[ Started: 2024-09-20 15:31:07 CEST ] [ CARNIVAL v2.7.2 for BioC-3.20 from https://github.com/saezlab/CARNIVAL@master (2b8887a 2023-12-06 13:18:32) ] [1] "Libraries: " "/home/omnipath/local/R/4.4-3.20" [3] "/home/omnipath/local/R/4.4" "/usr/lib/R/library" trying URL 'https://cran.uni-muenster.de/src/contrib/gert_2.1.2.tar.gz' Content type 'application/x-gzip' length 122632 bytes (119 KB) ================================================== downloaded 119 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/RtmpXx5rUW/R.INSTALL2f99f7661c516d/gert/libgit2-1.4.2-x86_64_linux/include Using PKG_LIBS=-L/tmp/RtmpXx5rUW/R.INSTALL2f99f7661c516d/gert/libgit2-1.4.2-x86_64_linux/lib -lstatgit2 -lrt -lpthread -lstatssh2 -lstatssl -lstatcrypto -ldl Configuration OK! ** libs using C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ 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/RtmpXx5rUW/R.INSTALL2f99f7661c516d/gert/libgit2-1.4.2-x86_64_linux/include -DR_NO_REMAP -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c branch.c -o branch.o gcc -I"/usr/share/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/RtmpXx5rUW/R.INSTALL2f99f7661c516d/gert/libgit2-1.4.2-x86_64_linux/include -DR_NO_REMAP -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c clone.c -o clone.o gcc -I"/usr/share/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/RtmpXx5rUW/R.INSTALL2f99f7661c516d/gert/libgit2-1.4.2-x86_64_linux/include -DR_NO_REMAP -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c commit.c -o commit.o gcc -I"/usr/share/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/RtmpXx5rUW/R.INSTALL2f99f7661c516d/gert/libgit2-1.4.2-x86_64_linux/include -DR_NO_REMAP -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c config.c -o config.o gcc -I"/usr/share/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/RtmpXx5rUW/R.INSTALL2f99f7661c516d/gert/libgit2-1.4.2-x86_64_linux/include -DR_NO_REMAP -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c conflicts.c -o conflicts.o gcc -I"/usr/share/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/RtmpXx5rUW/R.INSTALL2f99f7661c516d/gert/libgit2-1.4.2-x86_64_linux/include -DR_NO_REMAP -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c files.c -o files.o gcc -I"/usr/share/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/RtmpXx5rUW/R.INSTALL2f99f7661c516d/gert/libgit2-1.4.2-x86_64_linux/include -DR_NO_REMAP -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c ignore.c -o ignore.o gcc -I"/usr/share/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/RtmpXx5rUW/R.INSTALL2f99f7661c516d/gert/libgit2-1.4.2-x86_64_linux/include -DR_NO_REMAP -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c init.c -o init.o gcc -I"/usr/share/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/RtmpXx5rUW/R.INSTALL2f99f7661c516d/gert/libgit2-1.4.2-x86_64_linux/include -DR_NO_REMAP -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c merge.c -o merge.o gcc -I"/usr/share/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/RtmpXx5rUW/R.INSTALL2f99f7661c516d/gert/libgit2-1.4.2-x86_64_linux/include -DR_NO_REMAP -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c rebase.c -o rebase.o gcc -I"/usr/share/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/RtmpXx5rUW/R.INSTALL2f99f7661c516d/gert/libgit2-1.4.2-x86_64_linux/include -DR_NO_REMAP -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c stash.c -o stash.o gcc -I"/usr/share/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/RtmpXx5rUW/R.INSTALL2f99f7661c516d/gert/libgit2-1.4.2-x86_64_linux/include -DR_NO_REMAP -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c submodules.c -o submodules.o gcc -I"/usr/share/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/RtmpXx5rUW/R.INSTALL2f99f7661c516d/gert/libgit2-1.4.2-x86_64_linux/include -DR_NO_REMAP -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c tag.c -o tag.o gcc -I"/usr/share/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/RtmpXx5rUW/R.INSTALL2f99f7661c516d/gert/libgit2-1.4.2-x86_64_linux/include -DR_NO_REMAP -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c utils.c -o utils.o gcc -I"/usr/share/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/RtmpXx5rUW/R.INSTALL2f99f7661c516d/gert/libgit2-1.4.2-x86_64_linux/include -DR_NO_REMAP -DSTRICT_R_HEADERS -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c version.c -o version.o gcc -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -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/RtmpXx5rUW/R.INSTALL2f99f7661c516d/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/4.4-3.20/00LOCK-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) The downloaded source packages are in ‘/tmp/RtmplnoyxW/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 3.20 (BiocManager 1.30.25), R 4.4.1 (2024-06-14) Old packages: 'curl', 'jsonlite', 'magick', 'openssl', 'profvis' trying URL 'https://cloud.r-project.org/src/contrib/curl_5.2.3.tar.gz' Content type 'application/x-gzip' length 717168 bytes (700 KB) ================================================== downloaded 700 KB trying URL 'https://cloud.r-project.org/src/contrib/jsonlite_1.8.9.tar.gz' Content type 'application/x-gzip' length 1055633 bytes (1.0 MB) ================================================== downloaded 1.0 MB trying URL 'https://cloud.r-project.org/src/contrib/magick_2.8.5.tar.gz' Content type 'application/x-gzip' length 4596590 bytes (4.4 MB) ================================================== downloaded 4.4 MB trying URL 'https://cloud.r-project.org/src/contrib/openssl_2.2.2.tar.gz' Content type 'application/x-gzip' length 1208018 bytes (1.2 MB) ================================================== downloaded 1.2 MB trying URL 'https://cloud.r-project.org/src/contrib/profvis_0.4.0.tar.gz' Content type 'application/x-gzip' length 301123 bytes (294 KB) ================================================== downloaded 294 KB * installing *source* package ‘curl’ ... ** package ‘curl’ successfully unpacked and MD5 sums checked ** using staged installation Found pkg-config cflags and libs! Using PKG_CFLAGS=-I/usr/include/x86_64-linux-gnu Using PKG_LIBS=-lcurl ** libs using C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ rm -f curl.so callbacks.o curl.o download.o escape.o fetch.o findport.o form.o getdate.o handle.o ieproxy.o init.o interrupt.o multi.o nslookup.o options.o reflist.o split.o ssl.o typechecking.o utils.o version.o winidn.o writer.o gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -DR_NO_REMAP -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c callbacks.c -o callbacks.o gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -DR_NO_REMAP -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c curl.c -o curl.o gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -DR_NO_REMAP -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c download.c -o download.o gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -DR_NO_REMAP -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c escape.c -o escape.o gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -DR_NO_REMAP -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c fetch.c -o fetch.o gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -DR_NO_REMAP -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c findport.c -o findport.o gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -DR_NO_REMAP -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c form.c -o form.o gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -DR_NO_REMAP -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c getdate.c -o getdate.o gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -DR_NO_REMAP -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c handle.c -o handle.o gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -DR_NO_REMAP -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c ieproxy.c -o ieproxy.o gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -DR_NO_REMAP -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c init.c -o init.o gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -DR_NO_REMAP -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c interrupt.c -o interrupt.o gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -DR_NO_REMAP -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c multi.c -o multi.o gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -DR_NO_REMAP -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c nslookup.c -o nslookup.o gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -DR_NO_REMAP -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c options.c -o options.o gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -DR_NO_REMAP -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c reflist.c -o reflist.o gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -DR_NO_REMAP -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c split.c -o split.o gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -DR_NO_REMAP -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c ssl.c -o ssl.o gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -DR_NO_REMAP -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c typechecking.c -o typechecking.o gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -DR_NO_REMAP -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c utils.c -o utils.o gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -DR_NO_REMAP -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c version.c -o version.o gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -DR_NO_REMAP -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c winidn.c -o winidn.o gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -DR_NO_REMAP -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c writer.c -o writer.o gcc -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -o curl.so callbacks.o curl.o download.o escape.o fetch.o findport.o form.o getdate.o handle.o ieproxy.o init.o interrupt.o multi.o nslookup.o options.o reflist.o split.o ssl.o typechecking.o utils.o version.o winidn.o writer.o -lcurl -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.4-3.20/00LOCK-curl/00new/curl/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 (curl) * installing *source* package ‘jsonlite’ ... ** package ‘jsonlite’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c base64.c -o base64.o gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c collapse_array.c -o collapse_array.o gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c collapse_object.c -o collapse_object.o gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c collapse_pretty.c -o collapse_pretty.o gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c escape_chars.c -o escape_chars.o gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c integer64_to_na.c -o integer64_to_na.o gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c is_datelist.c -o is_datelist.o gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c is_recordlist.c -o is_recordlist.o gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c is_scalarlist.c -o is_scalarlist.o gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c modp_numtoa.c -o modp_numtoa.o gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c null_to_na.c -o null_to_na.o gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c num_to_char.c -o num_to_char.o gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c parse.c -o parse.o gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c prettify.c -o prettify.o gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c push_parser.c -o push_parser.o gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c r-base64.c -o r-base64.o gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c register.c -o register.o gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c row_collapse.c -o row_collapse.o gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c transpose_list.c -o transpose_list.o gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c validate.c -o validate.o gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c yajl/yajl.c -o yajl/yajl.o gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c yajl/yajl_alloc.c -o yajl/yajl_alloc.o gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c yajl/yajl_buf.c -o yajl/yajl_buf.o gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c yajl/yajl_encode.c -o yajl/yajl_encode.o gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c yajl/yajl_gen.c -o yajl/yajl_gen.o gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c yajl/yajl_lex.c -o yajl/yajl_lex.o gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c yajl/yajl_parser.c -o yajl/yajl_parser.o gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c yajl/yajl_tree.c -o yajl/yajl_tree.o ar rcs yajl/libstatyajl.a yajl/yajl.o yajl/yajl_alloc.o yajl/yajl_buf.o yajl/yajl_encode.o yajl/yajl_gen.o yajl/yajl_lex.o yajl/yajl_parser.o yajl/yajl_tree.o gcc -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -o jsonlite.so base64.o collapse_array.o collapse_object.o collapse_pretty.o escape_chars.o integer64_to_na.o is_datelist.o is_recordlist.o is_scalarlist.o modp_numtoa.o null_to_na.o num_to_char.o parse.o prettify.o push_parser.o r-base64.o register.o row_collapse.o transpose_list.o validate.o -Lyajl -lstatyajl -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.4-3.20/00LOCK-jsonlite/00new/jsonlite/libs ** R ** inst ** byte-compile and prepare package for lazy loading in method for ‘asJSON’ with signature ‘"AsIs"’: no definition for class “AsIs” in method for ‘asJSON’ with signature ‘"ITime"’: no definition for class “ITime” in method for ‘asJSON’ with signature ‘"hms"’: no definition for class “hms” in method for ‘asJSON’ with signature ‘"json"’: no definition for class “json” in method for ‘asJSON’ with signature ‘"integer64"’: no definition for class “integer64” in method for ‘asJSON’ with signature ‘"pairlist"’: no definition for class “pairlist” in method for ‘asJSON’ with signature ‘"blob"’: no definition for class “blob” in method for ‘asJSON’ with signature ‘"scalar"’: no definition for class “scalar” in method for ‘asJSON’ with signature ‘"sf"’: no definition for class “sf” in method for ‘asJSON’ with signature ‘"sfc"’: no definition for class “sfc” in method for ‘asJSON’ with signature ‘"vctrs_vctr"’: no definition for class “vctrs_vctr” ** 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 (jsonlite) * installing *source* package ‘openssl’ ... ** package ‘openssl’ successfully unpacked and MD5 sums checked ** using staged installation Found pkg-config cflags and libs! Using PKG_CFLAGS= Using PKG_LIBS=-l:libssl.so.3 -l:libcrypto.so.3 ** libs using C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ rm -f aes.o base64.o bignum.o cert.o compatibility.o diffie.o envelope.o error.o hash.o info.o keygen.o keys.o onload.o openssh.o password.o pbkdf.o pem.o pkcs12.o pkcs7.o rand.o rsa.o signing.o ssl.o stream.o write.o x25519.o openssl.so bcrypt/libstatbcrypt.a bcrypt/bcrypt_pbkdf.o bcrypt/blowfish.o gcc -I"/usr/share/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c aes.c -o aes.o gcc -I"/usr/share/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c base64.c -o base64.o gcc -I"/usr/share/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c bignum.c -o bignum.o gcc -I"/usr/share/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c cert.c -o cert.o gcc -I"/usr/share/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c compatibility.c -o compatibility.o gcc -I"/usr/share/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c diffie.c -o diffie.o gcc -I"/usr/share/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c envelope.c -o envelope.o gcc -I"/usr/share/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c error.c -o error.o gcc -I"/usr/share/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c hash.c -o hash.o gcc -I"/usr/share/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c info.c -o info.o gcc -I"/usr/share/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c keygen.c -o keygen.o gcc -I"/usr/share/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c keys.c -o keys.o gcc -I"/usr/share/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c onload.c -o onload.o gcc -I"/usr/share/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c openssh.c -o openssh.o gcc -I"/usr/share/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c password.c -o password.o gcc -I"/usr/share/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c pbkdf.c -o pbkdf.o gcc -I"/usr/share/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c pem.c -o pem.o gcc -I"/usr/share/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c pkcs12.c -o pkcs12.o gcc -I"/usr/share/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c pkcs7.c -o pkcs7.o gcc -I"/usr/share/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c rand.c -o rand.o gcc -I"/usr/share/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c rsa.c -o rsa.o gcc -I"/usr/share/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c signing.c -o signing.o gcc -I"/usr/share/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c ssl.c -o ssl.o gcc -I"/usr/share/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c stream.c -o stream.o gcc -I"/usr/share/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c write.c -o write.o gcc -I"/usr/share/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c x25519.c -o x25519.o gcc -I"/usr/share/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c bcrypt/bcrypt_pbkdf.c -o bcrypt/bcrypt_pbkdf.o gcc -I"/usr/share/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c bcrypt/blowfish.c -o bcrypt/blowfish.o ar rcs bcrypt/libstatbcrypt.a bcrypt/bcrypt_pbkdf.o bcrypt/blowfish.o gcc -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -o openssl.so aes.o base64.o bignum.o cert.o compatibility.o diffie.o envelope.o error.o hash.o info.o keygen.o keys.o onload.o openssh.o password.o pbkdf.o pem.o pkcs12.o pkcs7.o rand.o rsa.o signing.o ssl.o stream.o write.o x25519.o -Lbcrypt -lstatbcrypt -l:libssl.so.3 -l:libcrypto.so.3 -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.4-3.20/00LOCK-openssl/00new/openssl/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 (openssl) * installing *source* package ‘profvis’ ... ** package ‘profvis’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c pause.c -o pause.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c profvis-init.c -o profvis-init.o gcc -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -o profvis.so pause.o profvis-init.o -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.4-3.20/00LOCK-profvis/00new/profvis/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 (profvis) * installing *source* package ‘magick’ ... ** package ‘magick’ successfully unpacked and MD5 sums checked ** using staged installation Found pkg-config cflags and libs! Using PKG_CFLAGS=-I/usr/include/x86_64-linux-gnu/ImageMagick-6 -I/usr/include/ImageMagick-6 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 Using PKG_LIBS=-lMagick++-6.Q16 -lMagickWand-6.Q16 -lMagickCore-6.Q16 ** libs using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu/ImageMagick-6 -I/usr/include/ImageMagick-6 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include' -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu/ImageMagick-6 -I/usr/include/ImageMagick-6 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include' -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c animation.cpp -o animation.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu/ImageMagick-6 -I/usr/include/ImageMagick-6 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include' -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c attributes.cpp -o attributes.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu/ImageMagick-6 -I/usr/include/ImageMagick-6 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include' -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c base.cpp -o base.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu/ImageMagick-6 -I/usr/include/ImageMagick-6 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include' -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c color.cpp -o color.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu/ImageMagick-6 -I/usr/include/ImageMagick-6 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include' -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c composite.cpp -o composite.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu/ImageMagick-6 -I/usr/include/ImageMagick-6 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include' -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c config.cc -o config.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu/ImageMagick-6 -I/usr/include/ImageMagick-6 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include' -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c convolve.cpp -o convolve.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu/ImageMagick-6 -I/usr/include/ImageMagick-6 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include' -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c device.cpp -o device.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu/ImageMagick-6 -I/usr/include/ImageMagick-6 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include' -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c edges.cpp -o edges.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu/ImageMagick-6 -I/usr/include/ImageMagick-6 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include' -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c edit.cpp -o edit.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu/ImageMagick-6 -I/usr/include/ImageMagick-6 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include' -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c fonts.cpp -o fonts.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu/ImageMagick-6 -I/usr/include/ImageMagick-6 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include' -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c options.cpp -o options.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu/ImageMagick-6 -I/usr/include/ImageMagick-6 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include' -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c properties.cpp -o properties.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu/ImageMagick-6 -I/usr/include/ImageMagick-6 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include' -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c resize.cpp -o resize.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu/ImageMagick-6 -I/usr/include/ImageMagick-6 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include' -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c segment.cpp -o segment.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu/ImageMagick-6 -I/usr/include/ImageMagick-6 -fopenmp -DMAGICKCORE_HDRI_ENABLE=0 -DMAGICKCORE_QUANTUM_DEPTH=16 -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include' -fvisibility=hidden -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c transformations.cpp -o transformations.o g++ -std=gnu++17 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -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/4.4-3.20/00LOCK-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/RtmplnoyxW/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 3.20 (BiocManager 1.30.25), R 4.4.1 (2024-06-14) Warning message: package(s) not installed when version(s) same as or greater than current; use `force = TRUE` to re-install: 'BiocCheck' Skipping 4 packages ahead of CRAN: openssl, jsonlite, curl, BiocStyle [ Finished: 2024-09-20 15:32:37 CEST ]