[ Started: 2024-03-06 11:52:04 CET ] [ CARNIVAL v2.7.2 for BioC-3.18 from https://github.com/saezlab/CARNIVAL@master ] [1] "Libraries: " "/home/omnipath/local/R/4.3-3.18" [3] "/home/omnipath/local/R/4.3" "/usr/lib/R/library" trying URL 'https://cran.uni-muenster.de/src/contrib/lava_1.8.0.tar.gz' Content type 'application/x-gzip' length 1169695 bytes (1.1 MB) ================================================== downloaded 1.1 MB trying URL 'https://cran.uni-muenster.de/src/contrib/logger_0.3.0.tar.gz' Content type 'application/x-gzip' length 597396 bytes (583 KB) ================================================== downloaded 583 KB trying URL 'https://cran.uni-muenster.de/src/contrib/rmarkdown_2.26.tar.gz' Content type 'application/x-gzip' length 2189506 bytes (2.1 MB) ================================================== downloaded 2.1 MB * installing *source* package ‘lava’ ... ** package ‘lava’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data ** demo ** 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 (lava) * installing *source* package ‘logger’ ... ** package ‘logger’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** demo ** 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 (logger) * installing *source* package ‘rmarkdown’ ... ** package ‘rmarkdown’ 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 (rmarkdown) The downloaded source packages are in ‘/tmp/RtmpZkxm2U/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 3.18 (BiocManager 1.30.22), R 4.3.1 (2023-06-16) Old packages: 'S4Arrays' trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/S4Arrays_1.2.1.tar.gz' Content type 'application/x-gzip' length 282089 bytes (275 KB) ================================================== downloaded 275 KB * installing *source* package ‘S4Arrays’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c R_init_S4Arrays.c -o R_init_S4Arrays.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c abind.c -o abind.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c array_selection.c -o array_selection.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/S4Vectors/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c dim_tuning_utils.c -o dim_tuning_utils.o gcc -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o S4Arrays.so R_init_S4Arrays.o S4Vectors_stubs.o abind.o array_selection.o dim_tuning_utils.o -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.3-3.18/00LOCK-S4Arrays/00new/S4Arrays/libs ** R ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘rowsum’ in package ‘S4Arrays’ Creating a new generic function for ‘abind’ in package ‘S4Arrays’ ** 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 (S4Arrays) The downloaded source packages are in ‘/tmp/RtmpZkxm2U/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 3.18 (BiocManager 1.30.22), R 4.3.1 (2023-06-16) Warning message: package(s) not installed when version(s) same as or greater than current; use `force = TRUE` to re-install: 'BiocCheck' [ Finished: 2024-03-06 11:52:47 CET ]