[package - 122powerpc64-quarterly][math/R] Failed for R-4.0.4_1 in build
pkg-fallout at FreeBSD.org
pkg-fallout at FreeBSD.org
Tue Apr 27 03:58:27 UTC 2021
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 at 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 at 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 at 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 âchol2invâ from âbaseâ in package âMatrixâ
(from the saved implicit definition)
Creating a generic function for âchol2invâ from package âbaseâ in package âMatrixâ
Creating a generic function for âdiagâ from package âbaseâ in package âMatrixâ
Creating a generic function for âdropâ from package âbaseâ in package âMatrixâ
Creating a generic function for âcov2corâ from package âstatsâ in package âMatrixâ
Creating a generic function for âunnameâ from package âbaseâ in package âMatrixâ
Creating a generic function for ânormâ from package âbaseâ in package âMatrixâ
Creating a generic function for ârcondâ from âbaseâ in package âMatrixâ
(from the saved implicit definition)
Creating a generic function for ârcondâ from package âbaseâ in package âMatrixâ
in method for âcoerceâ with signature â"matrix.csr","dgRMatrix"â: no definition for class âmatrix.csrâ
in method for âcoerceâ with signature â"dgRMatrix","matrix.csr"â: no definition for class âmatrix.csrâ
in method for âcoerceâ with signature â"matrix.csc","dgCMatrix"â: no definition for class âmatrix.cscâ
in method for âcoerceâ with signature â"dgCMatrix","matrix.csc"â: no definition for class âmatrix.cscâ
in method for âcoerceâ with signature â"matrix.coo","dgTMatrix"â: no definition for class âmatrix.cooâ
in method for âcoerceâ with signature â"dgTMatrix","matrix.coo"â: no definition for class âmatrix.cooâ
in method for âcoerceâ with signature â"dsparseMatrix","matrix.csr"â: no definition for class âmatrix.csrâ
in method for âcoerceâ with signature â"matrix.csr","dgCMatrix"â: no definition for class âmatrix.csrâ
in method for âcoerceâ with signature â"matrix.coo","dgCMatrix"â: no definition for class âmatrix.cooâ
in method for âcoerceâ with signature â"matrix.csr","RsparseMatrix"â: no definition for class âmatrix.csrâ
in method for âcoerceâ with signature â"matrix.csc","CsparseMatrix"â: no definition for class âmatrix.cscâ
in method for âcoerceâ with signature â"matrix.coo","TsparseMatrix"â: no definition for class âmatrix.cooâ
in method for âcoerceâ with signature â"matrix.csr","CsparseMatrix"â: no definition for class âmatrix.csrâ
in method for âcoerceâ with signature â"matrix.coo","CsparseMatrix"â: no definition for class âmatrix.cooâ
in method for âcoerceâ with signature â"matrix.csc","TsparseMatrix"â: no definition for class âmatrix.cscâ
in method for âcoerceâ with signature â"matrix.csr","TsparseMatrix"â: no definition for class âmatrix.csrâ
in method for âcoerceâ with signature â"CsparseMatrix","matrix.csr"â: no definition for class âmatrix.csrâ
in method for âcoerceâ with signature â"CsparseMatrix","matrix.coo"â: no definition for class âmatrix.cooâ
in method for âcoerceâ with signature â"CsparseMatrix","matrix.csc"â: no definition for class âmatrix.cscâ
in method for âcoerceâ with signature â"matrix.csr","Matrix"â: no definition for class âmatrix.csrâ
in method for âcoerceâ with signature â"matrix.coo","Matrix"â: no definition for class âmatrix.cooâ
in method for âcoerceâ with signature â"matrix.csc","Matrix"â: no definition for class âmatrix.cscâ
Creating a generic function for âcolSumsâ from package âbaseâ in package âMatrixâ
Creating a generic function for âcolMeansâ from package âbaseâ in package âMatrixâ
Creating a generic function for ârowSumsâ from package âbaseâ in package âMatrixâ
Creating a generic function for ârowMeansâ from package âbaseâ in package âMatrixâ
in method for âcolSumsâ with signature âx="igCMatrix"â: no definition for class âigCMatrixâ
in method for ârowSumsâ with signature âx="igCMatrix"â: no definition for class âigCMatrixâ
in method for âcolMeansâ with signature âx="igCMatrix"â: no definition for class âigCMatrixâ
in method for ârowMeansâ with signature âx="igCMatrix"â: no definition for class âigCMatrixâ
Creating a generic function for âzapsmallâ from package âbaseâ in package âMatrixâ
Creating a generic function for âdiag<-â from package âbaseâ in package âMatrixâ
Creating a generic function for âcrossprodâ from package âbaseâ in package âMatrixâ
Creating a generic function for âtcrossprodâ from package âbaseâ in package âMatrixâ
Creating a generic function for âwhichâ from package âbaseâ in package âMatrixâ
in method for âcoerceâ with signature â"graphAM","sparseMatrix"â: no definition for class âgraphAMâ
in method for âcoerceâ with signature â"graph","CsparseMatrix"â: no definition for class âgraphâ
in method for âcoerceâ with signature â"graph","Matrix"â: no definition for class âgraphâ
in method for âcoerceâ with signature â"graphNEL","CsparseMatrix"â: no definition for class âgraphNELâ
in method for âcoerceâ with signature â"graphNEL","TsparseMatrix"â: no definition for class âgraphNELâ
in method for âcoerceâ with signature â"sparseMatrix","graph"â: no definition for class âgraphâ
in method for âcoerceâ with signature â"sparseMatrix","graphNEL"â: no definition for class âgraphNELâ
in method for âcoerceâ with signature â"TsparseMatrix","graphNEL"â: no definition for class âgraphNELâ
Creating a generic function for âqr.Râ from package âbaseâ in package âMatrixâ
Creating a generic function for âqr.Qâ from package âbaseâ in package âMatrixâ
Creating a generic function for âqr.qyâ from package âbaseâ in package âMatrixâ
Creating a generic function for âqr.qtyâ from package âbaseâ in package âMatrixâ
Creating a generic function for âqr.coefâ from package âbaseâ in package âMatrixâ
Creating a generic function for âqr.residâ from package âbaseâ in package âMatrixâ
Creating a generic function for âqr.fittedâ from package âbaseâ in package âMatrixâ
Creating a generic function for âtoeplitzâ from package âstatsâ in package âMatrixâ
** 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 âsurvivalâ ...
** package âsurvivalâ 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 âmgcvâ ...
** package âmgcvâ 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
More information about the freebsd-pkg-fallout
mailing list