalMatrix,diagonalMatrix-method [4069] [4070] Overfull \hbox (15.01662pt too wide) in paragraph at lines 5821--5823 \T1/ptm/m/it/10 (\T1/zi4/m/it/10 smooth.construct.ad.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , [4071] Overfull \hbox (20.8567pt too wide) in paragraph at lines 5975--5977 []\T1/zi4/m/it/10 all.equal,sparseVector,sparseVector-method [4072] Overfull \hbox (10.8567pt too wide) in paragraph at lines 6229--6231 []\T1/zi4/m/it/10 Arith,CsparseMatrix,CsparseMatrix-method Overfull \hbox (0.8567pt too wide) in paragraph at lines 6237--6239 []\T1/zi4/m/it/10 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6363--6365 []\T1/zi4/m/it/10 Arith,triangularMatrix,diagonalMatrix-method [4074] [4075] [4076] Overfull \hbox (15.01662pt too wide) in paragraph at lines 7032--7034 \T1/ptm/m/it/10 (\T1/zi4/m/it/10 smooth.construct.bs.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , [4077] [4078] [4079] [4080] [4081] [4082] [4083] [4084] Overfull \hbox (30.8567pt too wide) in paragraph at lines 8545--8547 []\T1/zi4/m/it/10 coerce,diagonalMatrix,symmetricMatrix-method Overfull \hbox (35.8567pt too wide) in paragraph at lines 8547--8549 []\T1/zi4/m/it/10 coerce,diagonalMatrix,triangularMatrix-method [4085] Overfull \hbox (10.8567pt too wide) in paragraph at lines 8567--8569 []\T1/zi4/m/it/10 coerce,generalMatrix,packedMatrix-method [4086] Overfull \hbox (0.8567pt too wide) in paragraph at lines 8713--8715 []\T1/zi4/m/it/10 coerce,matrix.coo,CsparseMatrix-method Overfull \hbox (0.8567pt too wide) in paragraph at lines 8721--8723 []\T1/zi4/m/it/10 coerce,matrix.coo,RsparseMatrix-method Overfull \hbox (0.8567pt too wide) in paragraph at lines 8725--8727 []\T1/zi4/m/it/10 coerce,matrix.coo,TsparseMatrix-method Overfull \hbox (0.8567pt too wide) in paragraph at lines 8727--8729 []\T1/zi4/m/it/10 coerce,matrix.csc,CsparseMatrix-method Overfull \hbox (0.8567pt too wide) in paragraph at lines 8733--8735 []\T1/zi4/m/it/10 coerce,matrix.csc,RsparseMatrix-method Overfull \hbox (0.8567pt too wide) in paragraph at lines 8737--8739 []\T1/zi4/m/it/10 coerce,matrix.csc,TsparseMatrix-method Overfull \hbox (0.8567pt too wide) in paragraph at lines 8739--8741 []\T1/zi4/m/it/10 coerce,matrix.csr,CsparseMatrix-method Overfull \hbox (0.8567pt too wide) in paragraph at lines 8747--8749 []\T1/zi4/m/it/10 coerce,matrix.csr,RsparseMatrix-method Overfull \hbox (0.8567pt too wide) in paragraph at lines 8751--8753 []\T1/zi4/m/it/10 coerce,matrix.csr,TsparseMatrix-method [4087] Overfull \hbox (10.8567pt too wide) in paragraph at lines 8775--8777 []\T1/zi4/m/it/10 coerce,sparseVector,CsparseMatrix-method Overfull \hbox (0.8567pt too wide) in paragraph at lines 8777--8779 []\T1/zi4/m/it/10 coerce,sparseVector,denseMatrix-method Overfull \hbox (10.8567pt too wide) in paragraph at lines 8779--8781 []\T1/zi4/m/it/10 coerce,sparseVector,dsparseVector-method Overfull \hbox (10.8567pt too wide) in paragraph at lines 8781--8783 []\T1/zi4/m/it/10 coerce,sparseVector,generalMatrix-method Overfull \hbox (10.8567pt too wide) in paragraph at lines 8783--8785 []\T1/zi4/m/it/10 coerce,sparseVector,isparseVector-method Overfull \hbox (10.8567pt too wide) in paragraph at lines 8785--8787 []\T1/zi4/m/it/10 coerce,sparseVector,lsparseVector-method Overfull \hbox (10.8567pt too wide) in paragraph at lines 8789--8791 []\T1/zi4/m/it/10 coerce,sparseVector,nsparseVector-method Overfull \hbox (10.8567pt too wide) in paragraph at lines 8791--8793 []\T1/zi4/m/it/10 coerce,sparseVector,RsparseMatrix-method Overfull \hbox (5.8567pt too wide) in paragraph at lines 8793--8795 []\T1/zi4/m/it/10 coerce,sparseVector,sparseMatrix-method Overfull \hbox (10.8567pt too wide) in paragraph at lines 8795--8797 []\T1/zi4/m/it/10 coerce,sparseVector,TsparseMatrix-method Overfull \hbox (15.8567pt too wide) in paragraph at lines 8797--8799 []\T1/zi4/m/it/10 coerce,sparseVector,unpackedMatrix-method Overfull \hbox (10.8567pt too wide) in paragraph at lines 8799--8801 []\T1/zi4/m/it/10 coerce,sparseVector,zsparseVector-method [4088] Overfull \hbox (20.8567pt too wide) in paragraph at lines 8975--8977 []\T1/zi4/m/it/10 Compare,CsparseMatrix,CsparseMatrix-method [4089] Overfull \hbox (40.8567pt too wide) in paragraph at lines 9007--9009 []\T1/zi4/m/it/10 Compare,triangularMatrix,diagonalMatrix-method [4090] [4091] Overfull \hbox (30.8567pt too wide) in paragraph at lines 9552--9554 []\T1/zi4/m/it/10 crossprod,CsparseMatrix,CsparseMatrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 9554--9556 []\T1/zi4/m/it/10 crossprod,CsparseMatrix,denseMatrix-method Overfull \hbox (35.8567pt too wide) in paragraph at lines 9556--9558 []\T1/zi4/m/it/10 crossprod,CsparseMatrix,diagonalMatrix-method Overfull \hbox (0.8567pt too wide) in paragraph at lines 9560--9562 []\T1/zi4/m/it/10 crossprod,CsparseMatrix,missing-method Overfull \hbox (30.8567pt too wide) in paragraph at lines 9562--9564 []\T1/zi4/m/it/10 crossprod,CsparseMatrix,RsparseMatrix-method Overfull \hbox (30.8567pt too wide) in paragraph at lines 9564--9566 []\T1/zi4/m/it/10 crossprod,CsparseMatrix,TsparseMatrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 9568--9570 []\T1/zi4/m/it/10 crossprod,denseMatrix,CsparseMatrix-method Overfull \hbox (10.8567pt too wide) in paragraph at lines 9570--9572 []\T1/zi4/m/it/10 crossprod,denseMatrix,denseMatrix-method Overfull \hbox (25.8567pt too wide) in paragraph at lines 9572--9574 []\T1/zi4/m/it/10 crossprod,denseMatrix,diagonalMatrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 9578--9580 []\T1/zi4/m/it/10 crossprod,denseMatrix,RsparseMatrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 9580--9582 []\T1/zi4/m/it/10 crossprod,denseMatrix,TsparseMatrix-method Overfull \hbox (35.8567pt too wide) in paragraph at lines 9584--9586 []\T1/zi4/m/it/10 crossprod,diagonalMatrix,CsparseMatrix-method Overfull \hbox (25.8567pt too wide) in paragraph at lines 9586--9588 []\T1/zi4/m/it/10 crossprod,diagonalMatrix,denseMatrix-method Overfull \hbox (40.8567pt too wide) in paragraph at lines 9588--9590 []\T1/zi4/m/it/10 crossprod,diagonalMatrix,diagonalMatrix-method [4092] Overfull \hbox (0.8567pt too wide) in paragraph at lines 9590--9592 []\T1/zi4/m/it/10 crossprod,diagonalMatrix,matrix-method Overfull \hbox (5.8567pt too wide) in paragraph at lines 9592--9594 []\T1/zi4/m/it/10 crossprod,diagonalMatrix,missing-method Overfull \hbox (35.8567pt too wide) in paragraph at lines 9594--9596 []\T1/zi4/m/it/10 crossprod,diagonalMatrix,RsparseMatrix-method Overfull \hbox (35.8567pt too wide) in paragraph at lines 9596--9598 []\T1/zi4/m/it/10 crossprod,diagonalMatrix,TsparseMatrix-method Overfull \hbox (0.8567pt too wide) in paragraph at lines 9598--9600 []\T1/zi4/m/it/10 crossprod,diagonalMatrix,vector-method Overfull \hbox (0.8567pt too wide) in paragraph at lines 9614--9616 []\T1/zi4/m/it/10 crossprod,matrix,diagonalMatrix-method Overfull \hbox (30.8567pt too wide) in paragraph at lines 9636--9638 []\T1/zi4/m/it/10 crossprod,RsparseMatrix,CsparseMatrix-method Overfull \hbox (20.8567pt too wide) in paragraph at lines 9638--9640 []\T1/zi4/m/it/10 crossprod,RsparseMatrix,denseMatrix-method Overfull \hbox (35.8567pt too wide) in paragraph at lines 9640--9642 []\T1/zi4/m/it/10 crossprod,RsparseMatrix,diagonalMatrix-method Overfull \hbox (0.8567pt too wide) in paragraph at lines 9644--9646 []\T1/zi4/m/it/10 crossprod,RsparseMatrix,missing-method Overfull \hbox (30.8567pt too wide) in paragraph at lines 9646--9648 []\T1/zi4/m/it/10 crossprod,RsparseMatrix,RsparseMatrix-method 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crossprod,TsparseMatrix,TsparseMatrix-method Overfull \hbox (0.8567pt too wide) in paragraph at lines 9684--9686 []\T1/zi4/m/it/10 crossprod,vector,diagonalMatrix-method [4093] Overfull \hbox (15.01662pt too wide) in paragraph at lines 9731--9733 \T1/ptm/m/it/10 (\T1/zi4/m/it/10 smooth.construct.cr.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (15.01662pt too wide) in paragraph at lines 9795--9797 \T1/ptm/m/it/10 (\T1/zi4/m/it/10 smooth.construct.cr.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (15.01662pt too wide) in paragraph at lines 9800--9802 \T1/ptm/m/it/10 (\T1/zi4/m/it/10 smooth.construct.ps.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (15.01662pt too wide) in paragraph at lines 9809--9811 \T1/ptm/m/it/10 (\T1/zi4/m/it/10 smooth.construct.bs.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , [4094] [4095] Overfull \hbox (5.8567pt too wide) in paragraph at lines 10174--10176 []\T1/zi4/m/it/10 determinant,BunchKaufman,logical-method Overfull 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[]\T1/zi4/m/it/10 dimnames<-,symmetricMatrix,NULL-method [4098] [4099] Overfull \hbox (15.01662pt too wide) in paragraph at lines 10967--10969 \T1/ptm/m/it/10 (\T1/zi4/m/it/10 smooth.construct.ds.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , [4100] [4101] [4102] [4103] [4104] Overfull \hbox (35.8567pt too wide) in paragraph at lines 11950--11952 []\T1/zi4/m/it/10 forceSymmetric,CsparseMatrix,character-method Overfull \hbox (25.8567pt too wide) in paragraph at lines 11952--11954 []\T1/zi4/m/it/10 forceSymmetric,CsparseMatrix,missing-method Overfull \hbox (25.8567pt too wide) in paragraph at lines 11954--11956 []\T1/zi4/m/it/10 forceSymmetric,denseMatrix,character-method Overfull \hbox (15.8567pt too wide) in paragraph at lines 11956--11958 []\T1/zi4/m/it/10 forceSymmetric,denseMatrix,missing-method Overfull \hbox (40.8567pt too wide) in paragraph at lines 11958--11960 []\T1/zi4/m/it/10 forceSymmetric,diagonalMatrix,character-method Overfull \hbox (30.8567pt too wide) in paragraph at 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forceSymmetric,TsparseMatrix,missing-method [4105] [4106] [4107] [4108] Overfull \hbox (15.01662pt too wide) in paragraph at lines 12969--12971 \T1/ptm/m/it/10 (\T1/zi4/m/it/10 smooth.construct.gp.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , [4109] [4110] [4111] [4112] [4113] [4114] [4115] [4116] Overfull \hbox (30.8567pt too wide) in paragraph at lines 14569--14571 []\T1/zi4/m/it/10 kronecker,CsparseMatrix,CsparseMatrix-method Overfull \hbox (35.8567pt too wide) in paragraph at lines 14571--14573 []\T1/zi4/m/it/10 kronecker,CsparseMatrix,diagonalMatrix-method Overfull \hbox (10.8567pt too wide) in paragraph at lines 14575--14577 []\T1/zi4/m/it/10 kronecker,denseMatrix,denseMatrix-method [4117] Overfull \hbox (35.8567pt too wide) in paragraph at lines 14579--14581 []\T1/zi4/m/it/10 kronecker,diagonalMatrix,CsparseMatrix-method Overfull \hbox (40.8567pt too wide) in paragraph at lines 14581--14583 []\T1/zi4/m/it/10 kronecker,diagonalMatrix,diagonalMatrix-method Overfull \hbox (15.8567pt 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kronecker,TsparseMatrix,diagonalMatrix-method Overfull \hbox (30.8567pt too wide) in paragraph at lines 14613--14615 []\T1/zi4/m/it/10 kronecker,TsparseMatrix,TsparseMatrix-method [4118] [4119] [4120] Overfull \hbox (10.8567pt too wide) in paragraph at lines 15451--15453 []\T1/zi4/m/it/10 Logic,CsparseMatrix,CsparseMatrix-method Overfull \hbox (5.8567pt too wide) in paragraph at lines 15459--15461 []\T1/zi4/m/it/10 Logic,ldenseMatrix,lsparseMatrix-method [4121] Overfull \hbox (5.8567pt too wide) in paragraph at lines 15481--15483 []\T1/zi4/m/it/10 Logic,lsparseMatrix,ldenseMatrix-method Overfull \hbox (10.8567pt too wide) in paragraph at lines 15483--15485 []\T1/zi4/m/it/10 Logic,lsparseMatrix,lsparseMatrix-method Overfull \hbox (10.8567pt too wide) in paragraph at lines 15485--15487 []\T1/zi4/m/it/10 Logic,lsparseVector,lsparseVector-method Overfull \hbox (0.8567pt too wide) in paragraph at lines 15517--15519 []\T1/zi4/m/it/10 Logic,sparseVector,sparseVector-method Overfull \hbox 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in paragraph at lines 17883--17885 \T1/ptm/m/it/10 (\T1/zi4/m/it/10 smooth.construct.ps.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , [4133] Overfull \hbox (33.3567pt too wide) in paragraph at lines 17918--17920 []\T1/zi4/m/it/10 package_native_routine_registration_skeleton\T1/ptm/m/n/10 , [4134] [4135] [4136] [4137] [4138] Overfull \hbox (15.01662pt too wide) in paragraph at lines 19274--19276 \T1/ptm/m/it/10 (\T1/zi4/m/it/10 smooth.construct.bs.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (15.01662pt too wide) in paragraph at lines 19281--19283 \T1/ptm/m/it/10 (\T1/zi4/m/it/10 smooth.construct.ds.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (15.01662pt too wide) in paragraph at lines 19283--19285 \T1/ptm/m/it/10 (\T1/zi4/m/it/10 smooth.construct.fs.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , [4139] Overfull \hbox (15.01662pt too wide) in paragraph at lines 19285--19287 \T1/ptm/m/it/10 (\T1/zi4/m/it/10 smooth.construct.gp.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (20.01662pt too wide) in paragraph at lines 19287--19289 \T1/ptm/m/it/10 (\T1/zi4/m/it/10 smooth.construct.mrf.smooth.spec\T1/ptm/m/it/1 0 )\T1/ptm/m/n/10 , Overfull \hbox (15.01662pt too wide) in paragraph at lines 19291--19293 \T1/ptm/m/it/10 (\T1/zi4/m/it/10 smooth.construct.re.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (20.01662pt too wide) in paragraph at lines 19297--19299 \T1/ptm/m/it/10 (\T1/zi4/m/it/10 smooth.construct.sos.smooth.spec\T1/ptm/m/it/1 0 )\T1/ptm/m/n/10 , Overfull \hbox (15.01662pt too wide) in paragraph at lines 19301--19303 \T1/ptm/m/it/10 (\T1/zi4/m/it/10 smooth.construct.sz.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , [4140] [4141] [4142] [4143] [4144] [4145] Overfull \hbox (20.8567pt too wide) in paragraph at lines 20397--20399 []\T1/zi4/m/it/10 R_AVAILABLE_PACKAGES_CACHE_CONTROL_MAX_AGE [4146] [4147] [4148] [4149] [4150] [4151] [4152] [4153] [4154] [4155] Overfull \hbox (15.01662pt too wide) in paragraph at lines 22362--22364 \T1/ptm/m/it/10 (\T1/zi4/m/it/10 smooth.construct.cr.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (15.01662pt too wide) in paragraph at lines 22364--22366 \T1/ptm/m/it/10 (\T1/zi4/m/it/10 smooth.construct.ps.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (15.01662pt too wide) in paragraph at lines 22367--22369 \T1/ptm/m/it/10 (\T1/zi4/m/it/10 smooth.construct.cr.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (15.01662pt too wide) in paragraph at lines 22384--22386 \T1/ptm/m/it/10 (\T1/zi4/m/it/10 smooth.construct.so.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (15.01662pt too wide) in paragraph at lines 22389--22391 \T1/ptm/m/it/10 (\T1/zi4/m/it/10 smooth.construct.so.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , Overfull \hbox (15.01662pt too wide) in paragraph at lines 22401--22403 \T1/ptm/m/it/10 (\T1/zi4/m/it/10 smooth.construct.tp.smooth.spec\T1/ptm/m/it/10 )\T1/ptm/m/n/10 , [4156] Overfull \hbox (5.8567pt 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(\T1/zi4/m/it/10 smooth.construct.sos.smooth.spec\T1/ptm/m/it/1 0 )\T1/ptm/m/n/10 , [4159] [4160] Overfull \hbox (5.8567pt too wide) in paragraph at lines 23269--23271 []\T1/zi4/m/it/10 summarize_check_packages_in_dir_depends Overfull \hbox (5.8567pt too wide) in paragraph at lines 23271--23273 []\T1/zi4/m/it/10 summarize_check_packages_in_dir_results Overfull \hbox (5.8567pt too wide) in paragraph at lines 23273--23275 []\T1/zi4/m/it/10 summarize_check_packages_in_dir_timings [4161] [4162] [4163] [4164] Overfull \hbox (35.8567pt too wide) in paragraph at lines 24107--24109 []\T1/zi4/m/it/10 tcrossprod,CsparseMatrix,CsparseMatrix-method Overfull \hbox (25.8567pt too wide) in paragraph at lines 24109--24111 []\T1/zi4/m/it/10 tcrossprod,CsparseMatrix,denseMatrix-method Overfull \hbox (40.8567pt too wide) in paragraph at lines 24111--24113 []\T1/zi4/m/it/10 tcrossprod,CsparseMatrix,diagonalMatrix-method Overfull \hbox (0.8567pt too wide) in paragraph at lines 24113--24115 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Transcript written on fullrefman.log. TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/local/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-FAQ.texi @setfilename R-FAQ.info This is pdfTeX, Version 3.141592653-2.6-1.40.26 (Web2C 2024) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-FAQ.t2d/pdf/xtr/R-FAQ.texi (/usr/local/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2024-02-10.22]: pdf, fonts, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, microtype, and turning on texinfo input format.) (/usr/local/share/texmf-dist/tex/texinfo/txi-en.tex) (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-defs.texi (/usr/local/share/texmf-dist/tex/texinfo/txi-en.tex)) [1{/usr/local/share/texmf -dist/fonts/map/pdftex/updmap/pdftex.map}] [-1] Chapter 1 Chapter 2 [1] Cross reference values unknown; you must run TeX again. [2] Underfull \hbox (badness 10000) in paragraph at lines 293--322 @textrm and sparc @reducedrm CPU[]@textrm s (e.g., [][]@texttt https:// buildd . debian. org/ build. php? & pkg=r-base[][]@textrm ), [3] [4] [5] [6] Underfull \hbox (badness 10000) in paragraph at lines 657--662 @textrm (doi: [][]10.1080/10618600.1996.10474713 (@texttt https:// doi. org/ 10. 1080/ 10618600. 1996. [7] [8] [9] Chapter 3 [10] [11] [12] [13] [14] [15] [16] [17] Underfull \hbox (badness 10000) in paragraph at lines 1530--1533 []@textrm See also [][]@texttt https:// en. wikipedia. org/ wiki/ R_progra mming_language# Underfull \hbox (badness 10000) in paragraph at lines 1530--1533 @texttt Commercialized_versions_of_R[][] @textrm for point-ers to com-mer-cial- ized ver-sions of Chapter 4 [18] Chapter 5 [19] [20] [21] Overfull \hbox (14.27353pt too wide) in paragraph at lines 1818--1818 []@smalltt MASS Support Functions and Datasets for Venables and Riple y s MASS[] [22] [23] Chapter 6 [24] [25] Chapter 7 [26] [27] [28] [29] [30] [31] [32] [33] [34] [35] [36] [37] Writing index file R-FAQ.fn [38] Underfull \hbox (badness 10000) in paragraph at lines 3134--3148 @textrm and @texttt error.bars.by()[] @textrm func-tions in the [][]@textbf psy ch @textrm (@texttt https:// CRAN. R-project. org/ [39] [40] [41] Chapter 8 [42] Chapter 9 [43] [44] [45] Chapter 10 [46] [47] ) (see the transcript file for additional information)< /usr/local/share/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt9.pfb> Output written on R-FAQ.pdf (49 pages, 351189 bytes). Transcript written on R-FAQ.log. This is pdfTeX, Version 3.141592653-2.6-1.40.26 (Web2C 2024) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-FAQ.t2d/pdf/xtr/R-FAQ.texi (/usr/local/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2024-02-10.22]: pdf, fonts, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, microtype, and turning on texinfo input format.) (/usr/local/share/texmf-dist/tex/texinfo/txi-en.tex) (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-defs.texi (/usr/local/share/texmf-dist/tex/texinfo/txi-en.tex)) [1{/usr/local/share/texmf -dist/fonts/map/pdftex/updmap/pdftex.map}] (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-FAQ.toc) (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-FAQ.toc [-1] [-2]) [-3] (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-FAQ.toc) (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-FAQ.toc) Chapter 1 (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-FAQ.aux) Chapter 2 [1] [2] Underfull \hbox (badness 10000) in paragraph at lines 293--322 @textrm and sparc @reducedrm CPU[]@textrm s (e.g., [][]@texttt https:// buildd . debian. org/ build. php? & pkg=r-base[][]@textrm ), [3] [4] [5] [6] Underfull \hbox (badness 10000) in paragraph at lines 657--662 @textrm (doi: [][]10.1080/10618600.1996.10474713 (@texttt https:// doi. org/ 10. 1080/ 10618600. 1996. 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R-project. org/ [39] [40] [41] Chapter 8 [42] Chapter 9 [43] [44] [45] Chapter 10 [46] [47] ) (see the transcript file for additional information)< /usr/local/share/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt9.pfb> Output written on R-FAQ.pdf (51 pages, 368242 bytes). Transcript written on R-FAQ.log. TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/local/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-admin.texi @setfilename R-admin.info This is pdfTeX, Version 3.141592653-2.6-1.40.26 (Web2C 2024) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-admin.t2d/pdf/xtr/R-admin. texi (/usr/local/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2024-02-10.22]: pdf, fonts, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, microtype, and turning on texinfo input format.) 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(Concept index) [80] No file R-admin.cps. (Environment variable index) [81] No file R-admin.ens. [82] ) (see the transcript file for additional information) pdfTeX warning (dest): name{\040Tcl/Tk\040headers\040and\040libraries} has been referenced but does not exist, replaced by a fixed one Output written on R-admin.pdf (85 pages, 472843 bytes). Transcript written on R-admin.log. This is pdfTeX, Version 3.141592653-2.6-1.40.26 (Web2C 2024) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-admin.t2d/pdf/xtr/R-admin. texi (/usr/local/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2024-02-10.22]: pdf, fonts, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, microtype, and turning on texinfo input format.) Writing index file R-admin.vr (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-defs.texi (/usr/local/share/texmf-dist/tex/texinfo/txi-en.tex)) (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/version.texi) [1{/usr/local/ share/texmf-dist/fonts/map/pdftex/updmap/pdftex.map}] [2] (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-admin.toc) (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-admin.toc [-1] [-2]) [-3] (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-admin.toc) (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-admin.toc) Chapter 1 (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-admin.aux) Writing index file R-admin.cp Writing index file R-admin.en [1] Chapter 2 [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] Chapter 3 [16] [17] [18] Chapter 4 [19] [20] [21] Chapter 5 [22] Chapter 6 [23] Overfull \hbox (14.94176pt too wide) in paragraph at lines 1917--1917 []@texttt [1] "datasets" "utils" "grDevices" "graphics" "stats" "met hods"[] [24] [25] Underfull \hbox (badness 6842) in paragraph at lines 2149--2157 []@texttt R CMD INSTALL[] @textrm works in Win-dows to in-stall source pack-age s. No ad-di- [26] Overfull \hbox (37.93651pt too wide) in paragraph at lines 2223--2223 []@texttt FLIBS = -L/Library/Frameworks/R.framework/Resources/lib -lgfortran - lquadmath[] [27] [28] Underfull \hbox (badness 10000) in paragraph at lines 2339--2344 @textrm (avoiding @texttt autoconf[]@textrm 's de-fault @texttt -g[]@textrm ). As from R 4.3.0, @texttt R CMD INSTALL[] @textrm and [29] [30] [31] Underfull \hbox (badness 10000) in paragraph at lines 2621--2627 []@texttt "mac.binary"[]@textrm : lo-cated at @texttt bin/macosx/big-sur-arm64 /contrib/@textttsl 4.y[] @textrm or [32] Overfull \hbox (20.69044pt too wide) in paragraph at lines 2675--2675 []@texttt R --arch @textttsl arch @texttt CMD check -l @textttsl libdir @textt t --extra-arch --install=check:@textttsl pkg@texttt .log @textttsl pkg[] Chapter 7 [33] [34] [35] Chapter 8 [36] Chapter 9 [37] [38] [39] Appendix A [40] [41] Overfull \hbox (49.43388pt too wide) in paragraph at lines 3246--3246 []@texttt ./configure --enable-utf --enable-unicode-properties --enable-jit -- disable-cpp[] [42] [43] [44] Underfull \hbox (badness 10000) in paragraph at lines 3459--3461 []@textrm Library @texttt libdeflate[] @textrm ([][]@texttt https:// github. com/ ebiggers/ libdeflate[][]@textrm ) is used by [45] Overfull \hbox (14.94176pt too wide) in paragraph at lines 3556--3556 []@texttt JAVA_HOME=/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.322.b06-6.fc34.x86_6 4/jre[] [46] [47] [48] [49] [50] [51] [52] [53] [54] Appendix B [55] [56] [57] [58] [59] [60] Appendix C [61] [62] [63] [64] Overfull \hbox (14.94176pt too wide) in paragraph at lines 4903--4903 []@texttt -Werror=format-security -Wp,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSER TIONS[] [65] [66] Overfull \hbox (26.43913pt too wide) in paragraph at lines 5103--5103 []@texttt !DEC$ ATTRIBUTES DLLEXPORT,C,REFERENCE,ALIAS: kdenestmlcvb :: kdenestmlcvb[] [67] Overfull \hbox (122.85329pt too wide) in paragraph at lines 5205--5205 []@texttt curl -OL https://mac.r-project.org/bin/darwin20/arm64/pcre2-10.44-da rwin.20-arm64.tar.xz[] Overfull \hbox (105.60722pt too wide) in paragraph at lines 5207--5207 []@texttt curl -OL https://mac.r-project.org/bin/darwin20/arm64/xz-5.6.3-darwi n.20-arm64.tar.xz[] [68] l.5254: Undefined cross reference ` Tcl/Tk headers and libraries-snt'. l.5254: Undefined cross reference ` Tcl/Tk headers and libraries-snt'. l.5254: Undefined cross reference ` Tcl/Tk headers and libraries-pg'. Overfull \hbox (60.93126pt too wide) in paragraph at lines 5328--5328 []@texttt curl -OL https://mac.r-project.org/tools/subversion-1.14.3-darwin.20 -arm64.tar.gz[] [69] Overfull \hbox (32.18782pt too wide) in paragraph at lines 5335--5335 []@texttt curl -OL https://mac.r-project.org/tools/subversion-1.14.3-darwin15. 6.tar.gz[] Overfull \hbox (170.15633pt too wide) in paragraph at lines 5365--5365 [] @texttt could not create compact unwind for _arcoef_: registers 23 and 24 not saved contiguously in frame[] Overfull \hbox (38.79282pt too wide) in paragraph at lines 5374--5375 [][][]@smallrm See [][]@smalltt https:// developer. apple. com/ documentati on/ xcode/ notarizing_macos_software_before_distribution[][]@smallrm .| [70] [71] [72] Overfull \hbox (72.77429pt too wide) in paragraph at lines 5642--5642 [][][][][]@smalltt https:// cran. r-project. org/ bin/ macosx/ RMacOSX-FA Q. html# Which-BLAS-is-used-and-how-can-it-be-changed_003f[][]| [73] Overfull \hbox (9.18199pt too wide) in paragraph at lines 1--5675 @texttt OpenMathLib/ OpenBLAS/ releases[][]@textrm ) by sym-link-ing @texttt /opt/OpenBLAS/lib/libopenblas.dylib[] [74] Underfull \hbox (badness 10000) in paragraph at lines 5750--5761 @texttt zulu-community/ ? os=macos& architecture=arm-64-bit& package=jdk[][ ] @textrm and from [75] [76] Overfull \hbox (48.12035pt too wide) in paragraph at lines 5911--5911 []@texttt /opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0/libgfortran.5. dylib \[] Overfull \hbox (48.12035pt too wide) in paragraph at lines 5916--5916 []@texttt /opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0/libquadmath.0. dylib \[] Overfull \hbox (25.1256pt too wide) in paragraph at lines 5934--5934 []@texttt PKG_LIBS = /usr/local/llvm/lib/libc++.a /usr/local/llvm/lib/libc++ab i.a[] Overfull \hbox (72.42863pt too wide) in paragraph at lines 5957--5957 []@texttt FC="/opt//gfortran/bin/gfortran -arch x86_64 -mtune=native -mmacosx- version-min=11"[] [77] [78] (Function and variable index) [79] (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-admin.vrs) (Concept index) [80] (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-admin.cps) (Environment variable index) [81] (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-admin.ens) [82] ) (see the transcript file for additional information) pdfTeX warning (dest): name{\040Tcl/Tk\040headers\040and\040libraries} has been referenced but does not exist, replaced by a fixed one Output written on R-admin.pdf (87 pages, 515660 bytes). Transcript written on R-admin.log. This is pdfTeX, Version 3.141592653-2.6-1.40.26 (Web2C 2024) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-admin.t2d/pdf/xtr/R-admin. texi (/usr/local/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2024-02-10.22]: pdf, fonts, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, microtype, and turning on texinfo input format.) Writing index file R-admin.vr (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-defs.texi (/usr/local/share/texmf-dist/tex/texinfo/txi-en.tex)) (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/version.texi) [1{/usr/local/ share/texmf-dist/fonts/map/pdftex/updmap/pdftex.map}] [2] (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-admin.toc) (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-admin.toc [-1] [-2]) [-3] (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-admin.toc) (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-admin.toc) Chapter 1 (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-admin.aux) Writing index file R-admin.cp Writing index file R-admin.en [1] Chapter 2 [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] Chapter 3 [16] [17] [18] Chapter 4 [19] [20] [21] Chapter 5 [22] Chapter 6 [23] Overfull \hbox (14.94176pt too wide) in paragraph at lines 1917--1917 []@texttt [1] "datasets" "utils" "grDevices" "graphics" "stats" "met hods"[] [24] [25] Underfull \hbox (badness 6842) in paragraph at lines 2149--2157 []@texttt R CMD INSTALL[] @textrm works in Win-dows to in-stall source pack-age s. No ad-di- [26] Overfull \hbox (37.93651pt too wide) in paragraph at lines 2223--2223 []@texttt FLIBS = -L/Library/Frameworks/R.framework/Resources/lib -lgfortran - lquadmath[] [27] [28] Underfull \hbox (badness 10000) in paragraph at lines 2339--2344 @textrm (avoiding @texttt autoconf[]@textrm 's de-fault @texttt -g[]@textrm ). As from R 4.3.0, @texttt R CMD INSTALL[] @textrm and [29] [30] [31] Underfull \hbox (badness 10000) in paragraph at lines 2621--2627 []@texttt "mac.binary"[]@textrm : lo-cated at @texttt bin/macosx/big-sur-arm64 /contrib/@textttsl 4.y[] @textrm or [32] Overfull \hbox (20.69044pt too wide) in paragraph at lines 2675--2675 []@texttt R --arch @textttsl arch @texttt CMD check -l @textttsl libdir @textt t --extra-arch --install=check:@textttsl pkg@texttt .log @textttsl pkg[] Chapter 7 [33] [34] [35] Chapter 8 [36] Chapter 9 [37] [38] [39] Appendix A [40] [41] Overfull \hbox (49.43388pt too wide) in paragraph at lines 3246--3246 []@texttt ./configure --enable-utf --enable-unicode-properties --enable-jit -- disable-cpp[] [42] [43] [44] Underfull \hbox (badness 10000) in paragraph at lines 3459--3461 []@textrm Library @texttt libdeflate[] @textrm ([][]@texttt https:// github. com/ ebiggers/ libdeflate[][]@textrm ) is used by [45] Overfull \hbox (14.94176pt too wide) in paragraph at lines 3556--3556 []@texttt JAVA_HOME=/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.322.b06-6.fc34.x86_6 4/jre[] [46] [47] [48] [49] [50] [51] [52] [53] [54] Appendix B [55] [56] [57] [58] [59] [60] Appendix C [61] [62] [63] [64] Overfull \hbox (14.94176pt too wide) in paragraph at lines 4903--4903 []@texttt -Werror=format-security -Wp,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSER TIONS[] [65] [66] Overfull \hbox (26.43913pt too wide) in paragraph at lines 5103--5103 []@texttt !DEC$ ATTRIBUTES DLLEXPORT,C,REFERENCE,ALIAS: kdenestmlcvb :: kdenestmlcvb[] [67] Overfull \hbox (122.85329pt too wide) in paragraph at lines 5205--5205 []@texttt curl -OL https://mac.r-project.org/bin/darwin20/arm64/pcre2-10.44-da rwin.20-arm64.tar.xz[] Overfull \hbox (105.60722pt too wide) in paragraph at lines 5207--5207 []@texttt curl -OL https://mac.r-project.org/bin/darwin20/arm64/xz-5.6.3-darwi n.20-arm64.tar.xz[] [68] l.5254: Undefined cross reference ` Tcl/Tk headers and libraries-snt'. l.5254: Undefined cross reference ` Tcl/Tk headers and libraries-snt'. l.5254: Undefined cross reference ` Tcl/Tk headers and libraries-pg'. Overfull \hbox (60.93126pt too wide) in paragraph at lines 5328--5328 []@texttt curl -OL https://mac.r-project.org/tools/subversion-1.14.3-darwin.20 -arm64.tar.gz[] [69] Overfull \hbox (32.18782pt too wide) in paragraph at lines 5335--5335 []@texttt curl -OL https://mac.r-project.org/tools/subversion-1.14.3-darwin15. 6.tar.gz[] Overfull \hbox (170.15633pt too wide) in paragraph at lines 5365--5365 [] @texttt could not create compact unwind for _arcoef_: registers 23 and 24 not saved contiguously in frame[] Overfull \hbox (38.79282pt too wide) in paragraph at lines 5374--5375 [][][]@smallrm See [][]@smalltt https:// developer. apple. com/ documentati on/ xcode/ notarizing_macos_software_before_distribution[][]@smallrm .| [70] [71] [72] Overfull \hbox (72.77429pt too wide) in paragraph at lines 5642--5642 [][][][][]@smalltt https:// cran. r-project. org/ bin/ macosx/ RMacOSX-FA Q. html# Which-BLAS-is-used-and-how-can-it-be-changed_003f[][]| [73] Overfull \hbox (9.18199pt too wide) in paragraph at lines 1--5675 @texttt OpenMathLib/ OpenBLAS/ releases[][]@textrm ) by sym-link-ing @texttt /opt/OpenBLAS/lib/libopenblas.dylib[] [74] Underfull \hbox (badness 10000) in paragraph at lines 5750--5761 @texttt zulu-community/ ? os=macos& architecture=arm-64-bit& package=jdk[][ ] @textrm and from [75] [76] Overfull \hbox (48.12035pt too wide) in paragraph at lines 5911--5911 []@texttt /opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0/libgfortran.5. dylib \[] Overfull \hbox (48.12035pt too wide) in paragraph at lines 5916--5916 []@texttt /opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0/libquadmath.0. dylib \[] Overfull \hbox (25.1256pt too wide) in paragraph at lines 5934--5934 []@texttt PKG_LIBS = /usr/local/llvm/lib/libc++.a /usr/local/llvm/lib/libc++ab i.a[] Overfull \hbox (72.42863pt too wide) in paragraph at lines 5957--5957 []@texttt FC="/opt//gfortran/bin/gfortran -arch x86_64 -mtune=native -mmacosx- version-min=11"[] [77] [78] (Function and variable index) [79] (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-admin.vrs) (Concept index) [80] (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-admin.cps) (Environment variable index) [81] (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-admin.ens) [82] ) (see the transcript file for additional information) pdfTeX warning (dest): name{\040Tcl/Tk\040headers\040and\040libraries} has been referenced but does not exist, replaced by a fixed one Output written on R-admin.pdf (87 pages, 515684 bytes). Transcript written on R-admin.log. TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/local/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-data.texi @setfilename R-data.info This is pdfTeX, Version 3.141592653-2.6-1.40.26 (Web2C 2024) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-data.t2d/pdf/xtr/R-data.te xi (/usr/local/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2024-02-10.22]: pdf, fonts, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, microtype, and turning on texinfo input format.) Writing index file R-data.vr (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-defs.texi (/usr/local/share/texmf-dist/tex/texinfo/txi-en.tex)) (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/version.texi) [1{/usr/local/ share/texmf-dist/fonts/map/pdftex/updmap/pdftex.map}] [2] [-1] (Acknowledgements) [1] Chapter 1 [2] Writing index file R-data.cp Cross reference values unknown; you must run TeX again. [3] [4] [5] Underfull \hbox (badness 10000) in paragraph at lines 441--444 []@textrm Function @texttt write.matrix[] @textrm in pack-age [][]@textbf MASS @textrm (@texttt https:// CRAN. R-project. org/ Underfull \hbox (badness 10000) in paragraph at lines 452--456 []@textrm Function @texttt write.foreign[] @textrm in pack-age [][]@textbf fore ign @textrm (@texttt https:// CRAN. R-project. org/ [6] Chapter 2 [7] [8] [9] [10] [11] [12] [13] Chapter 3 [14] [15] Chapter 4 [16] Underfull \hbox (badness 10000) in paragraph at lines 1226--1238 @textrm (@texttt https:// www. ibm. com/ products/ informix[]@textrm )[]; [][]Oracle (@texttt https:// www. oracle. com[]@textrm )[]; Underfull \hbox (badness 10000) in paragraph at lines 1226--1238 @textrm (@texttt https:// www. microsoft. com/ sql-server/ []@textrm )[] o n Win-dows) and aca-demic and [17] [18] [19] [20] [21] [22] Chapter 5 [23] Underfull \hbox (badness 10000) in paragraph at lines 1799--1805 []@textrm Packages [][]@textbf h5 @textrm (@texttt https:// CRAN. R-project. org/ package=h5[]@textrm )[], Bio-con-duc-tor's @textbf rhdf5@textrm , Chapter 6 [24] Chapter 7 [25] [26] [27] [28] [29] Chapter 8 [30] Chapter 9 [31] Appendix A [32] (Function and variable index) [33] No file R-data.vrs. (Concept index) [34] No file R-data.cps. [35] ) (see the transcript file for additional information) Output written on R-data.pdf (38 pages, 266554 bytes). Transcript written on R-data.log. This is pdfTeX, Version 3.141592653-2.6-1.40.26 (Web2C 2024) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-data.t2d/pdf/xtr/R-data.te xi (/usr/local/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2024-02-10.22]: pdf, fonts, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, microtype, and turning on texinfo input format.) Writing index file R-data.vr (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-defs.texi (/usr/local/share/texmf-dist/tex/texinfo/txi-en.tex)) (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/version.texi) [1{/usr/local/ share/texmf-dist/fonts/map/pdftex/updmap/pdftex.map}] [2] (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-data.toc) (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-data.toc [-1]) [-2] (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-data.toc) (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-data.toc) (Acknowledgements) (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-data.aux) [1] Chapter 1 [2] Writing index file R-data.cp [3] [4] [5] Underfull \hbox (badness 10000) in paragraph at lines 441--444 []@textrm Function @texttt write.matrix[] @textrm in pack-age [][]@textbf MASS @textrm (@texttt https:// CRAN. R-project. org/ Underfull \hbox (badness 10000) in paragraph at lines 452--456 []@textrm Function @texttt write.foreign[] @textrm in pack-age [][]@textbf fore ign @textrm (@texttt https:// CRAN. R-project. org/ [6] Chapter 2 [7] [8] [9] [10] [11] [12] [13] Chapter 3 [14] [15] Chapter 4 [16] Underfull \hbox (badness 10000) in paragraph at lines 1226--1238 @textrm (@texttt https:// www. ibm. com/ products/ informix[]@textrm )[]; [][]Oracle (@texttt https:// www. oracle. com[]@textrm )[]; Underfull \hbox (badness 10000) in paragraph at lines 1226--1238 @textrm (@texttt https:// www. microsoft. com/ sql-server/ []@textrm )[] o n Win-dows) and aca-demic and [17] [18] [19] [20] [21] [22] Chapter 5 [23] Underfull \hbox (badness 10000) in paragraph at lines 1799--1805 []@textrm Packages [][]@textbf h5 @textrm (@texttt https:// CRAN. R-project. org/ package=h5[]@textrm )[], Bio-con-duc-tor's @textbf rhdf5@textrm , Chapter 6 [24] Chapter 7 [25] [26] [27] [28] [29] Chapter 8 [30] Chapter 9 [31] Appendix A [32] (Function and variable index) [33] (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-data.vrs [34]) (Concept index) [35] (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-data.cps) [36] [37] ) (see the transcript file for additional information) Output written on R-data.pdf (41 pages, 302806 bytes). Transcript written on R-data.log. This is pdfTeX, Version 3.141592653-2.6-1.40.26 (Web2C 2024) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-data.t2d/pdf/xtr/R-data.te xi (/usr/local/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2024-02-10.22]: pdf, fonts, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, microtype, and turning on texinfo input format.) Writing index file R-data.vr (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-defs.texi (/usr/local/share/texmf-dist/tex/texinfo/txi-en.tex)) (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/version.texi) [1{/usr/local/ share/texmf-dist/fonts/map/pdftex/updmap/pdftex.map}] [2] (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-data.toc) (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-data.toc [-1]) [-2] (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-data.toc) (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-data.toc) (Acknowledgements) (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-data.aux) [1] Chapter 1 [2] Writing index file R-data.cp [3] [4] [5] Underfull \hbox (badness 10000) in paragraph at lines 441--444 []@textrm Function @texttt write.matrix[] @textrm in pack-age [][]@textbf MASS @textrm (@texttt https:// CRAN. R-project. org/ Underfull \hbox (badness 10000) in paragraph at lines 452--456 []@textrm Function @texttt write.foreign[] @textrm in pack-age [][]@textbf fore ign @textrm (@texttt https:// CRAN. R-project. org/ [6] Chapter 2 [7] [8] [9] [10] [11] [12] [13] Chapter 3 [14] [15] Chapter 4 [16] Underfull \hbox (badness 10000) in paragraph at lines 1226--1238 @textrm (@texttt https:// www. ibm. com/ products/ informix[]@textrm )[]; [][]Oracle (@texttt https:// www. oracle. com[]@textrm )[]; Underfull \hbox (badness 10000) in paragraph at lines 1226--1238 @textrm (@texttt https:// www. microsoft. com/ sql-server/ []@textrm )[] o n Win-dows) and aca-demic and [17] [18] [19] [20] [21] [22] Chapter 5 [23] Underfull \hbox (badness 10000) in paragraph at lines 1799--1805 []@textrm Packages [][]@textbf h5 @textrm (@texttt https:// CRAN. R-project. org/ package=h5[]@textrm )[], Bio-con-duc-tor's @textbf rhdf5@textrm , Chapter 6 [24] Chapter 7 [25] [26] [27] [28] [29] Chapter 8 [30] Chapter 9 [31] Appendix A [32] (Function and variable index) [33] (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-data.vrs [34]) (Concept index) [35] (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-data.cps) [36] [37] ) (see the transcript file for additional information) Output written on R-data.pdf (41 pages, 302811 bytes). Transcript written on R-data.log. TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/local/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-exts.texi @setfilename R-exts.info This is pdfTeX, Version 3.141592653-2.6-1.40.26 (Web2C 2024) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-exts.t2d/pdf/xtr/R-exts.te xi (/usr/local/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2024-02-10.22]: pdf, fonts, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, microtype, and turning on texinfo input format.) Writing index file R-exts.vr (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-defs.texi (/usr/local/share/texmf-dist/tex/texinfo/txi-en.tex)) (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/version.texi) [1{/usr/local/ share/texmf-dist/fonts/map/pdftex/updmap/pdftex.map}] [2] [-1] (Acknowledgements) Chapter 1 [1] Writing index file R-exts.cp Cross reference values unknown; you must run TeX again. [2] [3] [4] [5] [6] Underfull \hbox (badness 10000) in paragraph at lines 515--518 []@textrm The `@texttt Depends[]@textrm '[], `@texttt Imports[]@textrm '[], `@t exttt Suggests[]@textrm '[], `@texttt Enhances[]@textrm '[], `@texttt LinkingTo []@textrm '[] and [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] Underfull \hbox (badness 10000) in paragraph at lines 1325--1326 @texttt R_MAKEVARS_SITE[]@textrm , @textttsl R_HOME@texttt /etc/@textttsl R_ Underfull \hbox (badness 10000) in paragraph at lines 1326--1327 @texttt R_MAKEVARS_SITE[]@textrm , @textttsl R_HOME@texttt /etc/@textttsl R_ Underfull \hbox (badness 10000) in paragraph at lines 1329--1331 @texttt R_MAKEVARS_USER[]@textrm , @texttt ~/.R/Makevars- Underfull \hbox (badness 10000) in paragraph at lines 1331--1333 @texttt ~/.R/Makevars.win64[]@textrm , Underfull \hbox (badness 10000) in paragraph at lines 1339--1340 @texttt R_MAKEVARS_SITE[]@textrm , @textttsl R_HOME@texttt /etc/@textttsl R_ Underfull \hbox (badness 10000) in paragraph at lines 1340--1341 @texttt R_MAKEVARS_SITE[]@textrm , @textttsl R_HOME@texttt /etc/@textttsl R_ Underfull \hbox (badness 10000) in paragraph at lines 1343--1345 @texttt R_MAKEVARS_USER[]@textrm , @texttt ~/.R/Makevars- Underfull \hbox (badness 10000) in paragraph at lines 1345--1347 @texttt ~/.R/Makevars.win64[]@textrm , [17] [18] [19] [20] Overfull \hbox (95.42339pt too wide) in paragraph at lines 1609--1609 [] @texttt "--no-libs", "--no-help", "--no-demo", "--no-exec" , "--no-test-load")[] Overfull \hbox (72.42863pt too wide) in paragraph at lines 1610--1610 [] @texttt install.packages(pkg, lib, INSTALL_opts = opts, repos = NULL , quiet = TRUE)[] Overfull \hbox (20.69044pt too wide) in paragraph at lines 1611--1611 [] @texttt res[z] <- file.size(file.path(lib, pkg_name, "data", "Rdata. rdb"))[] [21] Underfull \hbox (badness 10000) in paragraph at lines 1642--1649 @texttt org/ package=amap[]@textrm )[]), Python or Tcl ([][]@textbf Simile @te xtrm (@texttt https:// CRAN. R-project. org/ [22] [23] [24] [25] [26] Overfull \hbox (32.18782pt too wide) in paragraph at lines 2048--2048 []@texttt $ pkg-config --exists libtiff-4 >= 4.1.0 --print-errors # check the status[] [27] [28] [29] Overfull \hbox (14.94176pt too wide) in paragraph at lines 2292--2292 []@texttt SLAMC_FFLAGS=$(R_XTRA_FFLAGS) $(FPICFLAGS) $(SHLIB_FFLAGS) $(SAFE_FF LAGS)[] [30] [31] [32] [33] [34] Overfull \hbox (67.78206pt too wide) in paragraph at lines 2699--2699 []@smalltt SOURCES = $(wildcard data/*.cpp network/*.cpp utils/*.cpp model/*.c pp model/*/*.cpp model/*/*/*.cpp)[] Overfull \hbox (53.60722pt too wide) in paragraph at lines 2701--2701 []@smalltt OBJECTS = siena07utilities.o siena07internals.o siena07setup.o sien a07models.o $(SOURCES:.cpp=.o)[] [35] [36] Overfull \hbox (16.92342pt too wide) in paragraph at lines 2839--2839 []@smalltt dnl for 64-bit ODBC need SQL[U]LEN, and it is unclear where they ar e defined.[] [37] [38] [39] Underfull \hbox (badness 7221) in paragraph at lines 3051--3057 [][][]@smallrm See [][]@smalltt https:// isocpp. org/ std/ standing-documen ts/ sd-6-sg10-feature-test-recommendations[][] @smallrm or [40] Overfull \hbox (60.93126pt too wide) in paragraph at lines 3138--3138 [] @texttt CXX="$(CXX17) $(CXX17STD)" CXXFLAGS="$(CXX17FLAGS) $(CXX 17PICFLAGS)")[] [41] [42] [43] Overfull \hbox (43.6852pt too wide) in paragraph at lines 3393--3393 []@texttt if test -z "$CMAKE"; then CMAKE=/Applications/CMake.app/Contents/bin /cmake; fi[] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] [54] [55] [56] [57] [58] [59] [60] [61] Overfull \hbox (20.69044pt too wide) in paragraph at lines 4793--4793 []@texttt importFrom("stats", approx, optim, pchisq, predict, qchisq, qnorm, s pline)[] [62] [63] [64] Overfull \hbox (81.29893pt too wide) in paragraph at lines 5029--5029 [] @texttt CXX="$(CXX)" CXXFLAGS="$(CXXFLAGS) $(CXXPICFLAGS) $(C_VISIB ILITY)" \[] Overfull \hbox (59.61772pt too wide) in paragraph at lines 5048--5048 []@texttt CXXFLAGS = ^^R"${RBIN}" CMD config CXXFLAGS^^R ^^R"${RBIN}" CMD conf ig CXXPICFLAGS^^R[] [65] [66] [67] [68] [69] [70] Overfull \hbox (53.86903pt too wide) in paragraph at lines 5532--5532 []@texttt jv <- .jcall("java/lang/System", "S", "getProperty", "java.runtime.v ersion")[] Overfull \hbox (48.12035pt too wide) in paragraph at lines 5534--5534 [] @texttt jvn <- as.numeric(paste0(strsplit(jv, "[.]")[[1L]][1:2], collapse = "."))[] Overfull \hbox (65.36641pt too wide) in paragraph at lines 5535--5535 [] @texttt if(jvn < 1.8) stop("Java >= 8 is needed for this package but not a vailable")[] [71] Overfull \hbox (76.86378pt too wide) in paragraph at lines 5550--5550 []@texttt java.lang.UnsupportedClassVersionError: ... Unsupported major.minor version 52.0[] [72] [73] [74] [75] [76] Overfull \hbox (14.94176pt too wide) in paragraph at lines 5930--5930 []@texttt "latin1=en_US:latin2=pl_PL:UTF-8=en_US.UTF-8:latin9=fr_FR.iso885915@ euro"[] [77] [78] Underfull \hbox (badness 10000) in paragraph at lines 6100--6103 @texttt gcc/ C-Extensions. html[][] @textrm and [][]@texttt https:// gcc. gnu. org/ onlinedocs/ gcc/ [79] Overfull \hbox (19.3769pt too wide) in paragraph at lines 6186--6186 []@texttt abs acos atan bind calloc ceil div exp fabs floor fmod free log mall oc[] [80] [81] Overfull \hbox (53.86903pt too wide) in paragraph at lines 6332--6332 []@texttt register storage class specifier is deprecated and incompatible with C++17[] [82] Overfull \hbox (13.62822pt too wide) in paragraph at lines 6397--6397 []@texttt #if defined (__unix__) || (defined (__APPLE__) && defined (__MACH__) )[] [83] Overfull \hbox (48.12035pt too wide) in paragraph at lines 6474--6474 []@texttt !DEC$ ATTRIBUTES DLLEXPORT,C,REFERENCE,ALIAS: kdenestmlcvb :: kdenestmlcvb[] Overfull \hbox (25.1256pt too wide) in paragraph at lines 6486--6486 []@texttt warning: argument 1 value 18446744073709551615 exceeds maximum object[] Overfull \hbox (94.10985pt too wide) in paragraph at lines 6501--6501 [] @texttt error("Actual: %0.f; Expected %0.f\n", (double) XLENGTH(Robj), ( double) nelem);[] [84] Underfull \hbox (badness 10000) in paragraph at lines 6552--6553 [][][]@smallrm See [][]@smalltt https:// prereleases. llvm. org/ 11. 0. 0 / rc2/ tools/ clang/ docs/ ReleaseNotes. html# [85] [86] [87] [88] [89] [90] Overfull \hbox (19.3769pt too wide) in paragraph at lines 7053--7053 []@texttt #define dngettext(pkg, String, StringP, N) (N == 1 ? String : String P)[] [91] [92] Chapter 2 [93] [94] [95] [96] [97] [98] [99] [100] [101] [102] [103] [104] [105] [106] Underfull \hbox (badness 10000) in paragraph at lines 8329--8336 []@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi lename@texttt }[] @textrm and [107] [108] [109] Underfull \hbox (badness 10000) in paragraph at lines 8541--8546 []@texttt echo=FALSE[] @textrm Whether the R code should be echoed. If @texttt TRUE[] @textit and [110] [111] [112] Chapter 3 [113] [114] [115] [116] [117] [118] [119] Overfull \hbox (43.6852pt too wide) in paragraph at lines 9312--9312 []@texttt 5497 1.9783 R findVarLocInFrame.part.0. lto_priv.0[] [120] Chapter 4 [121] [122] [123] Overfull \hbox (14.94176pt too wide) in paragraph at lines 9584--9584 []@texttt evaluation nested too deeply: infinite recursion / options(expressio ns=)?[] [124] Overfull \hbox (25.25755pt too wide) in paragraph at lines 9625--9625 []@smalltt Message: Error: no valid set of coefficients has been found: pleas e supply starting values[] [125] Overfull \hbox (20.53261pt too wide) in paragraph at lines 9729--9729 []@smalltt debugging in: glm.fit(x = X, y = Y, weights = weights, start = star t, etastart = etastart,[] Overfull \hbox (38.96663pt too wide) in paragraph at lines 9759--9768 []@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by e.g. @texttt debug(stats:::predict.Arima)[]@textrm . [126] [127] [128] [129] Underfull \hbox (badness 10000) in paragraph at lines 10031--10036 @smalltt developer. apple. com/ documentation/ xcode/ diagnosing-memory-th read-and-crash-issues-early[][]@smallrm . Underfull \hbox (badness 10000) in paragraph at lines 10029--10042 @texttt controlling-code-generation[][]@textrm , [][]@texttt https:// clang. llvm. org/ docs/ AddressSanitizer. Overfull \hbox (48.90796pt too wide) in paragraph at lines 10046--10047 [][][]@smallrm see [][]@smalltt https:// llvm. org/ devmtg/ 2014-04/ PDFs/ LightningTalks/ EuroLLVM%202014%20--%20container%20overflow. [130] [131] Overfull \hbox (78.17732pt too wide) in paragraph at lines 10195--10195 []@texttt setenv ASAN_OPTIONS alloc_dealloc_mismatch=0:detect_leaks=0:detect_odr_violation=0 [] Overfull \hbox (32.81921pt too wide) in paragraph at lines 10220--10223 [][]@smalltt https:// developer. apple. com/ documentation/ xcode/ diagno sing-memory-thread-and-crash-issues-early[][]@smallrm .| Overfull \hbox (33.15736pt too wide) in paragraph at lines 10233--10236 []@textrm This san-i-tizer may be com-bined with the Ad-dress San-i-tizer by @t exttt -fsanitize=undefined,address[] [132] [133] Underfull \hbox (badness 10000) in paragraph at lines 10332--10336 [][]@texttt https:// blog. llvm. org/ 2011/ 05/ what-every-c-programmer-s hould-know. html[][] Overfull \hbox (112.66945pt too wide) in paragraph at lines 10348--10348 []@texttt CC = clang -fsanitize=undefined -fno-sanitize=float-divide-by-zero - fno-omit-frame-pointer[] Overfull \hbox (170.15633pt too wide) in paragraph at lines 10349--10349 []@texttt CXX = clang++ -fsanitize=undefined -fno-sanitize=float-divide-by-zer o -fno-omit-frame-pointer -frtti[] Overfull \hbox (181.6537pt too wide) in paragraph at lines 10352--10352 []@texttt SAN_LIBS = $(UBSAN_DIR)/libclang_rt.ubsan_standalone.a $(UBSAN_DIR)/ libclang_rt.ubsan_standalone_cxx.a[] Overfull \hbox (37.93651pt too wide) in paragraph at lines 10360--10360 []@texttt SAN_LIBS = -L$(UBSAN_DIR) -Wl,-rpath,$(UBSAN_DIR) -lclang_rt.ubsan_s tandalone[] Overfull \hbox (2.03816pt too wide) in paragraph at lines 10404--10408 []@textrm See [][]@texttt https:// gcc. gnu. org/ onlinedocs/ gcc-10. 1. 0/ gcc/ Static-Analyzer-Options. [134] Overfull \hbox (72.42863pt too wide) in paragraph at lines 10427--10427 []@texttt Fortran runtime error: Index 1 of dimension 1 of array x above upper bound of 0[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 10472--10472 [] @texttt 2: possibleExtends(class(sloti), classi, ClassDef2 = getClassDef(cl assi,[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 10475--10475 [] @texttt 4: stopifnot(validObject(cu <- as(tu, "dtCMatrix")), validObject(t( cu)),[] [135] [136] Overfull \hbox (26.43913pt too wide) in paragraph at lines 10554--10554 []@texttt #5 0xb7d6c0a5 in do_random2 (call=0x94bf7d4, op=0x92580e8, args=0x9 698f98,[] [137] [138] [139] Underfull \hbox (badness 10000) in paragraph at lines 10797--10799 [][][]@smallrm See [][]@smalltt https:// svn. r-project. org/ R-dev-web/ t runk/ CRAN/ QA/ Simon/ R-build/ fixpathR[][]@smallrm : [140] Overfull \hbox (124.16682pt too wide) in paragraph at lines 10864--10864 []@texttt boot.f:61: warning: type of ddot does not match original declaration [-Wlto-type-mismatch][] Overfull \hbox (147.16158pt too wide) in paragraph at lines 10883--10883 []@texttt rkpk2.f:77:5: warning: type of dstup does not match original declaration [-Wlto-type-mismatch][] Overfull \hbox (141.41289pt too wide) in paragraph at lines 10894--10894 []@texttt reg.f:78:33: warning: type of dqrdc does not match original declaration [-Wlto-type-mismatch][] Overfull \hbox (14.94176pt too wide) in paragraph at lines 10914--10914 [] @tex ttt 1[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 10923--10923 [] @tex ttt 1[] Overfull \hbox (43.6852pt too wide) in paragraph at lines 10924--10924 []@texttt Warning: Type mismatch in argument jpvt at (1); passed REAL(8) to INTEGER(4)[] [141] Chapter 5 [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] Overfull \hbox (30.87428pt too wide) in paragraph at lines 11740--11740 [] @texttt double *w, int *iper, double *span, double *al pha,[] Overfull \hbox (51.66371pt too wide) in paragraph at lines 11804--11804 []@smalltt y[accept] <- .Call("spline_value", knots, coeff, ord, x[accept], de riv, PACKAGE = "splines")[] [153] [154] Overfull \hbox (60.93126pt too wide) in paragraph at lines 11968--11968 [] @texttt na_omit_xts_func fun = (na_omit_xts_func) R_GetCCallable("xts", "n a_omit_xts");[] [155] [156] [157] [158] [159] [160] Overfull \hbox (37.93651pt too wide) in paragraph at lines 12406--12406 []@texttt PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -Wl,-rpath,"$(PKGB_PATH)$(R_ARCH) " -lpackB[] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] Overfull \hbox (14.94176pt too wide) in paragraph at lines 13277--13277 [] @texttt if(ign == NA_LOGICAL) error(" ignore_quotes must be TRUE or FALSE");[] [172] Underfull \hbox (badness 10000) in paragraph at lines 13427--13431 []@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated 3[] @textrm are fast ver-sions of R's [173] [174] [175] [176] [177] [178] [179] Overfull \hbox (14.94176pt too wide) in paragraph at lines 13991--13991 [] @texttt // a version with (too) much PROTECT()ion .. "better safe than s orry"[] [180] [181] Overfull \hbox (14.94176pt too wide) in paragraph at lines 14115--14115 [] @texttt gradient = PROTECT(allocMatrix(REALSXP, LENGTH(ans), LENGTH(thet a)));[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 14120--14120 [] @texttt for(i = 0, start = 0; i < LENGTH(theta); i++, start += LENGTH(an s)) {[] [182] Overfull \hbox (14.94176pt too wide) in paragraph at lines 14175--14175 [] @texttt gradient = PROTECT(allocMatrix(REALSXP, LENGTH(ans), LENGTH(thet a)));[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 14188--14188 [] @texttt for(i = 0, start = 0; i < LENGTH(theta); i++, start += LENGTH(an s)) {[] [183] Overfull \hbox (26.43913pt too wide) in paragraph at lines 14287--14287 [] @texttt cmdexpr = PROTECT(R_ParseVector(cmdSexp, -1, &status, R_NilV alue));[] [184] [185] Overfull \hbox (14.94176pt too wide) in paragraph at lines 14436--14436 []@texttt void R_RegisterCFinalizerEx(SEXP s, R_CFinalizer_t fun, Rboolean one xit);[] [186] Overfull \hbox (43.6852pt too wide) in paragraph at lines 14527--14527 [] @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_ NilValue);[] [187] [188] Overfull \hbox (72.42863pt too wide) in paragraph at lines 14622--14622 []@texttt typedef enum {CE_NATIVE, CE_UTF8, CE_LATIN1, CE_BYTES, CE_SYMBOL, CE _ANY} cetype_t;[] Chapter 6 [189] [190] [191] [192] [193] [194] [195] [196] [197] Overfull \hbox (20.69044pt too wide) in paragraph at lines 15440--15440 [] @texttt call cmsg(msg//c_null_char) ! need to concatenate a nul term inator[] Underfull \hbox (badness 10000) in paragraph at lines 15458--15463 @texttt com/ content/ www/ us/ en/ docs/ fortran-compiler/ developer-gui de-reference/ [198] [199] [200] [201] [202] [203] [204] [205] [206] [207] Underfull \hbox (badness 10000) in paragraph at lines 16199--16203 []@texttt R_orderVector()[] @textrm cor-re-sponds to R's @texttt order(..., na .last, decreasing)[]@textrm . [208] Warning: unbalanced parentheses in @def... [209] [210] Overfull \hbox (14.94176pt too wide) in paragraph at lines 16396--16396 [] @texttt SEXP (*hndlr)(SEXP cond, void *hdata), void *hd ata);[] Overfull \hbox (66.67995pt too wide) in paragraph at lines 16403--16403 [] @texttt SEXP (*hndlr)(SEXP cond, void *hdata) , void *hdata)[] Overfull \hbox (26.43913pt too wide) in paragraph at lines 16432--16432 [] @texttt void (*clean)(void *data, Rboolean jump), void *cdata,[] [211] [212] [213] [214] [215] Chapter 7 [216] [217] Chapter 8 [218] [219] [220] Overfull \hbox (43.6852pt too wide) in paragraph at lines 17197--17197 []@texttt ## replace $(LIBR) $(LIBS) by $(STATIC_LIBR) if R was built with a s tatic libR[] [221] Overfull \hbox (20.69044pt too wide) in paragraph at lines 17240--17240 []@texttt extern int (*ptr_R_ReadConsole)(const char *, unsigned char *, int, int);[] Overfull \hbox (55.18257pt too wide) in paragraph at lines 17255--17255 []@texttt extern int (*ptr_R_EditFiles)(int, const char **, const char **, co nst char *);[] [222] [223] [224] [225] [226] [227] [228] [229] [230] (Function and variable index) [231] No file R-exts.vrs. (Concept index) [232] No file R-exts.cps. [233] ) (see the transcript file for additional information) Output written on R-exts.pdf (236 pages, 1003085 bytes). Transcript written on R-exts.log. This is pdfTeX, Version 3.141592653-2.6-1.40.26 (Web2C 2024) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-exts.t2d/pdf/xtr/R-exts.te xi (/usr/local/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2024-02-10.22]: pdf, fonts, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, microtype, and turning on texinfo input format.) Writing index file R-exts.vr (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-defs.texi (/usr/local/share/texmf-dist/tex/texinfo/txi-en.tex)) (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/version.texi) [1{/usr/local/ share/texmf-dist/fonts/map/pdftex/updmap/pdftex.map}] [2] (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-exts.toc) (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-exts.toc [-1] [-2] [-3] [-4]) [-5] (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-exts.toc) (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-exts.toc) (Acknowledgements) (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-exts.aux) Chapter 1 [1] Writing index file R-exts.cp [2] [3] [4] [5] [6] Underfull \hbox (badness 10000) in paragraph at lines 515--518 []@textrm The `@texttt Depends[]@textrm '[], `@texttt Imports[]@textrm '[], `@t exttt Suggests[]@textrm '[], `@texttt Enhances[]@textrm '[], `@texttt LinkingTo []@textrm '[] and [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] Underfull \hbox (badness 10000) in paragraph at lines 1325--1326 @texttt R_MAKEVARS_SITE[]@textrm , @textttsl R_HOME@texttt /etc/@textttsl R_ Underfull \hbox (badness 10000) in paragraph at lines 1326--1327 @texttt R_MAKEVARS_SITE[]@textrm , @textttsl R_HOME@texttt /etc/@textttsl R_ Underfull \hbox (badness 10000) in paragraph at lines 1329--1331 @texttt R_MAKEVARS_USER[]@textrm , @texttt ~/.R/Makevars- Underfull \hbox (badness 10000) in paragraph at lines 1331--1333 @texttt ~/.R/Makevars.win64[]@textrm , Underfull \hbox (badness 10000) in paragraph at lines 1339--1340 @texttt R_MAKEVARS_SITE[]@textrm , @textttsl R_HOME@texttt /etc/@textttsl R_ Underfull \hbox (badness 10000) in paragraph at lines 1340--1341 @texttt R_MAKEVARS_SITE[]@textrm , @textttsl R_HOME@texttt /etc/@textttsl R_ Underfull \hbox (badness 10000) in paragraph at lines 1343--1345 @texttt R_MAKEVARS_USER[]@textrm , @texttt ~/.R/Makevars- Underfull \hbox (badness 10000) in paragraph at lines 1345--1347 @texttt ~/.R/Makevars.win64[]@textrm , [17] [18] [19] [20] Overfull \hbox (95.42339pt too wide) in paragraph at lines 1609--1609 [] @texttt "--no-libs", "--no-help", "--no-demo", "--no-exec" , "--no-test-load")[] Overfull \hbox (72.42863pt too wide) in paragraph at lines 1610--1610 [] @texttt install.packages(pkg, lib, INSTALL_opts = opts, repos = NULL , quiet = TRUE)[] Overfull \hbox (20.69044pt too wide) in paragraph at lines 1611--1611 [] @texttt res[z] <- file.size(file.path(lib, pkg_name, "data", "Rdata. rdb"))[] [21] Underfull \hbox (badness 10000) in paragraph at lines 1642--1649 @texttt org/ package=amap[]@textrm )[]), Python or Tcl ([][]@textbf Simile @te xtrm (@texttt https:// CRAN. R-project. org/ [22] [23] [24] [25] [26] Overfull \hbox (32.18782pt too wide) in paragraph at lines 2048--2048 []@texttt $ pkg-config --exists libtiff-4 >= 4.1.0 --print-errors # check the status[] [27] [28] [29] Overfull \hbox (14.94176pt too wide) in paragraph at lines 2292--2292 []@texttt SLAMC_FFLAGS=$(R_XTRA_FFLAGS) $(FPICFLAGS) $(SHLIB_FFLAGS) $(SAFE_FF LAGS)[] [30] [31] [32] [33] [34] Overfull \hbox (67.78206pt too wide) in paragraph at lines 2699--2699 []@smalltt SOURCES = $(wildcard data/*.cpp network/*.cpp utils/*.cpp model/*.c pp model/*/*.cpp model/*/*/*.cpp)[] Overfull \hbox (53.60722pt too wide) in paragraph at lines 2701--2701 []@smalltt OBJECTS = siena07utilities.o siena07internals.o siena07setup.o sien a07models.o $(SOURCES:.cpp=.o)[] [35] [36] Overfull \hbox (16.92342pt too wide) in paragraph at lines 2839--2839 []@smalltt dnl for 64-bit ODBC need SQL[U]LEN, and it is unclear where they ar e defined.[] [37] [38] [39] Underfull \hbox (badness 7221) in paragraph at lines 3051--3057 [][][]@smallrm See [][]@smalltt https:// isocpp. org/ std/ standing-documen ts/ sd-6-sg10-feature-test-recommendations[][] @smallrm or [40] Overfull \hbox (60.93126pt too wide) in paragraph at lines 3138--3138 [] @texttt CXX="$(CXX17) $(CXX17STD)" CXXFLAGS="$(CXX17FLAGS) $(CXX 17PICFLAGS)")[] [41] [42] [43] Overfull \hbox (43.6852pt too wide) in paragraph at lines 3393--3393 []@texttt if test -z "$CMAKE"; then CMAKE=/Applications/CMake.app/Contents/bin /cmake; fi[] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] [54] [55] [56] [57] [58] [59] [60] [61] Overfull \hbox (20.69044pt too wide) in paragraph at lines 4793--4793 []@texttt importFrom("stats", approx, optim, pchisq, predict, qchisq, qnorm, s pline)[] [62] [63] [64] Overfull \hbox (81.29893pt too wide) in paragraph at lines 5029--5029 [] @texttt CXX="$(CXX)" CXXFLAGS="$(CXXFLAGS) $(CXXPICFLAGS) $(C_VISIB ILITY)" \[] Overfull \hbox (59.61772pt too wide) in paragraph at lines 5048--5048 []@texttt CXXFLAGS = ^^R"${RBIN}" CMD config CXXFLAGS^^R ^^R"${RBIN}" CMD conf ig CXXPICFLAGS^^R[] [65] [66] [67] [68] [69] [70] Overfull \hbox (53.86903pt too wide) in paragraph at lines 5532--5532 []@texttt jv <- .jcall("java/lang/System", "S", "getProperty", "java.runtime.v ersion")[] Overfull \hbox (48.12035pt too wide) in paragraph at lines 5534--5534 [] @texttt jvn <- as.numeric(paste0(strsplit(jv, "[.]")[[1L]][1:2], collapse = "."))[] Overfull \hbox (65.36641pt too wide) in paragraph at lines 5535--5535 [] @texttt if(jvn < 1.8) stop("Java >= 8 is needed for this package but not a vailable")[] [71] Overfull \hbox (76.86378pt too wide) in paragraph at lines 5550--5550 []@texttt java.lang.UnsupportedClassVersionError: ... Unsupported major.minor version 52.0[] [72] [73] [74] [75] [76] Overfull \hbox (14.94176pt too wide) in paragraph at lines 5930--5930 []@texttt "latin1=en_US:latin2=pl_PL:UTF-8=en_US.UTF-8:latin9=fr_FR.iso885915@ euro"[] [77] [78] Underfull \hbox (badness 10000) in paragraph at lines 6100--6103 @texttt gcc/ C-Extensions. html[][] @textrm and [][]@texttt https:// gcc. gnu. org/ onlinedocs/ gcc/ [79] Overfull \hbox (19.3769pt too wide) in paragraph at lines 6186--6186 []@texttt abs acos atan bind calloc ceil div exp fabs floor fmod free log mall oc[] [80] [81] Overfull \hbox (53.86903pt too wide) in paragraph at lines 6332--6332 []@texttt register storage class specifier is deprecated and incompatible with C++17[] [82] Overfull \hbox (13.62822pt too wide) in paragraph at lines 6397--6397 []@texttt #if defined (__unix__) || (defined (__APPLE__) && defined (__MACH__) )[] [83] Overfull \hbox (48.12035pt too wide) in paragraph at lines 6474--6474 []@texttt !DEC$ ATTRIBUTES DLLEXPORT,C,REFERENCE,ALIAS: kdenestmlcvb :: kdenestmlcvb[] Overfull \hbox (25.1256pt too wide) in paragraph at lines 6486--6486 []@texttt warning: argument 1 value 18446744073709551615 exceeds maximum object[] Overfull \hbox (94.10985pt too wide) in paragraph at lines 6501--6501 [] @texttt error("Actual: %0.f; Expected %0.f\n", (double) XLENGTH(Robj), ( double) nelem);[] [84] Underfull \hbox (badness 10000) in paragraph at lines 6552--6553 [][][]@smallrm See [][]@smalltt https:// prereleases. llvm. org/ 11. 0. 0 / rc2/ tools/ clang/ docs/ ReleaseNotes. html# [85] [86] [87] [88] [89] [90] Overfull \hbox (19.3769pt too wide) in paragraph at lines 7053--7053 []@texttt #define dngettext(pkg, String, StringP, N) (N == 1 ? String : String P)[] [91] [92] Chapter 2 [93] [94] [95] [96] [97] [98] [99] [100] [101] [102] [103] [104] [105] [106] Underfull \hbox (badness 10000) in paragraph at lines 8329--8336 []@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi lename@texttt }[] @textrm and [107] [108] [109] Underfull \hbox (badness 10000) in paragraph at lines 8541--8546 []@texttt echo=FALSE[] @textrm Whether the R code should be echoed. If @texttt TRUE[] @textit and [110] [111] [112] Chapter 3 [113] [114] [115] [116] [117] [118] [119] Overfull \hbox (43.6852pt too wide) in paragraph at lines 9312--9312 []@texttt 5497 1.9783 R findVarLocInFrame.part.0. lto_priv.0[] [120] Chapter 4 [121] [122] [123] Overfull \hbox (14.94176pt too wide) in paragraph at lines 9584--9584 []@texttt evaluation nested too deeply: infinite recursion / options(expressio ns=)?[] [124] Overfull \hbox (25.25755pt too wide) in paragraph at lines 9625--9625 []@smalltt Message: Error: no valid set of coefficients has been found: pleas e supply starting values[] [125] Overfull \hbox (20.53261pt too wide) in paragraph at lines 9729--9729 []@smalltt debugging in: glm.fit(x = X, y = Y, weights = weights, start = star t, etastart = etastart,[] Overfull \hbox (38.96663pt too wide) in paragraph at lines 9759--9768 []@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by e.g. @texttt debug(stats:::predict.Arima)[]@textrm . [126] [127] [128] [129] Underfull \hbox (badness 10000) in paragraph at lines 10031--10036 @smalltt developer. apple. com/ documentation/ xcode/ diagnosing-memory-th read-and-crash-issues-early[][]@smallrm . Underfull \hbox (badness 10000) in paragraph at lines 10029--10042 @texttt controlling-code-generation[][]@textrm , [][]@texttt https:// clang. llvm. org/ docs/ AddressSanitizer. Overfull \hbox (48.90796pt too wide) in paragraph at lines 10046--10047 [][][]@smallrm see [][]@smalltt https:// llvm. org/ devmtg/ 2014-04/ PDFs/ LightningTalks/ EuroLLVM%202014%20--%20container%20overflow. [130] [131] Overfull \hbox (78.17732pt too wide) in paragraph at lines 10195--10195 []@texttt setenv ASAN_OPTIONS alloc_dealloc_mismatch=0:detect_leaks=0:detect_odr_violation=0 [] Overfull \hbox (32.81921pt too wide) in paragraph at lines 10220--10223 [][]@smalltt https:// developer. apple. com/ documentation/ xcode/ diagno sing-memory-thread-and-crash-issues-early[][]@smallrm .| Overfull \hbox (33.15736pt too wide) in paragraph at lines 10233--10236 []@textrm This san-i-tizer may be com-bined with the Ad-dress San-i-tizer by @t exttt -fsanitize=undefined,address[] [132] [133] Underfull \hbox (badness 10000) in paragraph at lines 10332--10336 [][]@texttt https:// blog. llvm. org/ 2011/ 05/ what-every-c-programmer-s hould-know. html[][] Overfull \hbox (112.66945pt too wide) in paragraph at lines 10348--10348 []@texttt CC = clang -fsanitize=undefined -fno-sanitize=float-divide-by-zero - fno-omit-frame-pointer[] Overfull \hbox (170.15633pt too wide) in paragraph at lines 10349--10349 []@texttt CXX = clang++ -fsanitize=undefined -fno-sanitize=float-divide-by-zer o -fno-omit-frame-pointer -frtti[] Overfull \hbox (181.6537pt too wide) in paragraph at lines 10352--10352 []@texttt SAN_LIBS = $(UBSAN_DIR)/libclang_rt.ubsan_standalone.a $(UBSAN_DIR)/ libclang_rt.ubsan_standalone_cxx.a[] Overfull \hbox (37.93651pt too wide) in paragraph at lines 10360--10360 []@texttt SAN_LIBS = -L$(UBSAN_DIR) -Wl,-rpath,$(UBSAN_DIR) -lclang_rt.ubsan_s tandalone[] Overfull \hbox (2.03816pt too wide) in paragraph at lines 10404--10408 []@textrm See [][]@texttt https:// gcc. gnu. org/ onlinedocs/ gcc-10. 1. 0/ gcc/ Static-Analyzer-Options. [134] Overfull \hbox (72.42863pt too wide) in paragraph at lines 10427--10427 []@texttt Fortran runtime error: Index 1 of dimension 1 of array x above upper bound of 0[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 10472--10472 [] @texttt 2: possibleExtends(class(sloti), classi, ClassDef2 = getClassDef(cl assi,[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 10475--10475 [] @texttt 4: stopifnot(validObject(cu <- as(tu, "dtCMatrix")), validObject(t( cu)),[] [135] [136] Overfull \hbox (26.43913pt too wide) in paragraph at lines 10554--10554 []@texttt #5 0xb7d6c0a5 in do_random2 (call=0x94bf7d4, op=0x92580e8, args=0x9 698f98,[] [137] [138] [139] Underfull \hbox (badness 10000) in paragraph at lines 10797--10799 [][][]@smallrm See [][]@smalltt https:// svn. r-project. org/ R-dev-web/ t runk/ CRAN/ QA/ Simon/ R-build/ fixpathR[][]@smallrm : [140] Overfull \hbox (124.16682pt too wide) in paragraph at lines 10864--10864 []@texttt boot.f:61: warning: type of ddot does not match original declaration [-Wlto-type-mismatch][] Overfull \hbox (147.16158pt too wide) in paragraph at lines 10883--10883 []@texttt rkpk2.f:77:5: warning: type of dstup does not match original declaration [-Wlto-type-mismatch][] Overfull \hbox (141.41289pt too wide) in paragraph at lines 10894--10894 []@texttt reg.f:78:33: warning: type of dqrdc does not match original declaration [-Wlto-type-mismatch][] Overfull \hbox (14.94176pt too wide) in paragraph at lines 10914--10914 [] @tex ttt 1[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 10923--10923 [] @tex ttt 1[] Overfull \hbox (43.6852pt too wide) in paragraph at lines 10924--10924 []@texttt Warning: Type mismatch in argument jpvt at (1); passed REAL(8) to INTEGER(4)[] [141] Chapter 5 [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] Overfull \hbox (30.87428pt too wide) in paragraph at lines 11740--11740 [] @texttt double *w, int *iper, double *span, double *al pha,[] Overfull \hbox (51.66371pt too wide) in paragraph at lines 11804--11804 []@smalltt y[accept] <- .Call("spline_value", knots, coeff, ord, x[accept], de riv, PACKAGE = "splines")[] [153] [154] Overfull \hbox (60.93126pt too wide) in paragraph at lines 11968--11968 [] @texttt na_omit_xts_func fun = (na_omit_xts_func) R_GetCCallable("xts", "n a_omit_xts");[] [155] [156] [157] [158] [159] [160] Overfull \hbox (37.93651pt too wide) in paragraph at lines 12406--12406 []@texttt PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -Wl,-rpath,"$(PKGB_PATH)$(R_ARCH) " -lpackB[] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] Overfull \hbox (14.94176pt too wide) in paragraph at lines 13277--13277 [] @texttt if(ign == NA_LOGICAL) error(" ignore_quotes must be TRUE or FALSE");[] [172] Underfull \hbox (badness 10000) in paragraph at lines 13427--13431 []@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated 3[] @textrm are fast ver-sions of R's [173] [174] [175] [176] [177] [178] [179] Overfull \hbox (14.94176pt too wide) in paragraph at lines 13991--13991 [] @texttt // a version with (too) much PROTECT()ion .. "better safe than s orry"[] [180] [181] Overfull \hbox (14.94176pt too wide) in paragraph at lines 14115--14115 [] @texttt gradient = PROTECT(allocMatrix(REALSXP, LENGTH(ans), LENGTH(thet a)));[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 14120--14120 [] @texttt for(i = 0, start = 0; i < LENGTH(theta); i++, start += LENGTH(an s)) {[] [182] Overfull \hbox (14.94176pt too wide) in paragraph at lines 14175--14175 [] @texttt gradient = PROTECT(allocMatrix(REALSXP, LENGTH(ans), LENGTH(thet a)));[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 14188--14188 [] @texttt for(i = 0, start = 0; i < LENGTH(theta); i++, start += LENGTH(an s)) {[] [183] Overfull \hbox (26.43913pt too wide) in paragraph at lines 14287--14287 [] @texttt cmdexpr = PROTECT(R_ParseVector(cmdSexp, -1, &status, R_NilV alue));[] [184] [185] Overfull \hbox (14.94176pt too wide) in paragraph at lines 14436--14436 []@texttt void R_RegisterCFinalizerEx(SEXP s, R_CFinalizer_t fun, Rboolean one xit);[] [186] Overfull \hbox (43.6852pt too wide) in paragraph at lines 14527--14527 [] @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_ NilValue);[] [187] [188] Overfull \hbox (72.42863pt too wide) in paragraph at lines 14622--14622 []@texttt typedef enum {CE_NATIVE, CE_UTF8, CE_LATIN1, CE_BYTES, CE_SYMBOL, CE _ANY} cetype_t;[] Chapter 6 [189] [190] [191] [192] [193] [194] [195] [196] [197] Overfull \hbox (20.69044pt too wide) in paragraph at lines 15440--15440 [] @texttt call cmsg(msg//c_null_char) ! need to concatenate a nul term inator[] Underfull \hbox (badness 10000) in paragraph at lines 15458--15463 @texttt com/ content/ www/ us/ en/ docs/ fortran-compiler/ developer-gui de-reference/ [198] [199] [200] [201] [202] [203] [204] [205] [206] [207] Underfull \hbox (badness 10000) in paragraph at lines 16199--16203 []@texttt R_orderVector()[] @textrm cor-re-sponds to R's @texttt order(..., na .last, decreasing)[]@textrm . [208] Warning: unbalanced parentheses in @def... [209] [210] Overfull \hbox (14.94176pt too wide) in paragraph at lines 16396--16396 [] @texttt SEXP (*hndlr)(SEXP cond, void *hdata), void *hd ata);[] Overfull \hbox (66.67995pt too wide) in paragraph at lines 16403--16403 [] @texttt SEXP (*hndlr)(SEXP cond, void *hdata) , void *hdata)[] Overfull \hbox (26.43913pt too wide) in paragraph at lines 16432--16432 [] @texttt void (*clean)(void *data, Rboolean jump), void *cdata,[] [211] [212] [213] [214] [215] Chapter 7 [216] [217] Chapter 8 [218] [219] [220] Overfull \hbox (43.6852pt too wide) in paragraph at lines 17197--17197 []@texttt ## replace $(LIBR) $(LIBS) by $(STATIC_LIBR) if R was built with a s tatic libR[] [221] Overfull \hbox (20.69044pt too wide) in paragraph at lines 17240--17240 []@texttt extern int (*ptr_R_ReadConsole)(const char *, unsigned char *, int, int);[] Overfull \hbox (55.18257pt too wide) in paragraph at lines 17255--17255 []@texttt extern int (*ptr_R_EditFiles)(int, const char **, const char **, co nst char *);[] [222] [223] [224] [225] [226] [227] [228] [229] [230] (Function and variable index) [231] (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-exts.vrs [232] [233] [234] [235]) [236] (Concept index) [237] (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-exts.cps [238]) [239] ) (see the transcript file for additional information) Output written on R-exts.pdf (246 pages, 1068591 bytes). Transcript written on R-exts.log. This is pdfTeX, Version 3.141592653-2.6-1.40.26 (Web2C 2024) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-exts.t2d/pdf/xtr/R-exts.te xi (/usr/local/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2024-02-10.22]: pdf, fonts, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, microtype, and turning on texinfo input format.) Writing index file R-exts.vr (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-defs.texi (/usr/local/share/texmf-dist/tex/texinfo/txi-en.tex)) (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/version.texi) [1{/usr/local/ share/texmf-dist/fonts/map/pdftex/updmap/pdftex.map}] [2] (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-exts.toc) (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-exts.toc [-1] [-2] [-3] [-4]) [-5] (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-exts.toc) (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-exts.toc) (Acknowledgements) (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-exts.aux) Chapter 1 [1] Writing index file R-exts.cp [2] [3] [4] [5] [6] Underfull \hbox (badness 10000) in paragraph at lines 515--518 []@textrm The `@texttt Depends[]@textrm '[], `@texttt Imports[]@textrm '[], `@t exttt Suggests[]@textrm '[], `@texttt Enhances[]@textrm '[], `@texttt LinkingTo []@textrm '[] and [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] Underfull \hbox (badness 10000) in paragraph at lines 1325--1326 @texttt R_MAKEVARS_SITE[]@textrm , @textttsl R_HOME@texttt /etc/@textttsl R_ Underfull \hbox (badness 10000) in paragraph at lines 1326--1327 @texttt R_MAKEVARS_SITE[]@textrm , @textttsl R_HOME@texttt /etc/@textttsl R_ Underfull \hbox (badness 10000) in paragraph at lines 1329--1331 @texttt R_MAKEVARS_USER[]@textrm , @texttt ~/.R/Makevars- Underfull \hbox (badness 10000) in paragraph at lines 1331--1333 @texttt ~/.R/Makevars.win64[]@textrm , Underfull \hbox (badness 10000) in paragraph at lines 1339--1340 @texttt R_MAKEVARS_SITE[]@textrm , @textttsl R_HOME@texttt /etc/@textttsl R_ Underfull \hbox (badness 10000) in paragraph at lines 1340--1341 @texttt R_MAKEVARS_SITE[]@textrm , @textttsl R_HOME@texttt /etc/@textttsl R_ Underfull \hbox (badness 10000) in paragraph at lines 1343--1345 @texttt R_MAKEVARS_USER[]@textrm , @texttt ~/.R/Makevars- Underfull \hbox (badness 10000) in paragraph at lines 1345--1347 @texttt ~/.R/Makevars.win64[]@textrm , [17] [18] [19] [20] Overfull \hbox (95.42339pt too wide) in paragraph at lines 1609--1609 [] @texttt "--no-libs", "--no-help", "--no-demo", "--no-exec" , "--no-test-load")[] Overfull \hbox (72.42863pt too wide) in paragraph at lines 1610--1610 [] @texttt install.packages(pkg, lib, INSTALL_opts = opts, repos = NULL , quiet = TRUE)[] Overfull \hbox (20.69044pt too wide) in paragraph at lines 1611--1611 [] @texttt res[z] <- file.size(file.path(lib, pkg_name, "data", "Rdata. rdb"))[] [21] Underfull \hbox (badness 10000) in paragraph at lines 1642--1649 @texttt org/ package=amap[]@textrm )[]), Python or Tcl ([][]@textbf Simile @te xtrm (@texttt https:// CRAN. R-project. org/ [22] [23] [24] [25] [26] Overfull \hbox (32.18782pt too wide) in paragraph at lines 2048--2048 []@texttt $ pkg-config --exists libtiff-4 >= 4.1.0 --print-errors # check the status[] [27] [28] [29] Overfull \hbox (14.94176pt too wide) in paragraph at lines 2292--2292 []@texttt SLAMC_FFLAGS=$(R_XTRA_FFLAGS) $(FPICFLAGS) $(SHLIB_FFLAGS) $(SAFE_FF LAGS)[] [30] [31] [32] [33] [34] Overfull \hbox (67.78206pt too wide) in paragraph at lines 2699--2699 []@smalltt SOURCES = $(wildcard data/*.cpp network/*.cpp utils/*.cpp model/*.c pp model/*/*.cpp model/*/*/*.cpp)[] Overfull \hbox (53.60722pt too wide) in paragraph at lines 2701--2701 []@smalltt OBJECTS = siena07utilities.o siena07internals.o siena07setup.o sien a07models.o $(SOURCES:.cpp=.o)[] [35] [36] Overfull \hbox (16.92342pt too wide) in paragraph at lines 2839--2839 []@smalltt dnl for 64-bit ODBC need SQL[U]LEN, and it is unclear where they ar e defined.[] [37] [38] [39] Underfull \hbox (badness 7221) in paragraph at lines 3051--3057 [][][]@smallrm See [][]@smalltt https:// isocpp. org/ std/ standing-documen ts/ sd-6-sg10-feature-test-recommendations[][] @smallrm or [40] Overfull \hbox (60.93126pt too wide) in paragraph at lines 3138--3138 [] @texttt CXX="$(CXX17) $(CXX17STD)" CXXFLAGS="$(CXX17FLAGS) $(CXX 17PICFLAGS)")[] [41] [42] [43] Overfull \hbox (43.6852pt too wide) in paragraph at lines 3393--3393 []@texttt if test -z "$CMAKE"; then CMAKE=/Applications/CMake.app/Contents/bin /cmake; fi[] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] [54] [55] [56] [57] [58] [59] [60] [61] Overfull \hbox (20.69044pt too wide) in paragraph at lines 4793--4793 []@texttt importFrom("stats", approx, optim, pchisq, predict, qchisq, qnorm, s pline)[] [62] [63] [64] Overfull \hbox (81.29893pt too wide) in paragraph at lines 5029--5029 [] @texttt CXX="$(CXX)" CXXFLAGS="$(CXXFLAGS) $(CXXPICFLAGS) $(C_VISIB ILITY)" \[] Overfull \hbox (59.61772pt too wide) in paragraph at lines 5048--5048 []@texttt CXXFLAGS = ^^R"${RBIN}" CMD config CXXFLAGS^^R ^^R"${RBIN}" CMD conf ig CXXPICFLAGS^^R[] [65] [66] [67] [68] [69] [70] Overfull \hbox (53.86903pt too wide) in paragraph at lines 5532--5532 []@texttt jv <- .jcall("java/lang/System", "S", "getProperty", "java.runtime.v ersion")[] Overfull \hbox (48.12035pt too wide) in paragraph at lines 5534--5534 [] @texttt jvn <- as.numeric(paste0(strsplit(jv, "[.]")[[1L]][1:2], collapse = "."))[] Overfull \hbox (65.36641pt too wide) in paragraph at lines 5535--5535 [] @texttt if(jvn < 1.8) stop("Java >= 8 is needed for this package but not a vailable")[] [71] Overfull \hbox (76.86378pt too wide) in paragraph at lines 5550--5550 []@texttt java.lang.UnsupportedClassVersionError: ... Unsupported major.minor version 52.0[] [72] [73] [74] [75] [76] Overfull \hbox (14.94176pt too wide) in paragraph at lines 5930--5930 []@texttt "latin1=en_US:latin2=pl_PL:UTF-8=en_US.UTF-8:latin9=fr_FR.iso885915@ euro"[] [77] [78] Underfull \hbox (badness 10000) in paragraph at lines 6100--6103 @texttt gcc/ C-Extensions. html[][] @textrm and [][]@texttt https:// gcc. gnu. org/ onlinedocs/ gcc/ [79] Overfull \hbox (19.3769pt too wide) in paragraph at lines 6186--6186 []@texttt abs acos atan bind calloc ceil div exp fabs floor fmod free log mall oc[] [80] [81] Overfull \hbox (53.86903pt too wide) in paragraph at lines 6332--6332 []@texttt register storage class specifier is deprecated and incompatible with C++17[] [82] Overfull \hbox (13.62822pt too wide) in paragraph at lines 6397--6397 []@texttt #if defined (__unix__) || (defined (__APPLE__) && defined (__MACH__) )[] [83] Overfull \hbox (48.12035pt too wide) in paragraph at lines 6474--6474 []@texttt !DEC$ ATTRIBUTES DLLEXPORT,C,REFERENCE,ALIAS: kdenestmlcvb :: kdenestmlcvb[] Overfull \hbox (25.1256pt too wide) in paragraph at lines 6486--6486 []@texttt warning: argument 1 value 18446744073709551615 exceeds maximum object[] Overfull \hbox (94.10985pt too wide) in paragraph at lines 6501--6501 [] @texttt error("Actual: %0.f; Expected %0.f\n", (double) XLENGTH(Robj), ( double) nelem);[] [84] Underfull \hbox (badness 10000) in paragraph at lines 6552--6553 [][][]@smallrm See [][]@smalltt https:// prereleases. llvm. org/ 11. 0. 0 / rc2/ tools/ clang/ docs/ ReleaseNotes. html# [85] [86] [87] [88] [89] [90] Overfull \hbox (19.3769pt too wide) in paragraph at lines 7053--7053 []@texttt #define dngettext(pkg, String, StringP, N) (N == 1 ? String : String P)[] [91] [92] Chapter 2 [93] [94] [95] [96] [97] [98] [99] [100] [101] [102] [103] [104] [105] [106] Underfull \hbox (badness 10000) in paragraph at lines 8329--8336 []@textrm The two com-monly used sim-ple forms are @texttt \figure{@textttsl fi lename@texttt }[] @textrm and [107] [108] [109] Underfull \hbox (badness 10000) in paragraph at lines 8541--8546 []@texttt echo=FALSE[] @textrm Whether the R code should be echoed. If @texttt TRUE[] @textit and [110] [111] [112] Chapter 3 [113] [114] [115] [116] [117] [118] [119] Overfull \hbox (43.6852pt too wide) in paragraph at lines 9312--9312 []@texttt 5497 1.9783 R findVarLocInFrame.part.0. lto_priv.0[] [120] Chapter 4 [121] [122] [123] Overfull \hbox (14.94176pt too wide) in paragraph at lines 9584--9584 []@texttt evaluation nested too deeply: infinite recursion / options(expressio ns=)?[] [124] Overfull \hbox (25.25755pt too wide) in paragraph at lines 9625--9625 []@smalltt Message: Error: no valid set of coefficients has been found: pleas e supply starting values[] [125] Overfull \hbox (20.53261pt too wide) in paragraph at lines 9729--9729 []@smalltt debugging in: glm.fit(x = X, y = Y, weights = weights, start = star t, etastart = etastart,[] Overfull \hbox (38.96663pt too wide) in paragraph at lines 9759--9768 []@texttt debug[] @textrm can be used for hid-den func-tions and S3 meth-ods by e.g. @texttt debug(stats:::predict.Arima)[]@textrm . [126] [127] [128] [129] Underfull \hbox (badness 10000) in paragraph at lines 10031--10036 @smalltt developer. apple. com/ documentation/ xcode/ diagnosing-memory-th read-and-crash-issues-early[][]@smallrm . Underfull \hbox (badness 10000) in paragraph at lines 10029--10042 @texttt controlling-code-generation[][]@textrm , [][]@texttt https:// clang. llvm. org/ docs/ AddressSanitizer. Overfull \hbox (48.90796pt too wide) in paragraph at lines 10046--10047 [][][]@smallrm see [][]@smalltt https:// llvm. org/ devmtg/ 2014-04/ PDFs/ LightningTalks/ EuroLLVM%202014%20--%20container%20overflow. [130] [131] Overfull \hbox (78.17732pt too wide) in paragraph at lines 10195--10195 []@texttt setenv ASAN_OPTIONS alloc_dealloc_mismatch=0:detect_leaks=0:detect_odr_violation=0 [] Overfull \hbox (32.81921pt too wide) in paragraph at lines 10220--10223 [][]@smalltt https:// developer. apple. com/ documentation/ xcode/ diagno sing-memory-thread-and-crash-issues-early[][]@smallrm .| Overfull \hbox (33.15736pt too wide) in paragraph at lines 10233--10236 []@textrm This san-i-tizer may be com-bined with the Ad-dress San-i-tizer by @t exttt -fsanitize=undefined,address[] [132] [133] Underfull \hbox (badness 10000) in paragraph at lines 10332--10336 [][]@texttt https:// blog. llvm. org/ 2011/ 05/ what-every-c-programmer-s hould-know. html[][] Overfull \hbox (112.66945pt too wide) in paragraph at lines 10348--10348 []@texttt CC = clang -fsanitize=undefined -fno-sanitize=float-divide-by-zero - fno-omit-frame-pointer[] Overfull \hbox (170.15633pt too wide) in paragraph at lines 10349--10349 []@texttt CXX = clang++ -fsanitize=undefined -fno-sanitize=float-divide-by-zer o -fno-omit-frame-pointer -frtti[] Overfull \hbox (181.6537pt too wide) in paragraph at lines 10352--10352 []@texttt SAN_LIBS = $(UBSAN_DIR)/libclang_rt.ubsan_standalone.a $(UBSAN_DIR)/ libclang_rt.ubsan_standalone_cxx.a[] Overfull \hbox (37.93651pt too wide) in paragraph at lines 10360--10360 []@texttt SAN_LIBS = -L$(UBSAN_DIR) -Wl,-rpath,$(UBSAN_DIR) -lclang_rt.ubsan_s tandalone[] Overfull \hbox (2.03816pt too wide) in paragraph at lines 10404--10408 []@textrm See [][]@texttt https:// gcc. gnu. org/ onlinedocs/ gcc-10. 1. 0/ gcc/ Static-Analyzer-Options. [134] Overfull \hbox (72.42863pt too wide) in paragraph at lines 10427--10427 []@texttt Fortran runtime error: Index 1 of dimension 1 of array x above upper bound of 0[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 10472--10472 [] @texttt 2: possibleExtends(class(sloti), classi, ClassDef2 = getClassDef(cl assi,[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 10475--10475 [] @texttt 4: stopifnot(validObject(cu <- as(tu, "dtCMatrix")), validObject(t( cu)),[] [135] [136] Overfull \hbox (26.43913pt too wide) in paragraph at lines 10554--10554 []@texttt #5 0xb7d6c0a5 in do_random2 (call=0x94bf7d4, op=0x92580e8, args=0x9 698f98,[] [137] [138] [139] Underfull \hbox (badness 10000) in paragraph at lines 10797--10799 [][][]@smallrm See [][]@smalltt https:// svn. r-project. org/ R-dev-web/ t runk/ CRAN/ QA/ Simon/ R-build/ fixpathR[][]@smallrm : [140] Overfull \hbox (124.16682pt too wide) in paragraph at lines 10864--10864 []@texttt boot.f:61: warning: type of ddot does not match original declaration [-Wlto-type-mismatch][] Overfull \hbox (147.16158pt too wide) in paragraph at lines 10883--10883 []@texttt rkpk2.f:77:5: warning: type of dstup does not match original declaration [-Wlto-type-mismatch][] Overfull \hbox (141.41289pt too wide) in paragraph at lines 10894--10894 []@texttt reg.f:78:33: warning: type of dqrdc does not match original declaration [-Wlto-type-mismatch][] Overfull \hbox (14.94176pt too wide) in paragraph at lines 10914--10914 [] @tex ttt 1[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 10923--10923 [] @tex ttt 1[] Overfull \hbox (43.6852pt too wide) in paragraph at lines 10924--10924 []@texttt Warning: Type mismatch in argument jpvt at (1); passed REAL(8) to INTEGER(4)[] [141] Chapter 5 [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] Overfull \hbox (30.87428pt too wide) in paragraph at lines 11740--11740 [] @texttt double *w, int *iper, double *span, double *al pha,[] Overfull \hbox (51.66371pt too wide) in paragraph at lines 11804--11804 []@smalltt y[accept] <- .Call("spline_value", knots, coeff, ord, x[accept], de riv, PACKAGE = "splines")[] [153] [154] Overfull \hbox (60.93126pt too wide) in paragraph at lines 11968--11968 [] @texttt na_omit_xts_func fun = (na_omit_xts_func) R_GetCCallable("xts", "n a_omit_xts");[] [155] [156] [157] [158] [159] [160] Overfull \hbox (37.93651pt too wide) in paragraph at lines 12406--12406 []@texttt PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -Wl,-rpath,"$(PKGB_PATH)$(R_ARCH) " -lpackB[] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] Overfull \hbox (14.94176pt too wide) in paragraph at lines 13277--13277 [] @texttt if(ign == NA_LOGICAL) error(" ignore_quotes must be TRUE or FALSE");[] [172] Underfull \hbox (badness 10000) in paragraph at lines 13427--13431 []@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated 3[] @textrm are fast ver-sions of R's [173] [174] [175] [176] [177] [178] [179] Overfull \hbox (14.94176pt too wide) in paragraph at lines 13991--13991 [] @texttt // a version with (too) much PROTECT()ion .. "better safe than s orry"[] [180] [181] Overfull \hbox (14.94176pt too wide) in paragraph at lines 14115--14115 [] @texttt gradient = PROTECT(allocMatrix(REALSXP, LENGTH(ans), LENGTH(thet a)));[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 14120--14120 [] @texttt for(i = 0, start = 0; i < LENGTH(theta); i++, start += LENGTH(an s)) {[] [182] Overfull \hbox (14.94176pt too wide) in paragraph at lines 14175--14175 [] @texttt gradient = PROTECT(allocMatrix(REALSXP, LENGTH(ans), LENGTH(thet a)));[] Overfull \hbox (14.94176pt too wide) in paragraph at lines 14188--14188 [] @texttt for(i = 0, start = 0; i < LENGTH(theta); i++, start += LENGTH(an s)) {[] [183] Overfull \hbox (26.43913pt too wide) in paragraph at lines 14287--14287 [] @texttt cmdexpr = PROTECT(R_ParseVector(cmdSexp, -1, &status, R_NilV alue));[] [184] [185] Overfull \hbox (14.94176pt too wide) in paragraph at lines 14436--14436 []@texttt void R_RegisterCFinalizerEx(SEXP s, R_CFinalizer_t fun, Rboolean one xit);[] [186] Overfull \hbox (43.6852pt too wide) in paragraph at lines 14527--14527 [] @texttt ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_ NilValue);[] [187] [188] Overfull \hbox (72.42863pt too wide) in paragraph at lines 14622--14622 []@texttt typedef enum {CE_NATIVE, CE_UTF8, CE_LATIN1, CE_BYTES, CE_SYMBOL, CE _ANY} cetype_t;[] Chapter 6 [189] [190] [191] [192] [193] [194] [195] [196] [197] Overfull \hbox (20.69044pt too wide) in paragraph at lines 15440--15440 [] @texttt call cmsg(msg//c_null_char) ! need to concatenate a nul term inator[] Underfull \hbox (badness 10000) in paragraph at lines 15458--15463 @texttt com/ content/ www/ us/ en/ docs/ fortran-compiler/ developer-gui de-reference/ [198] [199] [200] [201] [202] [203] [204] [205] [206] [207] Underfull \hbox (badness 10000) in paragraph at lines 16199--16203 []@texttt R_orderVector()[] @textrm cor-re-sponds to R's @texttt order(..., na .last, decreasing)[]@textrm . [208] Warning: unbalanced parentheses in @def... [209] [210] Overfull \hbox (14.94176pt too wide) in paragraph at lines 16396--16396 [] @texttt SEXP (*hndlr)(SEXP cond, void *hdata), void *hd ata);[] Overfull \hbox (66.67995pt too wide) in paragraph at lines 16403--16403 [] @texttt SEXP (*hndlr)(SEXP cond, void *hdata) , void *hdata)[] Overfull \hbox (26.43913pt too wide) in paragraph at lines 16432--16432 [] @texttt void (*clean)(void *data, Rboolean jump), void *cdata,[] [211] [212] [213] [214] [215] Chapter 7 [216] [217] Chapter 8 [218] [219] [220] Overfull \hbox (43.6852pt too wide) in paragraph at lines 17197--17197 []@texttt ## replace $(LIBR) $(LIBS) by $(STATIC_LIBR) if R was built with a s tatic libR[] [221] Overfull \hbox (20.69044pt too wide) in paragraph at lines 17240--17240 []@texttt extern int (*ptr_R_ReadConsole)(const char *, unsigned char *, int, int);[] Overfull \hbox (55.18257pt too wide) in paragraph at lines 17255--17255 []@texttt extern int (*ptr_R_EditFiles)(int, const char **, const char **, co nst char *);[] [222] [223] [224] [225] [226] [227] [228] [229] [230] (Function and variable index) [231] (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-exts.vrs [232] [233] [234] [235]) [236] (Concept index) [237] (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-exts.cps [238]) [239] ) (see the transcript file for additional information) Output written on R-exts.pdf (246 pages, 1068581 bytes). Transcript written on R-exts.log. TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/local/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-intro.texi @setfilename R-intro.info This is pdfTeX, Version 3.141592653-2.6-1.40.26 (Web2C 2024) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-intro.t2d/pdf/xtr/R-intro. texi (/usr/local/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2024-02-10.22]: pdf, fonts, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, microtype, and turning on texinfo input format.) Writing index file R-intro.vr (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-defs.texi (/usr/local/share/texmf-dist/tex/texinfo/txi-en.tex)) (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/version.texi) [1{/usr/local/ share/texmf-dist/fonts/map/pdftex/updmap/pdftex.map}] [2] [-1] (Preface) Cross reference values unknown; you must run TeX again. Chapter 1 [1] Writing index file R-intro.cp [2] [3] [4] [5] Chapter 2 [6] [7] [8] [9] [10] [11] [12] Chapter 3 [13] [14] [15] Chapter 4 [16] [17] Chapter 5 [18] [19] [20] [21] [22] [23] [24] [25] [26] [27] Chapter 6 [28] [29] [30] [31] Chapter 7 [32] [33] [34] Chapter 8 [35] [36] [37] [38] [39] [40] [41] Chapter 9 [42] [43] Chapter 10 [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] Chapter 11 [54] [55] [56] [57] [58] [59] [60] Underfull \hbox (badness 10000) in paragraph at lines 4838--4840 @texttt logit[]@textrm , @texttt probit[]@textrm , @texttt cloglog[]@textrm , @texttt identity[]@textrm , [61] [62] [63] [64] [65] Underfull \hbox (badness 10000) in paragraph at lines 5253--5263 [][]@textbf Mixed mod-els. @textrm The rec-om-mended [][]@textbf nlme @textrm (@texttt https:// CRAN. R-project. org/ [66] Chapter 12 [67] [68] [69] [70] [71] Overfull \hbox (26.43913pt too wide) in paragraph at lines 5733--5733 []@texttt > text(x, y, expression(paste(bgroup("(", atop(n, x), ")"), p^x, q^{ n-x})))[] [72] [73] [74] [75] [76] [77] [78] [79] [80] [81] Chapter 13 [82] Underfull \hbox (badness 10000) in paragraph at lines 6444--6449 []@textrm Users con-nected to the In-ter-net can use the @texttt install.packag es()[] @textrm and [83] Chapter 14 [84] [85] Underfull \hbox (badness 10000) in paragraph at lines 6652--6657 []@textrm Windows' UNC filepaths (such as @texttt \\server\dir1\dir2\file[] @t extrm and [86] Appendix A [87] [88] [89] [90] Appendix B [91] [92] [93] [94] [95] [96] [97] [98] Appendix C [99] [100] Appendix D [101] No file R-intro.vrs. Appendix E [102] No file R-intro.cps. Appendix F [103] [104] ) (see the transcript file for additional information) Output written on R-intro.pdf (107 pages, 572269 bytes). Transcript written on R-intro.log. This is pdfTeX, Version 3.141592653-2.6-1.40.26 (Web2C 2024) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-intro.t2d/pdf/xtr/R-intro. texi (/usr/local/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2024-02-10.22]: pdf, fonts, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, microtype, and turning on texinfo input format.) Writing index file R-intro.vr (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-defs.texi (/usr/local/share/texmf-dist/tex/texinfo/txi-en.tex)) (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/version.texi) [1{/usr/local/ share/texmf-dist/fonts/map/pdftex/updmap/pdftex.map}] [2] (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-intro.toc) (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-intro.toc [-1] [-2] [-3]) [-4] (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-intro.toc) (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-intro.toc) (Preface) (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-intro.aux) Chapter 1 [1] Writing index file R-intro.cp [2] [3] [4] [5] Chapter 2 [6] [7] [8] [9] [10] [11] [12] Chapter 3 [13] [14] [15] Chapter 4 [16] [17] Chapter 5 [18] [19] [20] [21] [22] [23] [24] [25] [26] [27] Chapter 6 [28] [29] [30] [31] Chapter 7 [32] [33] [34] Chapter 8 [35] [36] [37] [38] [39] [40] [41] Chapter 9 [42] [43] Chapter 10 [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] Chapter 11 [54] [55] [56] [57] [58] [59] [60] Underfull \hbox (badness 10000) in paragraph at lines 4838--4840 @texttt logit[]@textrm , @texttt probit[]@textrm , @texttt cloglog[]@textrm , @texttt identity[]@textrm , [61] [62] [63] [64] [65] Underfull \hbox (badness 10000) in paragraph at lines 5253--5263 [][]@textbf Mixed mod-els. @textrm The rec-om-mended [][]@textbf nlme @textrm (@texttt https:// CRAN. R-project. org/ [66] Chapter 12 [67] [68] [69] [70] [71] Overfull \hbox (26.43913pt too wide) in paragraph at lines 5733--5733 []@texttt > text(x, y, expression(paste(bgroup("(", atop(n, x), ")"), p^x, q^{ n-x})))[] [72] [73] [74] [75] [76] [77] [78] [79] [80] [81] Chapter 13 [82] Underfull \hbox (badness 10000) in paragraph at lines 6444--6449 []@textrm Users con-nected to the In-ter-net can use the @texttt install.packag es()[] @textrm and [83] Chapter 14 [84] [85] Underfull \hbox (badness 10000) in paragraph at lines 6652--6657 []@textrm Windows' UNC filepaths (such as @texttt \\server\dir1\dir2\file[] @t extrm and [86] Appendix A [87] [88] [89] [90] Appendix B [91] [92] [93] [94] [95] [96] [97] [98] Appendix C [99] [100] Appendix D [101] (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-intro.vrs [102] [103]) Appendix E [104] (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-intro.cps [105]) Appendix F [106] [107] ) (see the transcript file for additional information) Output written on R-intro.pdf (113 pages, 623956 bytes). Transcript written on R-intro.log. This is pdfTeX, Version 3.141592653-2.6-1.40.26 (Web2C 2024) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-intro.t2d/pdf/xtr/R-intro. texi (/usr/local/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2024-02-10.22]: pdf, fonts, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, microtype, and turning on texinfo input format.) Writing index file R-intro.vr (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-defs.texi (/usr/local/share/texmf-dist/tex/texinfo/txi-en.tex)) (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/version.texi) [1{/usr/local/ share/texmf-dist/fonts/map/pdftex/updmap/pdftex.map}] [2] (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-intro.toc) (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-intro.toc [-1] [-2] [-3]) [-4] (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-intro.toc) (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-intro.toc) (Preface) (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-intro.aux) Chapter 1 [1] Writing index file R-intro.cp [2] [3] [4] [5] Chapter 2 [6] [7] [8] [9] [10] [11] [12] Chapter 3 [13] [14] [15] Chapter 4 [16] [17] Chapter 5 [18] [19] [20] [21] [22] [23] [24] [25] [26] [27] Chapter 6 [28] [29] [30] [31] Chapter 7 [32] [33] [34] Chapter 8 [35] [36] [37] [38] [39] [40] [41] Chapter 9 [42] [43] Chapter 10 [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] Chapter 11 [54] [55] [56] [57] [58] [59] [60] Underfull \hbox (badness 10000) in paragraph at lines 4838--4840 @texttt logit[]@textrm , @texttt probit[]@textrm , @texttt cloglog[]@textrm , @texttt identity[]@textrm , [61] [62] [63] [64] [65] Underfull \hbox (badness 10000) in paragraph at lines 5253--5263 [][]@textbf Mixed mod-els. @textrm The rec-om-mended [][]@textbf nlme @textrm (@texttt https:// CRAN. R-project. org/ [66] Chapter 12 [67] [68] [69] [70] [71] Overfull \hbox (26.43913pt too wide) in paragraph at lines 5733--5733 []@texttt > text(x, y, expression(paste(bgroup("(", atop(n, x), ")"), p^x, q^{ n-x})))[] [72] [73] [74] [75] [76] [77] [78] [79] [80] [81] Chapter 13 [82] Underfull \hbox (badness 10000) in paragraph at lines 6444--6449 []@textrm Users con-nected to the In-ter-net can use the @texttt install.packag es()[] @textrm and [83] Chapter 14 [84] [85] Underfull \hbox (badness 10000) in paragraph at lines 6652--6657 []@textrm Windows' UNC filepaths (such as @texttt \\server\dir1\dir2\file[] @t extrm and [86] Appendix A [87] [88] [89] [90] Appendix B [91] [92] [93] [94] [95] [96] [97] [98] Appendix C [99] [100] Appendix D [101] (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-intro.vrs [102] [103]) Appendix E [104] (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-intro.cps [105]) Appendix F [106] [107] ) (see the transcript file for additional information) Output written on R-intro.pdf (113 pages, 623977 bytes). Transcript written on R-intro.log. TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/local/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-ints.texi @setfilename R-ints.info This is pdfTeX, Version 3.141592653-2.6-1.40.26 (Web2C 2024) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-ints.t2d/pdf/xtr/R-ints.te xi (/usr/local/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2024-02-10.22]: pdf, fonts, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, microtype, and turning on texinfo input format.) Writing index file R-ints.vr (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-defs.texi (/usr/local/share/texmf-dist/tex/texinfo/txi-en.tex)) (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/version.texi) [1{/usr/local/ share/texmf-dist/fonts/map/pdftex/updmap/pdftex.map}] [2] [-1] Chapter 1 Writing index file R-ints.cp [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] Overfull \hbox (49.43388pt too wide) in paragraph at lines 1497--1497 [] @texttt length(nM <- asNamespace("Matrix") ) # 941 for M atrix 1.2-6[] Overfull \hbox (78.17732pt too wide) in paragraph at lines 1498--1498 [] @texttt length(meth <- grep("^[.]__T__", names(nM), value=TRUE))# 107 gener ics with methods[] Overfull \hbox (66.67995pt too wide) in paragraph at lines 1499--1499 [] @texttt length(meth.Ops <- nM$^^R.__T__Ops:base^^R) # 71 methods for the Ops (group)generic[] Overfull \hbox (158.65895pt too wide) in paragraph at lines 1500--1500 [] @texttt head(sort(names(meth.Ops))) ## "abIndex#abIndex" ... "ANY#ddiMatrix " "ANY#ldiMatrix" "ANY#Matrix"[] [19] [20] [21] [22] [23] [24] Chapter 2 [25] Overfull \hbox (26.43913pt too wide) in paragraph at lines 2018--2018 [] @texttt if (!is.character(x)) x <- structure(as.character(x), names = na mes(x))[] [26] [27] [28] [29] Chapter 3 [30] [31] Chapter 4 [32] [33] Chapter 5 [34] Chapter 6 [35] [36] [37] [38] [39] [40] Underfull \hbox (badness 10000) in paragraph at lines 3136--3142 []@textrm The @texttt glyphs[] @textrm com-po-nent re-ports whether ren-der-in g glyphs (e.g., via [41] [42] [43] [44] [45] [46] [47] [48] Chapter 7 [49] Underfull \hbox (badness 10000) in paragraph at lines 3790--3799 @textrm it uses @texttt /Library/Frameworks/R.framework/R[]@textrm . This is a sym-bolic link, Underfull \hbox (badness 10000) in paragraph at lines 3790--3799 @texttt /Library/Frameworks/R.framework/Versions/Current/Resources/lib/libR.dyl ib[]@textrm , [50] Overfull \hbox (16.81319pt too wide) in paragraph at lines 3841--3845 []@textrm The de-fault path for a per-sonal li-brary di-rec-tory is set as @te xttt ~/Library/R/arch/x.y/library[]@textrm . Chapter 8 [51] [52] [53] [54] [55] Underfull \hbox (badness 10000) in paragraph at lines 4179--4187 []@textrm A string with comma-separated @textttsl name@texttt =@textttsl value [] @textrm pairs (with @textsl value[] @textrm a Underfull \hbox (badness 10000) in paragraph at lines 4179--4187 @textrm log-i-cal con-stant) giv-ing ad-di-tional ar-gu-ments for the [][]@tex tbf codetools Underfull \hbox (badness 10000) in paragraph at lines 4179--4187 @textrm (@texttt https:// CRAN. R-project. org/ package=codetools[]@textrm )[] func-tions used Underfull \hbox (badness 10000) in paragraph at lines 4179--4187 @textrm to us-ing @texttt skipWith = TRUE[]@textrm , @texttt suppressPartialMa tchArgs = FALSE[] @textrm and [56] [57] [58] [59] [60] [61] Underfull \hbox (badness 10000) in paragraph at lines 4551--4556 @texttt blog. r-project. org/ 2022/ 04/ 08/ enhancements-to-html-documen tation/ [62] [63] [64] [65] Chapter 9 [66] [67] Chapter 10 [68] Chapter 11 [69] Chapter 12 [70] [71] (Function and variable index) [72] [73] No file R-ints.vrs. (Concept index) [74] No file R-ints.cps. [75] ) (see the transcript file for additional information) Output written on R-ints.pdf (78 pages, 420733 bytes). Transcript written on R-ints.log. This is pdfTeX, Version 3.141592653-2.6-1.40.26 (Web2C 2024) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-ints.t2d/pdf/xtr/R-ints.te xi (/usr/local/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2024-02-10.22]: pdf, fonts, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, microtype, and turning on texinfo input format.) Writing index file R-ints.vr (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-defs.texi (/usr/local/share/texmf-dist/tex/texinfo/txi-en.tex)) (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/version.texi) [1{/usr/local/ share/texmf-dist/fonts/map/pdftex/updmap/pdftex.map}] [2] (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-ints.toc) (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-ints.toc [-1] [-2]) [-3] (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-ints.toc) (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-ints.toc) Chapter 1 (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-ints.aux) Writing index file R-ints.cp [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] Overfull \hbox (49.43388pt too wide) in paragraph at lines 1497--1497 [] @texttt length(nM <- asNamespace("Matrix") ) # 941 for M atrix 1.2-6[] Overfull \hbox (78.17732pt too wide) in paragraph at lines 1498--1498 [] @texttt length(meth <- grep("^[.]__T__", names(nM), value=TRUE))# 107 gener ics with methods[] Overfull \hbox (66.67995pt too wide) in paragraph at lines 1499--1499 [] @texttt length(meth.Ops <- nM$^^R.__T__Ops:base^^R) # 71 methods for the Ops (group)generic[] Overfull \hbox (158.65895pt too wide) in paragraph at lines 1500--1500 [] @texttt head(sort(names(meth.Ops))) ## "abIndex#abIndex" ... "ANY#ddiMatrix " "ANY#ldiMatrix" "ANY#Matrix"[] [19] [20] [21] [22] [23] [24] Chapter 2 [25] Overfull \hbox (26.43913pt too wide) in paragraph at lines 2018--2018 [] @texttt if (!is.character(x)) x <- structure(as.character(x), names = na mes(x))[] [26] [27] [28] [29] Chapter 3 [30] [31] Chapter 4 [32] [33] Chapter 5 [34] Chapter 6 [35] [36] [37] [38] [39] [40] Underfull \hbox (badness 10000) in paragraph at lines 3136--3142 []@textrm The @texttt glyphs[] @textrm com-po-nent re-ports whether ren-der-in g glyphs (e.g., via [41] [42] [43] [44] [45] [46] [47] [48] Chapter 7 [49] Underfull \hbox (badness 10000) in paragraph at lines 3790--3799 @textrm it uses @texttt /Library/Frameworks/R.framework/R[]@textrm . This is a sym-bolic link, Underfull \hbox (badness 10000) in paragraph at lines 3790--3799 @texttt /Library/Frameworks/R.framework/Versions/Current/Resources/lib/libR.dyl ib[]@textrm , [50] Overfull \hbox (16.81319pt too wide) in paragraph at lines 3841--3845 []@textrm The de-fault path for a per-sonal li-brary di-rec-tory is set as @te xttt ~/Library/R/arch/x.y/library[]@textrm . Chapter 8 [51] [52] [53] [54] [55] Underfull \hbox (badness 10000) in paragraph at lines 4179--4187 []@textrm A string with comma-separated @textttsl name@texttt =@textttsl value [] @textrm pairs (with @textsl value[] @textrm a Underfull \hbox (badness 10000) in paragraph at lines 4179--4187 @textrm log-i-cal con-stant) giv-ing ad-di-tional ar-gu-ments for the [][]@tex tbf codetools Underfull \hbox (badness 10000) in paragraph at lines 4179--4187 @textrm (@texttt https:// CRAN. R-project. org/ package=codetools[]@textrm )[] func-tions used Underfull \hbox (badness 10000) in paragraph at lines 4179--4187 @textrm to us-ing @texttt skipWith = TRUE[]@textrm , @texttt suppressPartialMa tchArgs = FALSE[] @textrm and [56] [57] [58] [59] [60] [61] Underfull \hbox (badness 10000) in paragraph at lines 4551--4556 @texttt blog. r-project. org/ 2022/ 04/ 08/ enhancements-to-html-documen tation/ [62] [63] [64] [65] Chapter 9 [66] [67] Chapter 10 [68] Chapter 11 [69] Chapter 12 [70] [71] (Function and variable index) [72] [73] (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-ints.vrs [74] [75]) (Concept index) [76] (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-ints.cps) [77] ) (see the transcript file for additional information) Output written on R-ints.pdf (82 pages, 469335 bytes). Transcript written on R-ints.log. This is pdfTeX, Version 3.141592653-2.6-1.40.26 (Web2C 2024) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-ints.t2d/pdf/xtr/R-ints.te xi (/usr/local/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2024-02-10.22]: pdf, fonts, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, microtype, and turning on texinfo input format.) Writing index file R-ints.vr (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-defs.texi (/usr/local/share/texmf-dist/tex/texinfo/txi-en.tex)) (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/version.texi) [1{/usr/local/ share/texmf-dist/fonts/map/pdftex/updmap/pdftex.map}] [2] (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-ints.toc) (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-ints.toc [-1] [-2]) [-3] (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-ints.toc) (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-ints.toc) Chapter 1 (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-ints.aux) Writing index file R-ints.cp [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] Overfull \hbox (49.43388pt too wide) in paragraph at lines 1497--1497 [] @texttt length(nM <- asNamespace("Matrix") ) # 941 for M atrix 1.2-6[] Overfull \hbox (78.17732pt too wide) in paragraph at lines 1498--1498 [] @texttt length(meth <- grep("^[.]__T__", names(nM), value=TRUE))# 107 gener ics with methods[] Overfull \hbox (66.67995pt too wide) in paragraph at lines 1499--1499 [] @texttt length(meth.Ops <- nM$^^R.__T__Ops:base^^R) # 71 methods for the Ops (group)generic[] Overfull \hbox (158.65895pt too wide) in paragraph at lines 1500--1500 [] @texttt head(sort(names(meth.Ops))) ## "abIndex#abIndex" ... "ANY#ddiMatrix " "ANY#ldiMatrix" "ANY#Matrix"[] [19] [20] [21] [22] [23] [24] Chapter 2 [25] Overfull \hbox (26.43913pt too wide) in paragraph at lines 2018--2018 [] @texttt if (!is.character(x)) x <- structure(as.character(x), names = na mes(x))[] [26] [27] [28] [29] Chapter 3 [30] [31] Chapter 4 [32] [33] Chapter 5 [34] Chapter 6 [35] [36] [37] [38] [39] [40] Underfull \hbox (badness 10000) in paragraph at lines 3136--3142 []@textrm The @texttt glyphs[] @textrm com-po-nent re-ports whether ren-der-in g glyphs (e.g., via [41] [42] [43] [44] [45] [46] [47] [48] Chapter 7 [49] Underfull \hbox (badness 10000) in paragraph at lines 3790--3799 @textrm it uses @texttt /Library/Frameworks/R.framework/R[]@textrm . This is a sym-bolic link, Underfull \hbox (badness 10000) in paragraph at lines 3790--3799 @texttt /Library/Frameworks/R.framework/Versions/Current/Resources/lib/libR.dyl ib[]@textrm , [50] Overfull \hbox (16.81319pt too wide) in paragraph at lines 3841--3845 []@textrm The de-fault path for a per-sonal li-brary di-rec-tory is set as @te xttt ~/Library/R/arch/x.y/library[]@textrm . Chapter 8 [51] [52] [53] [54] [55] Underfull \hbox (badness 10000) in paragraph at lines 4179--4187 []@textrm A string with comma-separated @textttsl name@texttt =@textttsl value [] @textrm pairs (with @textsl value[] @textrm a Underfull \hbox (badness 10000) in paragraph at lines 4179--4187 @textrm log-i-cal con-stant) giv-ing ad-di-tional ar-gu-ments for the [][]@tex tbf codetools Underfull \hbox (badness 10000) in paragraph at lines 4179--4187 @textrm (@texttt https:// CRAN. R-project. org/ package=codetools[]@textrm )[] func-tions used Underfull \hbox (badness 10000) in paragraph at lines 4179--4187 @textrm to us-ing @texttt skipWith = TRUE[]@textrm , @texttt suppressPartialMa tchArgs = FALSE[] @textrm and [56] [57] [58] [59] [60] [61] Underfull \hbox (badness 10000) in paragraph at lines 4551--4556 @texttt blog. r-project. org/ 2022/ 04/ 08/ enhancements-to-html-documen tation/ [62] [63] [64] [65] Chapter 9 [66] [67] Chapter 10 [68] Chapter 11 [69] Chapter 12 [70] [71] (Function and variable index) [72] [73] (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-ints.vrs [74] [75]) (Concept index) [76] (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-ints.cps) [77] ) (see the transcript file for additional information) Output written on R-ints.pdf (82 pages, 469326 bytes). Transcript written on R-ints.log. TEXINPUTS=".:$TEXINPUTS" LC_COLLATE=C /usr/local/bin/texi2dvi --texinfo="@set UseExternalXrefs " --pdf R-lang.texi @setfilename R-lang.info This is pdfTeX, Version 3.141592653-2.6-1.40.26 (Web2C 2024) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-lang.t2d/pdf/xtr/R-lang.te xi (/usr/local/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2024-02-10.22]: pdf, fonts, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, microtype, and turning on texinfo input format.) Writing index file R-lang.vr (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-defs.texi (/usr/local/share/texmf-dist/tex/texinfo/txi-en.tex)) (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/version.texi) [1{/usr/local/ share/texmf-dist/fonts/map/pdftex/updmap/pdftex.map}] [2] [-1] Chapter 1 Writing index file R-lang.cp Chapter 2 [1] [2] Cross reference values unknown; you must run TeX again. Overfull \hbox (8.41086pt too wide) in paragraph at lines 305--306 @textbf storage.mode| [3] [4] [5] [6] [7] [8] Chapter 3 [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] Chapter 4 [24] [25] [26] [27] Chapter 5 [28] [29] [30] [31] [32] [33] [34] Chapter 6 [35] [36] [37] [38] [39] [40] [41] [42] [43] Chapter 7 [44] [45] Chapter 8 [46] [47] Chapter 9 [48] [49] [50] Chapter 10 [51] [52] [53] [54] [55] [56] [57] [58] (Function and Variable Index) [59] No file R-lang.vrs. (Concept Index) [60] No file R-lang.cps. Appendix A [61] [62] ) (see the transcript file for additional information) Output written on R-lang.pdf (65 pages, 348667 bytes). Transcript written on R-lang.log. This is pdfTeX, Version 3.141592653-2.6-1.40.26 (Web2C 2024) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-lang.t2d/pdf/xtr/R-lang.te xi (/usr/local/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2024-02-10.22]: pdf, fonts, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, microtype, and turning on texinfo input format.) Writing index file R-lang.vr (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-defs.texi (/usr/local/share/texmf-dist/tex/texinfo/txi-en.tex)) (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/version.texi) [1{/usr/local/ share/texmf-dist/fonts/map/pdftex/updmap/pdftex.map}] [2] (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-lang.toc) (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-lang.toc [-1] [-2]) [-3] [-4] (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-lang.toc) (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-lang.toc) Chapter 1 (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-lang.aux) Writing index file R-lang.cp Chapter 2 [1] [2] Overfull \hbox (8.41086pt too wide) in paragraph at lines 305--306 @textbf storage.mode| [3] [4] [5] [6] [7] [8] Chapter 3 [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] Chapter 4 [24] [25] [26] [27] Chapter 5 [28] [29] [30] [31] [32] [33] [34] Chapter 6 [35] [36] [37] [38] [39] [40] [41] [42] [43] Chapter 7 [44] [45] Chapter 8 [46] [47] Chapter 9 [48] [49] [50] Chapter 10 [51] [52] [53] [54] [55] [56] [57] [58] (Function and Variable Index) [59] (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-lang.vrs [60]) (Concept Index) [61] (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-lang.cps) [62] Appendix A [63] [64] ) (see the transcript file for additional information) Output written on R-lang.pdf (70 pages, 391298 bytes). Transcript written on R-lang.log. This is pdfTeX, Version 3.141592653-2.6-1.40.26 (Web2C 2024) (preloaded format=pdfetex) restricted \write18 enabled. entering extended mode (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-lang.t2d/pdf/xtr/R-lang.te xi (/usr/local/share/texmf-dist/tex/texinfo/texinfo.tex Loading texinfo [version 2024-02-10.22]: pdf, fonts, glyphs, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, microtype, and turning on texinfo input format.) Writing index file R-lang.vr (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-defs.texi (/usr/local/share/texmf-dist/tex/texinfo/txi-en.tex)) (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/version.texi) [1{/usr/local/ share/texmf-dist/fonts/map/pdftex/updmap/pdftex.map}] [2] (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-lang.toc) (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-lang.toc [-1] [-2]) [-3] [-4] (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-lang.toc) (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-lang.toc) Chapter 1 (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-lang.aux) Writing index file R-lang.cp Chapter 2 [1] [2] Overfull \hbox (8.41086pt too wide) in paragraph at lines 305--306 @textbf storage.mode| [3] [4] [5] [6] [7] [8] Chapter 3 [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] Chapter 4 [24] [25] [26] [27] Chapter 5 [28] [29] [30] [31] [32] [33] [34] Chapter 6 [35] [36] [37] [38] [39] [40] [41] [42] [43] Chapter 7 [44] [45] Chapter 8 [46] [47] Chapter 9 [48] [49] [50] Chapter 10 [51] [52] [53] [54] [55] [56] [57] [58] (Function and Variable Index) [59] (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-lang.vrs [60]) (Concept Index) [61] (/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual/R-lang.cps) [62] Appendix A [63] [64] ) (see the transcript file for additional information) Output written on R-lang.pdf (70 pages, 391294 bytes). Transcript written on R-lang.log. installing R manuals in PDF format ... gmake[1]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.4.3/doc/manual' ====> Compressing man pages (compress-man) ===> Installing ldconfig configuration file =========================================================================== =================================================== ===== env: 'PKG_NOTES=build_timestamp ports_top_git_hash ports_top_checkout_unclean port_git_hash port_checkout_unclean built_by' 'PKG_NOTE_build_timestamp=2025-03-02T23:26:47+00:00' 'PKG_NOTE_ports_top_git_hash=0a0e18a32b6a' 'PKG_NOTE_ports_top_checkout_unclean=no' 'PKG_NOTE_port_git_hash=df81348d70a6' 'PKG_NOTE_port_checkout_unclean=no' 'PKG_NOTE_built_by=poudriere-git-3.4.99.20250209' PKG_NO_VERSION_FOR_DEPS=1 NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building packages for R-4.4.3 ===> Building R-4.4.3 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for R-4.4.3 build of math/R | R-4.4.3 ended at 2025-03-02T17:41:27-06:00 build time: 00:14:40