[ Started: 2023-09-26 23:58:26 CEST ] [ CARNIVAL v2.7.2 for BioC-3.16 from https://github.com/saezlab/CARNIVAL@master ] [1] "Libraries: " "/home/omnipath/local/R/4.2-3.16" [3] "/home/omnipath/local/R/4.2" "/usr/lib/R/library" trying URL 'https://cran.uni-muenster.de/src/contrib/magick_2.8.0.tar.gz' Content type 'application/x-gzip' length 4599626 bytes (4.4 MB) ================================================== downloaded 4.4 MB * installing *source* package ‘magick’ ... ** package ‘magick’ successfully unpacked and MD5 sums checked ** using staged installation Found pkg-config cflags and libs! Using PKG_CFLAGS=-fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 Using PKG_LIBS=-lMagick++-6.Q16 -lMagickWand-6.Q16 -lMagickCore-6.Q16 ** libs g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c animation.cpp -o animation.o g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c attributes.cpp -o attributes.o g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c base.cpp -o base.o g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c color.cpp -o color.o g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c composite.cpp -o composite.o g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c config.cc -o config.o g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c convolve.cpp -o convolve.o g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c device.cpp -o device.o g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c edges.cpp -o edges.o g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c edit.cpp -o edit.o g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c fonts.cpp -o fonts.o g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c options.cpp -o options.o g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c properties.cpp -o properties.o g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c resize.cpp -o resize.o g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c segment.cpp -o segment.o g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I/usr/include/x86_64-linux-gnu//ImageMagick-6 -I/usr/include/ImageMagick-6 -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c transformations.cpp -o transformations.o g++ -std=gnu++14 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o magick.so RcppExports.o animation.o attributes.o base.o color.o composite.o config.o convolve.o device.o edges.o edit.o fonts.o options.o properties.o resize.o segment.o transformations.o -lMagick++-6.Q16 -lMagickWand-6.Q16 -lMagickCore-6.Q16 -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.2-3.16/00LOCK-magick/00new/magick/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (magick) The downloaded source packages are in ‘/tmp/RtmpoTE9cs/downloaded_packages’ Bioconductor version '3.16' is out-of-date; the current release version '3.17' is available with R version '4.3'; see https://bioconductor.org/install 'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details. Replacement repositories: CRAN: https://cloud.r-project.org Bioconductor version 3.16 (BiocManager 1.30.22), R 4.2.3 (2023-03-15) Old packages: 'gert', 'withr' trying URL 'https://cloud.r-project.org/src/contrib/gert_2.0.0.tar.gz' Content type 'application/x-gzip' length 122720 bytes (119 KB) ================================================== downloaded 119 KB trying URL 'https://cloud.r-project.org/src/contrib/withr_2.5.1.tar.gz' Content type 'application/x-gzip' length 102318 bytes (99 KB) ================================================== downloaded 99 KB * installing *source* package ‘gert’ ... ** package ‘gert’ successfully unpacked and MD5 sums checked ** using staged installation Found OpenSSL3 Using static libgit2 for Linux x86_64 Using PKG_CFLAGS=-DSTATIC_LIBGIT2 -I/tmp/Rtmp4hoT3Z/R.INSTALL3ab4096aa80545/gert/libgit2-1.4.2-x86_64_linux/include Using PKG_LIBS=-L/tmp/Rtmp4hoT3Z/R.INSTALL3ab4096aa80545/gert/libgit2-1.4.2-x86_64_linux/lib -lstatgit2 -lrt -lpthread -lstatssh2 -lstatssl -lstatcrypto -ldl Configuration OK! ** libs rm -f gert.so branch.o clone.o commit.o config.o conflicts.o files.o ignore.o init.o merge.o rebase.o stash.o submodules.o tag.o utils.o version.o gcc -I"/usr/share/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/Rtmp4hoT3Z/R.INSTALL3ab4096aa80545/gert/libgit2-1.4.2-x86_64_linux/include -DR_NO_REMAP -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c branch.c -o branch.o gcc -I"/usr/share/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/Rtmp4hoT3Z/R.INSTALL3ab4096aa80545/gert/libgit2-1.4.2-x86_64_linux/include -DR_NO_REMAP -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c clone.c -o clone.o gcc -I"/usr/share/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/Rtmp4hoT3Z/R.INSTALL3ab4096aa80545/gert/libgit2-1.4.2-x86_64_linux/include -DR_NO_REMAP -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c commit.c -o commit.o gcc -I"/usr/share/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/Rtmp4hoT3Z/R.INSTALL3ab4096aa80545/gert/libgit2-1.4.2-x86_64_linux/include -DR_NO_REMAP -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c config.c -o config.o gcc -I"/usr/share/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/Rtmp4hoT3Z/R.INSTALL3ab4096aa80545/gert/libgit2-1.4.2-x86_64_linux/include -DR_NO_REMAP -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c conflicts.c -o conflicts.o gcc -I"/usr/share/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/Rtmp4hoT3Z/R.INSTALL3ab4096aa80545/gert/libgit2-1.4.2-x86_64_linux/include -DR_NO_REMAP -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c files.c -o files.o gcc -I"/usr/share/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/Rtmp4hoT3Z/R.INSTALL3ab4096aa80545/gert/libgit2-1.4.2-x86_64_linux/include -DR_NO_REMAP -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c ignore.c -o ignore.o gcc -I"/usr/share/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/Rtmp4hoT3Z/R.INSTALL3ab4096aa80545/gert/libgit2-1.4.2-x86_64_linux/include -DR_NO_REMAP -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c init.c -o init.o gcc -I"/usr/share/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/Rtmp4hoT3Z/R.INSTALL3ab4096aa80545/gert/libgit2-1.4.2-x86_64_linux/include -DR_NO_REMAP -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c merge.c -o merge.o gcc -I"/usr/share/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/Rtmp4hoT3Z/R.INSTALL3ab4096aa80545/gert/libgit2-1.4.2-x86_64_linux/include -DR_NO_REMAP -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c rebase.c -o rebase.o gcc -I"/usr/share/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/Rtmp4hoT3Z/R.INSTALL3ab4096aa80545/gert/libgit2-1.4.2-x86_64_linux/include -DR_NO_REMAP -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c stash.c -o stash.o gcc -I"/usr/share/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/Rtmp4hoT3Z/R.INSTALL3ab4096aa80545/gert/libgit2-1.4.2-x86_64_linux/include -DR_NO_REMAP -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c submodules.c -o submodules.o gcc -I"/usr/share/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/Rtmp4hoT3Z/R.INSTALL3ab4096aa80545/gert/libgit2-1.4.2-x86_64_linux/include -DR_NO_REMAP -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c tag.c -o tag.o gcc -I"/usr/share/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/Rtmp4hoT3Z/R.INSTALL3ab4096aa80545/gert/libgit2-1.4.2-x86_64_linux/include -DR_NO_REMAP -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c utils.c -o utils.o gcc -I"/usr/share/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/Rtmp4hoT3Z/R.INSTALL3ab4096aa80545/gert/libgit2-1.4.2-x86_64_linux/include -DR_NO_REMAP -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c version.c -o version.o gcc -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o gert.so branch.o clone.o commit.o config.o conflicts.o files.o ignore.o init.o merge.o rebase.o stash.o submodules.o tag.o utils.o version.o -L/tmp/Rtmp4hoT3Z/R.INSTALL3ab4096aa80545/gert/libgit2-1.4.2-x86_64_linux/lib -lstatgit2 -lrt -lpthread -lstatssh2 -lstatssl -lstatcrypto -ldl -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.2-3.16/00LOCK-gert/00new/gert/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (gert) * installing *source* package ‘withr’ ... ** package ‘withr’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (withr) The downloaded source packages are in ‘/tmp/RtmpoTE9cs/downloaded_packages’ 'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details. Replacement repositories: CRAN: https://cloud.r-project.org Bioconductor version 3.16 (BiocManager 1.30.22), R 4.2.3 (2023-03-15) Warning message: package(s) not installed when version(s) same as or greater than current; use `force = TRUE` to re-install: 'BiocCheck' Skipping 1 packages ahead of CRAN: withr [ Finished: 2023-09-26 23:59:53 CEST ]