Date: Tue, 27 Apr 2021 03:58:26 GMT From: pkg-fallout@FreeBSD.org To: pkg-fallout@FreeBSD.org Subject: [package - 122powerpc64-quarterly][math/R] Failed for R-4.0.4_1 in build Message-ID: <202104270358.13R3wQlg093380@pylon.nyi.freebsd.org>
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You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: jrm@FreeBSD.org Log URL: http://pylon.nyi.freebsd.org/data/122powerpc64-quarterly/a6d30d977779/logs/R-4.0.4_1.log Build URL: http://pylon.nyi.freebsd.org/build.html?mastername=122powerpc64-quarterly&build=a6d30d977779 Log: =>> Building math/R build started at Tue Apr 27 03:16:06 UTC 2021 port directory: /usr/ports/math/R package name: R-4.0.4_1 building for: FreeBSD 122powerpc64-quarterly-job-05 12.2-RELEASE FreeBSD 12.2-RELEASE powerpc maintained by: jrm@FreeBSD.org Makefile ident: Poudriere version: 3.2.8-8-gaf08dbda Host OSVERSION: 1400003 Jail OSVERSION: 1202000 Job Id: 05 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1202000 UNAME_v=FreeBSD 12.2-RELEASE UNAME_r=12.2-RELEASE BLOCKSIZE=K MAIL=/var/mail/root STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin LOCALBASE=/usr/local USER=root LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.2.8-8-gaf08dbda MASTERMNT=/usr/local/poudriere/data/.m/122powerpc64-quarterly/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/122powerpc64-quarterly/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=122powerpc64-quarterly SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/122powerpc64-quarterly/ref/.p SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= DEPENDS_ARGS= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ===> The following configuration options are available for R-4.0.4_1: ICU=on: Unicode support via ICU INFO=on: Build and/or install GNU info pages LDOUBLE=on: Long double data type LETTER=off: 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=off: 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-- --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-tcltk --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 ac_cv_path_KPSEWHICH="" ac_cv_path_MAKEINDEX="" ac_cv_path_PDFLATEX="" ac_cv_path_PDFTEX="" ac_cv_path_TEX="" ac_cv_path_TEXI2DVI="" MAKE=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 F77="gfortran10" FC="gfortran10" FFLAGS="-O -Wl,-rpath=/usr/local/lib/gcc10" FCFLAGS="-Wl,-rpath=/usr/local/lib/gcc10" XDG_DATA_HOME=/wrkdirs/usr/ports/math/R/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/math/R/work 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 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="/u sr/local/bin/readelf" SIZE="/usr/local/bin/size" STRINGS="/usr/local/bin/strings" CMAKE_PREFIX_PATH="/usr/local" LANG=en_US.UTF-8 LC_ALL=en_US.UTF-8 CONFIG_SITE=/usr/ports/Templates/config.site lt_cv_sys_max_cmd_len=524288 --End CONFIGURE_ENV-- --MAKE_ENV-- PERL_USE_UNSAFE_INC=1 F77="gfortran10" FC="gfortran10" FFLAGS="-O -Wl,-rpath=/usr/local/lib/gcc10" FCFLAGS="-Wl,-rpath=/usr/local/lib/gcc10" XDG_DATA_HOME=/wrkdirs/usr/ports/math/R/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/math/R/work 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 NO_PIE=yes 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" LANG=en_US.UTF-8 LC_ALL=en_US.UTF-8 PREFIX=/usr/local LOCALBASE=/usr/local CC="gcc10" CFLAGS="-O2 -pipe -DLIBICONV_PLUG -fstack-protector-str ong -Wl,-rpath=/usr/local/lib/gcc10 -isystem /usr/local/include -fno-strict-aliasing " CPP="cpp10" CPPFLAGS="-DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include" LDFLAGS=" -L/usr/local/lib -Wl,-rpath=/usr/local/lib/gcc10 -L/usr/local/lib/gcc10 -B/usr/local/bin -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10 -L/usr/local/lib/gcc10 " LIBS="-L/usr/local/lib" CXX="g++10" CXXFLAGS="-O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10 -DLIBICONV_PLUG -Wl,-rpath=/usr/local/lib/gcc10 -isystem /usr/local/include " MANPREFIX="/usr/local" 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=4.0.4 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="@comment " NO_LETTER="" 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="@comment " NO_TEXDOCS="" TIFF="" NO_TIFF="@comment " X11="" NO_X11="@comment " GTK2_VERSION="2.10.0" GTK3_VERSION="3.0.0" OSREL=12.2 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PERL_VERSION=5.32.1 PERL_VER=5.32 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/5.32 DOCSDIR="share/doc/R" EXAMPLESDIR="s hare/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="@comment " NO_LETTER="" 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="@comment " NO_TEXDOCS="" 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 PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### /usr/local/etc/poudriere.d/make.conf #### # XXX: We really need this but cannot use it while 'make checksum' does not # try the next mirror on checksum failure. It currently retries the same # failed mirror and then fails rather then trying another. It *does* # try the next if the size is mismatched though. #MASTER_SITE_FREEBSD=yes # Build ALLOW_MAKE_JOBS_PACKAGES with 2 jobs MAKE_JOBS_NUMBER=2 #### /usr/ports/Mk/Scripts/ports_env.sh #### _CCVERSION_921dbbb2=cc (GCC) 4.2.1 20070831 patched [FreeBSD] Copyright (C) 2007 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. _ALTCCVERSION_921dbbb2=none _CXXINTERNAL_acaad9ca=Using built-in specs. Target: powerpc64-undermydesk-freebsd Configured with: FreeBSD/powerpc64 system compiler Thread model: posix gcc version 4.2.1 20070831 patched [FreeBSD] "/usr/bin/ld" "--eh-frame-hdr" "-Qy" "-melf64ppc_fbsd" "--enable-new-dtags" "-dynamic-linker" "/libexec/ld-elf.so.1" "/usr/lib/crt1.o" "/usr/lib/crti.o" "/usr/lib/crtbegin.o" "-L/usr/lib" "-L/usr/lib" "/dev/null" "-lstdc++" "-lm" "-lgcc_s" "-lgcc" "-lc" "-lgcc_s" "-lgcc" "/usr/lib/crtsavres.o" "/usr/lib/crtend.o" "/usr/lib/crtn.o" CC_OUTPUT_921dbbb2_58173849=yes CC_OUTPUT_921dbbb2_9bdba57c=yes CC_OUTPUT_921dbbb2_6a4fe7f5=cc1: error: unrecognized command line option "-std=c11" CC_OUTPUT_921dbbb2_6bcac02b=yes CC_OUTPUT_921dbbb2_67d20829=yes CC_OUTPUT_921dbbb2_bfa62e83=cc1: error: unrecognized command line option "-std=gnu11" CC_OUTPUT_921dbbb2_f0b4d593=yes CC_OUTPUT_921dbbb2_308abb44=cc1plus: error: unrecognized command line option "-std=c++0x" CC_OUTPUT_921dbbb2_f00456e5=cc1plus: error: unrecognized command line option "-std=c++11" CC_OUTPUT_921dbbb2_65ad290d=cc1plus: error: unrecognized command line option "-std=c++14" CC_OUTPUT_921dbbb2_f2776b26=cc1plus: error: unrecognized command line option "-std=c++17" CC_OUTPUT_921dbbb2_b2657cc3=yes CC_OUTPUT_921dbbb2_380987f7=cc1plus: error: unrecognized command line option "-std=gnu++11" CC_OUTPUT_921dbbb2_160933ec=cc1plus: error: unrecognized command line option "-std=gnu++14" CC_OUTPUT_921dbbb2_fb62803b=cc1plus: error: unrecognized command line option "-std=gnu++17" _OBJC_CCVERSION_921dbbb2=cc (GCC) 4.2.1 20070831 patched [FreeBSD] Copyright (C) 2007 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. _OBJC_ALTCCVERSION_921dbbb2=none ARCH=powerpc64 PPC_ABI=ELFv1 OPSYS=FreeBSD _OSRELEASE=12.2-RELEASE OSREL=12.2 OSVERSION=1202000 PYTHONBASE=/usr/local CONFIGURE_MAX_CMD_LEN=524288 HAVE_PORTS_ENV=1 #### Misc Poudriere #### 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) 89999 open files (-n) 1024 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 --End resource limits-- =======================<phase: check-sanity >============================ ===> License GPLv2 accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===> R-4.0.4_1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.16.3.txz [122powerpc64-quarterly-job-05] Installing pkg-1.16.3... [122powerpc64-quarterly-job-05] Extracting pkg-1.16.3: .......... done ===> R-4.0.4_1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of R-4.0.4_1 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by R-4.0.4_1 for building =========================================================================== =======================<phase: checksum >============================ ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by R-4.0.4_1 for building => SHA256 Checksum OK for R-4.0.4.tar.gz. =========================================================================== =======================<phase: extract-depends>============================ =========================================================================== =======================<phase: extract >============================ ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by R-4.0.4_1 for building ===> Extracting for R-4.0.4_1 => SHA256 Checksum OK for R-4.0.4.tar.gz. =========================================================================== =======================<phase: patch-depends >============================ =========================================================================== =======================<phase: patch >============================ <snip> /usr/local/bin/ar -rucs ../SuiteSparse_config.a SuiteSparse_config.o /usr/local/bin/ar: `u' modifier ignored since `D' is the default (see `U') gmake[5]: Leaving directory '/tmp/RtmpT3k263/R.INSTALL177f53ee9786f/Matrix/src/SuiteSparse_config' gcc10 -shared -L/wrkdirs/usr/ports/math/R/work/R-4.0.4/lib -L/usr/local/lib -Wl,-rpath=/usr/local/lib/gcc10 -L/usr/local/lib/gcc10 -B/usr/local/bin -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10 -L/usr/local/lib/gcc10 -o Matrix.so CHMfactor.o Csparse.o TMatrix_as.o Tsparse.o init.o Mutils.o chm_common.o cs.o cs_utils.o dense.o dgCMatrix.o dgTMatrix.o dgeMatrix.o dpoMatrix.o dppMatrix.o dsCMatrix.o dsyMatrix.o dspMatrix.o dtCMatrix.o dtTMatrix.o dtrMatrix.o dtpMatrix.o factorizations.o ldense.o lgCMatrix.o sparseQR.o abIndex.o CHOLMOD.a COLAMD.a AMD.a SuiteSparse_config.a -L/wrkdirs/usr/ports/math/R/work/R-4.0.4/lib -lRlapack -L/wrkdirs/usr/ports/math/R/work/R-4.0.4/lib -lRblas -lgfortran -lm -lssp_nonshared -L/wrkdirs/usr/ports/math/R/work/R-4.0.4/lib -lR gmake[4]: Leaving directory '/tmp/RtmpT3k263/R.INSTALL177f53ee9786f/Matrix/src' installing to /wrkdirs/usr/ports/math/R/work/R-4.0.4/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 ‘drop’ from package ‘base’ in package ‘Matrix’ Creating a generic function for ‘cov2cor’ from package ‘stats’ 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’ in method for ‘coerce’ with signature ‘"matrix.csr","dgRMatrix"’: no definition for class “matrix.csr” in method for ‘coerce’ with signature ‘"dgRMatrix","matrix.csr"’: no definition for class “matrix.csr” in method for ‘coerce’ with signature ‘"matrix.csc","dgCMatrix"’: no definition for class “matrix.csc” in method for ‘coerce’ with signature ‘"dgCMatrix","matrix.csc"’: no definition for class “matrix.csc” in method for ‘coerce’ with signature ‘"matrix.coo","dgTMatrix"’: no definition for class “matrix.coo” in method for ‘coerce’ with signature ‘"dgTMatrix","matrix.coo"’: no definition for class “matrix.coo” in method for ‘coerce’ with signature ‘"dsparseMatrix","matrix.csr"’: no definition for class “matrix.csr” 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.csr","RsparseMatrix"’: no definition for class “matrix.csr” in method for ‘coerce’ with signature ‘"matrix.csc","CsparseMatrix"’: no definition for class “matrix.csc” in method for ‘coerce’ with signature ‘"matrix.coo","TsparseMatrix"’: no definition for class “matrix.coo” in method for ‘coerce’ with signature ‘"matrix.csr","CsparseMatrix"’: 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.csc","TsparseMatrix"’: no definition for class “matrix.csc” in method for ‘coerce’ with signature ‘"matrix.csr","TsparseMatrix"’: no definition for class “matrix.csr” in method for ‘coerce’ with signature ‘"CsparseMatrix","matrix.csr"’: no definition for class “matrix.csr” in method for ‘coerce’ with signature ‘"CsparseMatrix","matrix.coo"’: no definition for class “matrix.coo” in method for ‘coerce’ with signature ‘"CsparseMatrix","matrix.csc"’: 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 ‘"matrix.csc","Matrix"’: no definition for class “matrix.csc” 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’ in method for ‘colSums’ with signature ‘x="igCMatrix"’: no definition for class “igCMatrix” in method for ‘rowSums’ with signature ‘x="igCMatrix"’: no definition for class “igCMatrix” in method for ‘colMeans’ with signature ‘x="igCMatrix"’: no definition for class “igCMatrix” in method for ‘rowMeans’ with signature ‘x="igCMatrix"’: no definition for class “igCMatrix” Creating a generic function for ‘zapsmall’ from package ‘base’ in package ‘Matrix’ Creating a generic function for ‘diag<-’ from package ‘base’ in package ‘Matrix’ Creating a generic function for ‘crossprod’ from package ‘base’ in package ‘Matrix’ Creating a generic function for ‘tcrossprod’ from package ‘base’ in package ‘Matrix’ Creating a generic function for ‘which’ from package ‘base’ in package ‘Matrix’ in method for ‘coerce’ with signature ‘"graphAM","sparseMatrix"’: no definition for class “graphAM” in method for ‘coerce’ with signature ‘"graph","CsparseMatrix"’: no definition for class “graph” in method for ‘coerce’ with signature ‘"graph","Matrix"’: no definition for class “graph” in method for ‘coerce’ with signature ‘"graphNEL","CsparseMatrix"’: no definition for class “graphNEL” in method for ‘coerce’ with signature ‘"graphNEL","TsparseMatrix"’: no definition for class “graphNEL” in method for ‘coerce’ with signature ‘"sparseMatrix","graph"’: no definition for class “graph” in method for ‘coerce’ with signature ‘"sparseMatrix","graphNEL"’: no definition for class “graphNEL” in method for ‘coerce’ with signature ‘"TsparseMatrix","graphNEL"’: no definition for class “graphNEL” Creating a generic function for ‘qr.R’ from package ‘base’ in package ‘Matrix’ Creating a generic function for ‘qr.Q’ from package ‘base’ in package ‘Matrix’ Creating a generic function for ‘qr.qy’ 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.coef’ 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.fitted’ from package ‘base’ in package ‘Matrix’ Creating a generic function for ‘toeplitz’ from package ‘stats’ 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 gmake[4]: Entering directory '/tmp/RtmpSKJVP0/R.INSTALL111e9118f91b0/survival/src' gcc10 -I"/wrkdirs/usr/ports/math/R/work/R-4.0.4/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fPIC -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10 -isystem /usr/local/include -fno-strict-aliasing -c agexact.c -o agexact.o gcc10 -I"/wrkdirs/usr/ports/math/R/work/R-4.0.4/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fPIC -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10 -isystem /usr/local/include -fno-strict-aliasing -c agfit4.c -o agfit4.o gcc10 -I"/wrkdirs/usr/ports/math/R/work/R-4.0.4/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fPIC -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10 -isystem /usr/local/include -fno-strict-aliasing -c agfit5.c -o agfit5.o gcc10 -I"/wrkdirs/usr/ports/math/R/work/R-4.0.4/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fPIC -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10 -isystem /usr/local/include -fno-strict-aliasing -c agmart.c -o agmart.o gcc10 -I"/wrkdirs/usr/ports/math/R/work/R-4.0.4/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fPIC -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10 -isystem /usr/local/include -fno-strict-aliasing -c agmart3.c -o agmart3.o gcc10 -I"/wrkdirs/usr/ports/math/R/work/R-4.0.4/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fPIC -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10 -isystem /usr/local/include -fno-strict-aliasing -c agscore2.c -o agscore2.o gcc10 -I"/wrkdirs/usr/ports/math/R/work/R-4.0.4/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fPIC -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10 -isystem /usr/local/include -fno-strict-aliasing -c agsurv3.c -o agsurv3.o gcc10 -I"/wrkdirs/usr/ports/math/R/work/R-4.0.4/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fPIC -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10 -isystem /usr/local/include -fno-strict-aliasing -c agsurv4.c -o agsurv4.o gcc10 -I"/wrkdirs/usr/ports/math/R/work/R-4.0.4/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fPIC -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10 -isystem /usr/local/include -fno-strict-aliasing -c agsurv5.c -o agsurv5.o gcc10 -I"/wrkdirs/usr/ports/math/R/work/R-4.0.4/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fPIC -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10 -isystem /usr/local/include -fno-strict-aliasing -c cdecomp.c -o cdecomp.o gcc10 -I"/wrkdirs/usr/ports/math/R/work/R-4.0.4/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fPIC -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10 -isystem /usr/local/include -fno-strict-aliasing -c chinv2.c -o chinv2.o gcc10 -I"/wrkdirs/usr/ports/math/R/work/R-4.0.4/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fPIC -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10 -isystem /usr/local/include -fno-strict-aliasing -c chinv3.c -o chinv3.o gcc10 -I"/wrkdirs/usr/ports/math/R/work/R-4.0.4/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fPIC -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10 -isystem /usr/local/include -fno-strict-aliasing -c cholesky2.c -o cholesky2.o gcc10 -I"/wrkdirs/usr/ports/math/R/work/R-4.0.4/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fPIC -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10 -isystem /usr/local/include -fno-strict-aliasing -c cholesky3.c -o cholesky3.o gcc10 -I"/wrkdirs/usr/ports/math/R/work/R-4.0.4/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fPIC -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10 -isystem /usr/local/include -fno-strict-aliasing -c cholesky5.c -o cholesky5.o gcc10 -I"/wrkdirs/usr/ports/math/R/work/R-4.0.4/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fPIC -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10 -isystem /usr/local/include -fno-strict-aliasing -c chsolve2.c -o chsolve2.o gcc10 -I"/wrkdirs/usr/ports/math/R/work/R-4.0.4/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fPIC -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10 -isystem /usr/local/include -fno-strict-aliasing -c chsolve3.c -o chsolve3.o gcc10 -I"/wrkdirs/usr/ports/math/R/work/R-4.0.4/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fPIC -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10 -isystem /usr/local/include -fno-strict-aliasing -c chsolve5.c -o chsolve5.o gcc10 -I"/wrkdirs/usr/ports/math/R/work/R-4.0.4/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fPIC -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10 -isystem /usr/local/include -fno-strict-aliasing -c collapse.c -o collapse.o gcc10 -I"/wrkdirs/usr/ports/math/R/work/R-4.0.4/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fPIC -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10 -isystem /usr/local/include -fno-strict-aliasing -c concordance1.c -o concordance1.o gcc10 -I"/wrkdirs/usr/ports/math/R/work/R-4.0.4/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fPIC -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10 -isystem /usr/local/include -fno-strict-aliasing -c concordance3.c -o concordance3.o gcc10 -I"/wrkdirs/usr/ports/math/R/work/R-4.0.4/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fPIC -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10 -isystem /usr/local/include -fno-strict-aliasing -c cox_Rcallback.c -o cox_Rcallback.o gcc10 -I"/wrkdirs/usr/ports/math/R/work/R-4.0.4/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fPIC -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10 -isystem /usr/local/include -fno-strict-aliasing -c coxcount1.c -o coxcount1.o gcc10 -I"/wrkdirs/usr/ports/math/R/work/R-4.0.4/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fPIC -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10 -isystem /usr/local/include -fno-strict-aliasing -c coxdetail.c -o coxdetail.o gcc10 -I"/wrkdirs/usr/ports/math/R/work/R-4.0.4/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fPIC -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10 -isystem /usr/local/include -fno-strict-aliasing -c coxexact.c -o coxexact.o gcc10 -I"/wrkdirs/usr/ports/math/R/work/R-4.0.4/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fPIC -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10 -isystem /usr/local/include -fno-strict-aliasing -c coxfit5.c -o coxfit5.o gcc10 -I"/wrkdirs/usr/ports/math/R/work/R-4.0.4/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fPIC -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10 -isystem /usr/local/include -fno-strict-aliasing -c coxfit6.c -o coxfit6.o gcc10 -I"/wrkdirs/usr/ports/math/R/work/R-4.0.4/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fPIC -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10 -isystem /usr/local/include -fno-strict-aliasing -c coxmart.c -o coxmart.o gcc10 -I"/wrkdirs/usr/ports/math/R/work/R-4.0.4/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fPIC -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10 -isystem /usr/local/include -fno-strict-aliasing -c coxmart2.c -o coxmart2.o gcc10 -I"/wrkdirs/usr/ports/math/R/work/R-4.0.4/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fPIC -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10 -isystem /usr/local/include -fno-strict-aliasing -c coxph_wtest.c -o coxph_wtest.o gcc10 -I"/wrkdirs/usr/ports/math/R/work/R-4.0.4/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fPIC -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10 -isystem /usr/local/include -fno-strict-aliasing -c coxsafe.c -o coxsafe.o gcc10 -I"/wrkdirs/usr/ports/math/R/work/R-4.0.4/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fPIC -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10 -isystem /usr/local/include -fno-strict-aliasing -c coxscho.c -o coxscho.o gcc10 -I"/wrkdirs/usr/ports/math/R/work/R-4.0.4/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fPIC -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10 -isystem /usr/local/include -fno-strict-aliasing -c coxscore2.c -o coxscore2.o gcc10 -I"/wrkdirs/usr/ports/math/R/work/R-4.0.4/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fPIC -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10 -isystem /usr/local/include -fno-strict-aliasing -c coxsurv1.c -o coxsurv1.o gcc10 -I"/wrkdirs/usr/ports/math/R/work/R-4.0.4/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fPIC -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10 -isystem /usr/local/include -fno-strict-aliasing -c coxsurv2.c -o coxsurv2.o gcc10 -I"/wrkdirs/usr/ports/math/R/work/R-4.0.4/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fPIC -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10 -isystem /usr/local/include -fno-strict-aliasing -c dmatrix.c -o dmatrix.o gcc10 -I"/wrkdirs/usr/ports/math/R/work/R-4.0.4/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fPIC -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10 -isystem /usr/local/include -fno-strict-aliasing -c doloop.c -o doloop.o gcc10 -I"/wrkdirs/usr/ports/math/R/work/R-4.0.4/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fPIC -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10 -isystem /usr/local/include -fno-strict-aliasing -c finegray.c -o finegray.o gcc10 -I"/wrkdirs/usr/ports/math/R/work/R-4.0.4/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fPIC -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10 -isystem /usr/local/include -fno-strict-aliasing -c gchol.c -o gchol.o gcc10 -I"/wrkdirs/usr/ports/math/R/work/R-4.0.4/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fPIC -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10 -isystem /usr/local/include -fno-strict-aliasing -c init.c -o init.o gcc10 -I"/wrkdirs/usr/ports/math/R/work/R-4.0.4/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fPIC -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10 -isystem /usr/local/include -fno-strict-aliasing -c multicheck.c -o multicheck.o gcc10 -I"/wrkdirs/usr/ports/math/R/work/R-4.0.4/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fPIC -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10 -isystem /usr/local/include -fno-strict-aliasing -c norisk.c -o norisk.o gcc10 -I"/wrkdirs/usr/ports/math/R/work/R-4.0.4/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fPIC -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10 -isystem /usr/local/include -fno-strict-aliasing -c pyears1.c -o pyears1.o gcc10 -I"/wrkdirs/usr/ports/math/R/work/R-4.0.4/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fPIC -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10 -isystem /usr/local/include -fno-strict-aliasing -c pyears2.c -o pyears2.o gcc10 -I"/wrkdirs/usr/ports/math/R/work/R-4.0.4/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fPIC -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10 -isystem /usr/local/include -fno-strict-aliasing -c pyears3b.c -o pyears3b.o gcc10 -I"/wrkdirs/usr/ports/math/R/work/R-4.0.4/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fPIC -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10 -isystem /usr/local/include -fno-strict-aliasing -c pystep.c -o pystep.o gcc10 -I"/wrkdirs/usr/ports/math/R/work/R-4.0.4/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fPIC -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10 -isystem /usr/local/include -fno-strict-aliasing -c survConcordance.c -o survConcordance.o gcc10 -I"/wrkdirs/usr/ports/math/R/work/R-4.0.4/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fPIC -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10 -isystem /usr/local/include -fno-strict-aliasing -c survdiff2.c -o survdiff2.o gcc10 -I"/wrkdirs/usr/ports/math/R/work/R-4.0.4/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fPIC -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10 -isystem /usr/local/include -fno-strict-aliasing -c survfit4.c -o survfit4.o gcc10 -I"/wrkdirs/usr/ports/math/R/work/R-4.0.4/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fPIC -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10 -isystem /usr/local/include -fno-strict-aliasing -c survfitci.c -o survfitci.o gcc10 -I"/wrkdirs/usr/ports/math/R/work/R-4.0.4/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fPIC -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10 -isystem /usr/local/include -fno-strict-aliasing -c survfitkm.c -o survfitkm.o gcc10 -I"/wrkdirs/usr/ports/math/R/work/R-4.0.4/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fPIC -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10 -isystem /usr/local/include -fno-strict-aliasing -c survfitresid.c -o survfitresid.o gcc10 -I"/wrkdirs/usr/ports/math/R/work/R-4.0.4/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fPIC -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10 -isystem /usr/local/include -fno-strict-aliasing -c survpenal.c -o survpenal.o gcc10 -I"/wrkdirs/usr/ports/math/R/work/R-4.0.4/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fPIC -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10 -isystem /usr/local/include -fno-strict-aliasing -c survreg6.c -o survreg6.o gcc10 -I"/wrkdirs/usr/ports/math/R/work/R-4.0.4/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fPIC -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10 -isystem /usr/local/include -fno-strict-aliasing -c survreg7.c -o survreg7.o gcc10 -I"/wrkdirs/usr/ports/math/R/work/R-4.0.4/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fPIC -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10 -isystem /usr/local/include -fno-strict-aliasing -c survregc1.c -o survregc1.o gcc10 -I"/wrkdirs/usr/ports/math/R/work/R-4.0.4/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fPIC -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10 -isystem /usr/local/include -fno-strict-aliasing -c survregc2.c -o survregc2.o gcc10 -I"/wrkdirs/usr/ports/math/R/work/R-4.0.4/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fPIC -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10 -isystem /usr/local/include -fno-strict-aliasing -c survsplit.c -o survsplit.o gcc10 -I"/wrkdirs/usr/ports/math/R/work/R-4.0.4/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fPIC -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10 -isystem /usr/local/include -fno-strict-aliasing -c tmerge.c -o tmerge.o gcc10 -I"/wrkdirs/usr/ports/math/R/work/R-4.0.4/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fPIC -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10 -isystem /usr/local/include -fno-strict-aliasing -c zph1.c -o zph1.o gcc10 -I"/wrkdirs/usr/ports/math/R/work/R-4.0.4/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fPIC -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10 -isystem /usr/local/include -fno-strict-aliasing -c zph2.c -o zph2.o gcc10 -shared -L/wrkdirs/usr/ports/math/R/work/R-4.0.4/lib -L/usr/local/lib -Wl,-rpath=/usr/local/lib/gcc10 -L/usr/local/lib/gcc10 -B/usr/local/bin -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10 -L/usr/local/lib/gcc10 -o survival.so agexact.o agfit4.o agfit5.o agmart.o agmart3.o agscore2.o agsurv3.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 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 dmatrix.o doloop.o finegray.o gchol.o init.o multicheck.o norisk.o pyears1.o pyears2.o pyears3b.o pystep.o survConcordance.o survdiff2.o survfit4.o survfitci.o survfitkm.o survfitresid.o survpenal.o survreg6.o survreg7.o survregc1.o survregc2.o survsplit.o tmerge.o zph1.o zph2.o -L/wrkdirs/usr/ports/math/R/work/R-4.0.4/lib -lR gmake[4]: Leaving directory '/tmp/RtmpSKJVP0/R.INSTALL111e9118f91b0/survival/src' installing to /wrkdirs/usr/ports/math/R/work/R-4.0.4/library/survival/libs ** R ** data *** moving datasets to lazyload DB Killed gmake[3]: *** [Makefile:53: survival.ts] Error 1 gmake[3]: *** Waiting for unfinished jobs.... * installing *source* package ‘mgcv’ ... ** package ‘mgcv’ successfully unpacked and MD5 sums checked ** using non-staged installation ** libs gmake[4]: Entering directory '/tmp/RtmpzZc2u1/R.INSTALL111eb4e65d241/mgcv/src' gcc10 -I"/wrkdirs/usr/ports/math/R/work/R-4.0.4/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fPIC -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10 -isystem /usr/local/include -fno-strict-aliasing -c coxph.c -o coxph.o gcc10 -I"/wrkdirs/usr/ports/math/R/work/R-4.0.4/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fPIC -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10 -isystem /usr/local/include -fno-strict-aliasing -c davies.c -o davies.o gcc10 -I"/wrkdirs/usr/ports/math/R/work/R-4.0.4/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fPIC -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10 -isystem /usr/local/include -fno-strict-aliasing -c discrete.c -o discrete.o gcc10 -I"/wrkdirs/usr/ports/math/R/work/R-4.0.4/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fPIC -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10 -isystem /usr/local/include -fno-strict-aliasing -c gdi.c -o gdi.o gcc10 -I"/wrkdirs/usr/ports/math/R/work/R-4.0.4/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fPIC -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10 -isystem /usr/local/include -fno-strict-aliasing -c init.c -o init.o gcc10 -I"/wrkdirs/usr/ports/math/R/work/R-4.0.4/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fPIC -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10 -isystem /usr/local/include -fno-strict-aliasing -c magic.c -o magic.o gcc10 -I"/wrkdirs/usr/ports/math/R/work/R-4.0.4/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fPIC -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10 -isystem /usr/local/include -fno-strict-aliasing -c mat.c -o mat.o gcc10 -I"/wrkdirs/usr/ports/math/R/work/R-4.0.4/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fPIC -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10 -isystem /usr/local/include -fno-strict-aliasing -c matrix.c -o matrix.o gcc10 -I"/wrkdirs/usr/ports/math/R/work/R-4.0.4/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fPIC -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10 -isystem /usr/local/include -fno-strict-aliasing -c mgcv.c -o mgcv.o gcc10 -I"/wrkdirs/usr/ports/math/R/work/R-4.0.4/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fPIC -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10 -isystem /usr/local/include -fno-strict-aliasing -c misc.c -o misc.o gcc10 -I"/wrkdirs/usr/ports/math/R/work/R-4.0.4/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fPIC -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10 -isystem /usr/local/include -fno-strict-aliasing -c mvn.c -o mvn.o gcc10 -I"/wrkdirs/usr/ports/math/R/work/R-4.0.4/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fPIC -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10 -isystem /usr/local/include -fno-strict-aliasing -c qp.c -o qp.o gcc10 -I"/wrkdirs/usr/ports/math/R/work/R-4.0.4/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fPIC -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10 -isystem /usr/local/include -fno-strict-aliasing -c soap.c -o soap.o gcc10 -I"/wrkdirs/usr/ports/math/R/work/R-4.0.4/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fPIC -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10 -isystem /usr/local/include -fno-strict-aliasing -c sparse-smooth.c -o sparse-smooth.o gcc10 -I"/wrkdirs/usr/ports/math/R/work/R-4.0.4/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fPIC -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10 -isystem /usr/local/include -fno-strict-aliasing -c sparse.c -o sparse.o gcc10 -I"/wrkdirs/usr/ports/math/R/work/R-4.0.4/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fPIC -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10 -isystem /usr/local/include -fno-strict-aliasing -c tprs.c -o tprs.o gcc10 -shared -L/wrkdirs/usr/ports/math/R/work/R-4.0.4/lib -L/usr/local/lib -Wl,-rpath=/usr/local/lib/gcc10 -L/usr/local/lib/gcc10 -B/usr/local/bin -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10 -L/usr/local/lib/gcc10 -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 qp.o soap.o sparse-smooth.o sparse.o tprs.o -L/wrkdirs/usr/ports/math/R/work/R-4.0.4/lib -lRlapack -L/wrkdirs/usr/ports/math/R/work/R-4.0.4/lib -lRblas -lgfortran -lm -lssp_nonshared -fopenmp -L/wrkdirs/usr/ports/math/R/work/R-4.0.4/lib -lR gmake[4]: Leaving directory '/tmp/RtmpzZc2u1/R.INSTALL111eb4e65d241/mgcv/src' installing to /wrkdirs/usr/ports/math/R/work/R-4.0.4/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[3]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.0.4/src/library/Recommended' gmake[2]: *** [Makefile:39: recommended-packages] Error 2 gmake[2]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.0.4/src/library/Recommended' gmake[1]: *** [Makefile:77: stamp-recommended] Error 2 gmake[1]: Leaving directory '/wrkdirs/usr/ports/math/R/work/R-4.0.4' ===> Compilation failed unexpectedly. Try to set MAKE_JOBS_UNSAFE=yes and rebuild before reporting the failure to the maintainer. *** Error code 1 Stop. make: stopped in /usr/ports/math/R
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