[ Started: 2026-10-14 17:32:14 CEST ] [ CARNIVAL v2.5.1 for BioC-3.24 from https://github.com/saezlab/CARNIVAL@dev (81a0120 2022-03-17 09:59:10) ] [ R version 4.6.1 Patched (2026-10-12 r90666) -- "Happy Hop" at /opt/R-4.6-patched/bin ] [1] "Libraries: " "/home/omnipath/local/R/4.6-3.24" [3] "/home/omnipath/local/R/4.6" "/opt/R-4.6-patched/lib/R/library" trying URL 'https://cran.uni-muenster.de/src/contrib/lambda.r_1.2.6.tar.gz' Content type 'application/x-gzip' length 25603 bytes (25 KB) ================================================== downloaded 25 KB * installing *source* package ‘lambda.r’ ... ** this is package ‘lambda.r’ version ‘1.2.6’ ** package ‘lambda.r’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded 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 (lambda.r) The downloaded source packages are in ‘/tmp/Rtmpuq31dI/downloaded_packages’ Bioconductor version 3.24 (BiocManager 1.30.27), R 4.6.1 Patched (2026-10-12 r90666) Old packages: 'curl', 'FactoMineR', 'gert' trying URL 'https://cloud.r-project.org/src/contrib/curl_8.1.0.tar.gz' trying URL 'https://cloud.r-project.org/src/contrib/FactoMineR_2.18.tar.gz' trying URL 'https://cloud.r-project.org/src/contrib/gert_2.5.0.tar.gz' * installing *source* package ‘curl’ ... ** this is package ‘curl’ version ‘8.1.0’ ** 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 13.3.0-6ubuntu2~24.04.1) 13.3.0’ gcc -std=gnu2x -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c callbacks.c -o callbacks.o gcc -std=gnu2x -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c curl.c -o curl.o gcc -std=gnu2x -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c download.c -o download.o gcc -std=gnu2x -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c dryrun.c -o dryrun.o gcc -std=gnu2x -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c escape.c -o escape.o gcc -std=gnu2x -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c fetch.c -o fetch.o gcc -std=gnu2x -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c findport.c -o findport.o gcc -std=gnu2x -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c form.c -o form.o gcc -std=gnu2x -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c getdate.c -o getdate.o gcc -std=gnu2x -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c handle.c -o handle.o gcc -std=gnu2x -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c ieproxy.c -o ieproxy.o gcc -std=gnu2x -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c init.c -o init.o gcc -std=gnu2x -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c interrupt.c -o interrupt.o gcc -std=gnu2x -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c multi.c -o multi.o gcc -std=gnu2x -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c nslookup.c -o nslookup.o gcc -std=gnu2x -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c options.c -o options.o gcc -std=gnu2x -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c reflist.c -o reflist.o gcc -std=gnu2x -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c split.c -o split.o gcc -std=gnu2x -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c ssl.c -o ssl.o gcc -std=gnu2x -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c typechecking.c -o typechecking.o gcc -std=gnu2x -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c urlparser.c -o urlparser.o gcc -std=gnu2x -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c utils.c -o utils.o gcc -std=gnu2x -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c version.c -o version.o gcc -std=gnu2x -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c winidn.c -o winidn.o gcc -std=gnu2x -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c writer.c -o writer.o gcc -std=gnu2x -shared -L/opt/R-4.6-patched/lib/R/lib -L/usr/local/lib -o curl.so callbacks.o curl.o download.o dryrun.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 urlparser.o utils.o version.o winidn.o writer.o -lcurl -L/opt/R-4.6-patched/lib/R/lib -lR installing to /home/omnipath/local/R/4.6-3.24/00LOCK-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 ‘FactoMineR’ ... ** this is package ‘FactoMineR’ version ‘2.18’ ** package ‘FactoMineR’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’ gcc -std=gnu2x -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c disjonctif.c -o disjonctif.o gcc -std=gnu2x -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c init.c -o init.o gcc -std=gnu2x -shared -L/opt/R-4.6-patched/lib/R/lib -L/usr/local/lib -o FactoMineR.so disjonctif.o init.o -L/opt/R-4.6-patched/lib/R/lib -lR installing to /home/omnipath/local/R/4.6-3.24/00LOCK-FactoMineR/00new/FactoMineR/libs ** R ** data ** 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 (FactoMineR) * installing *source* package ‘gert’ ... ** this is package ‘gert’ version ‘2.5.0’ ** package ‘gert’ successfully unpacked and MD5 sums checked ** using staged installation Found pkg-config cflags and libs! Using PKG_CFLAGS= Using PKG_LIBS=-lgit2 Configuration OK! ** libs using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’ gcc -std=gnu2x -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c branch.c -o branch.o gcc -std=gnu2x -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c clone.c -o clone.o gcc -std=gnu2x -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c commit.c -o commit.o gcc -std=gnu2x -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c config.c -o config.o gcc -std=gnu2x -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c conflicts.c -o conflicts.o gcc -std=gnu2x -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c files.c -o files.o gcc -std=gnu2x -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c ignore.c -o ignore.o gcc -std=gnu2x -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c init.c -o init.o gcc -std=gnu2x -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c merge.c -o merge.o gcc -std=gnu2x -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c rebase.c -o rebase.o gcc -std=gnu2x -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c stash.c -o stash.o gcc -std=gnu2x -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c submodules.c -o submodules.o gcc -std=gnu2x -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c tag.c -o tag.o gcc -std=gnu2x -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c utils.c -o utils.o gcc -std=gnu2x -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c version.c -o version.o gcc -std=gnu2x -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c worktree.c -o worktree.o gcc -std=gnu2x -shared -L/opt/R-4.6-patched/lib/R/lib -L/usr/local/lib -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 worktree.o -lgit2 -L/opt/R-4.6-patched/lib/R/lib -lR installing to /home/omnipath/local/R/4.6-3.24/00LOCK-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/Rtmpuq31dI/downloaded_packages’ Bioconductor version 3.24 (BiocManager 1.30.27), R 4.6.1 Patched (2026-10-12 r90666) 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: curl [ Finished: 2026-10-14 17:32:59 CEST ]