[ Started: 2026-10-17 17:32:21 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" Bioconductor version 3.24 (BiocManager 1.30.27), R 4.6.1 Patched (2026-10-12 r90666) Old packages: 'GSVA', 'RcppArmadillo', 'readxl', 'rsvd' trying URL 'https://bioconductor.org/packages/3.24/bioc/src/contrib/GSVA_2.7.25.tar.gz' trying URL 'https://cloud.r-project.org/src/contrib/RcppArmadillo_15.6.2-1.tar.gz' trying URL 'https://cloud.r-project.org/src/contrib/readxl_1.6.0.tar.gz' trying URL 'https://cloud.r-project.org/src/contrib/rsvd_1.0.6.tar.gz' * installing *source* package ‘GSVA’ ... ** this is package ‘GSVA’ version ‘2.7.25’ ** package ‘GSVA’ 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'/home/omnipath/local/R/4.6-3.24/cli/include' -I/usr/local/include -fpic -g -O2 -c average.c -o average.o gcc -std=gnu2x -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.6-3.24/cli/include' -I/usr/local/include -fpic -g -O2 -c ecdfvals.c -o ecdfvals.o gcc -std=gnu2x -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.6-3.24/cli/include' -I/usr/local/include -fpic -g -O2 -c kcdfvals.c -o kcdfvals.o gcc -std=gnu2x -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.6-3.24/cli/include' -I/usr/local/include -fpic -g -O2 -c kernel_estimation.c -o kernel_estimation.o gcc -std=gnu2x -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.6-3.24/cli/include' -I/usr/local/include -fpic -g -O2 -c ks_test.c -o ks_test.o gcc -std=gnu2x -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.6-3.24/cli/include' -I/usr/local/include -fpic -g -O2 -c register_cmethods.c -o register_cmethods.o gcc -std=gnu2x -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.6-3.24/cli/include' -I/usr/local/include -fpic -g -O2 -c row_rngs_nzrngs.c -o row_rngs_nzrngs.o gcc -std=gnu2x -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.6-3.24/cli/include' -I/usr/local/include -fpic -g -O2 -c utils.c -o utils.o gcc -std=gnu2x -shared -L/opt/R-4.6-patched/lib/R/lib -L/usr/local/lib -o GSVA.so average.o ecdfvals.o kcdfvals.o kernel_estimation.o ks_test.o register_cmethods.o row_rngs_nzrngs.o utils.o -L/opt/R-4.6-patched/lib/R/lib -lR installing to /home/omnipath/local/R/4.6-3.24/00LOCK-GSVA/00new/GSVA/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 (GSVA) * installing *source* package ‘RcppArmadillo’ ... ** this is package ‘RcppArmadillo’ version ‘15.6.2-1’ ** package ‘RcppArmadillo’ successfully unpacked and MD5 sums checked ** using staged installation checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C++... yes checking whether g++ -std=gnu++20 accepts -g... yes checking for g++ -std=gnu++20 option to enable C++11 features... -std=gnu++11 checking how to run the C++ preprocessor... g++ -std=gnu++20 -std=gnu++11 -E checking whether the compiler supports GNU C++... (cached) yes checking whether g++ -std=gnu++20 -std=gnu++11 accepts -g... (cached) yes checking for g++ -std=gnu++20 -std=gnu++11 option to enable C++11 features... (cached) -std=gnu++11 checking what system we are on... running Linux on x86_64 checking whether we have a suitable tempdir... /tmp checking whether on Linux... yes checking whether R CMD SHLIB can already compile OpenMP programs... yes checking whether on macOS... no checking for OpenMP... found and suitable configure: creating ./config.status config.status: creating inst/include/RcppArmadillo/config/RcppArmadilloConfigGenerated.h config.status: creating src/Makevars ** libs using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’ g++ -std=gnu++20 -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG -I../inst/include -DARMA_USE_CURRENT -I'/home/omnipath/local/R/4.6-3.24/Rcpp/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppArmadillo.cpp -o RcppArmadillo.o g++ -std=gnu++20 -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG -I../inst/include -DARMA_USE_CURRENT -I'/home/omnipath/local/R/4.6-3.24/Rcpp/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++20 -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG -I../inst/include -DARMA_USE_CURRENT -I'/home/omnipath/local/R/4.6-3.24/Rcpp/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c fastLm.cpp -o fastLm.o g++ -std=gnu++20 -shared -L/opt/R-4.6-patched/lib/R/lib -L/usr/local/lib -o RcppArmadillo.so RcppArmadillo.o RcppExports.o fastLm.o -fopenmp -llapack -L/opt/R-4.6-patched/lib/R/lib -lRblas -lgfortran -lm -lquadmath -L/opt/R-4.6-patched/lib/R/lib -lR installing to /home/omnipath/local/R/4.6-3.24/00LOCK-RcppArmadillo/00new/RcppArmadillo/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 (RcppArmadillo) * installing *source* package ‘readxl’ ... ** this is package ‘readxl’ version ‘1.6.0’ ** package ‘readxl’ 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’ using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’ g++ -std=gnu++20 -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG -Iunix -I. -I'/home/omnipath/local/R/4.6-3.24/cpp11/include' -I'/home/omnipath/local/R/4.6-3.24/progress/include' -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c cpp11.cpp -o cpp11.o g++ -std=gnu++20 -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG -Iunix -I. -I'/home/omnipath/local/R/4.6-3.24/cpp11/include' -I'/home/omnipath/local/R/4.6-3.24/progress/include' -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c XlsWorkBook.cpp -o XlsWorkBook.o g++ -std=gnu++20 -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG -Iunix -I. -I'/home/omnipath/local/R/4.6-3.24/cpp11/include' -I'/home/omnipath/local/R/4.6-3.24/progress/include' -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c XlsxWorkBook.cpp -o XlsxWorkBook.o g++ -std=gnu++20 -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG -Iunix -I. -I'/home/omnipath/local/R/4.6-3.24/cpp11/include' -I'/home/omnipath/local/R/4.6-3.24/progress/include' -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c zip.cpp -o zip.o g++ -std=gnu++20 -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG -Iunix -I. -I'/home/omnipath/local/R/4.6-3.24/cpp11/include' -I'/home/omnipath/local/R/4.6-3.24/progress/include' -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c Read.cpp -o Read.o g++ -std=gnu++20 -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG -Iunix -I. -I'/home/omnipath/local/R/4.6-3.24/cpp11/include' -I'/home/omnipath/local/R/4.6-3.24/progress/include' -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c Decrypt.cpp -o Decrypt.o gcc -std=gnu2x -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG -Iunix -I. -I'/home/omnipath/local/R/4.6-3.24/cpp11/include' -I'/home/omnipath/local/R/4.6-3.24/progress/include' -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c cran.c -o cran.o gcc -std=gnu2x -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG -Iunix -I. -I'/home/omnipath/local/R/4.6-3.24/cpp11/include' -I'/home/omnipath/local/R/4.6-3.24/progress/include' -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c aes128.c -o aes128.o gcc -std=gnu2x -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG -Iunix -I. -I'/home/omnipath/local/R/4.6-3.24/cpp11/include' -I'/home/omnipath/local/R/4.6-3.24/progress/include' -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c aes192.c -o aes192.o gcc -std=gnu2x -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG -Iunix -I. -I'/home/omnipath/local/R/4.6-3.24/cpp11/include' -I'/home/omnipath/local/R/4.6-3.24/progress/include' -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c aes256.c -o aes256.o gcc -std=gnu2x -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG -Iunix -I. -I'/home/omnipath/local/R/4.6-3.24/cpp11/include' -I'/home/omnipath/local/R/4.6-3.24/progress/include' -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c libxls/xlstool.c -o libxls/xlstool.o gcc -std=gnu2x -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG -Iunix -I. -I'/home/omnipath/local/R/4.6-3.24/cpp11/include' -I'/home/omnipath/local/R/4.6-3.24/progress/include' -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c libxls/endian.c -o libxls/endian.o gcc -std=gnu2x -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG -Iunix -I. -I'/home/omnipath/local/R/4.6-3.24/cpp11/include' -I'/home/omnipath/local/R/4.6-3.24/progress/include' -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c libxls/ole.c -o libxls/ole.o gcc -std=gnu2x -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG -Iunix -I. -I'/home/omnipath/local/R/4.6-3.24/cpp11/include' -I'/home/omnipath/local/R/4.6-3.24/progress/include' -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c libxls/xls.c -o libxls/xls.o gcc -std=gnu2x -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG -Iunix -I. -I'/home/omnipath/local/R/4.6-3.24/cpp11/include' -I'/home/omnipath/local/R/4.6-3.24/progress/include' -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c libxls/locale.c -o libxls/locale.o g++ -std=gnu++20 -shared -L/opt/R-4.6-patched/lib/R/lib -L/usr/local/lib -o readxl.so cpp11.o XlsWorkBook.o XlsxWorkBook.o zip.o Read.o Decrypt.o cran.o aes128.o aes192.o aes256.o libxls/xlstool.o libxls/endian.o libxls/ole.o libxls/xls.o libxls/locale.o -L/opt/R-4.6-patched/lib/R/lib -lR installing to /home/omnipath/local/R/4.6-3.24/00LOCK-readxl/00new/readxl/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 (readxl) * installing *source* package ‘rsvd’ ... ** this is package ‘rsvd’ version ‘1.0.6’ ** package ‘rsvd’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** 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 (rsvd) The downloaded source packages are in ‘/tmp/RtmpSTM59U/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' [ Finished: 2026-10-17 17:34:13 CEST ]