[ Started: 2025-08-11 07:44:17 CEST ] [ OmnipathR v3.16.0 for BioC-3.21 from https://git.bioconductor.org/packages/OmnipathR@RELEASE_3_21 (08e98a0 2025-04-15 11:51:33) ] [1] "Libraries: " "/home/omnipath/local/R/4.5-3.21" [3] "/home/omnipath/local/R/4.5" "/usr/lib/R/library" trying URL 'https://cran.uni-muenster.de/src/contrib/FactoMineR_2.12.tar.gz' Content type 'application/x-gzip' length 2837924 bytes (2.7 MB) ================================================== downloaded 2.7 MB * installing *source* package ‘FactoMineR’ ... ** this is package ‘FactoMineR’ version ‘2.12’ ** package ‘FactoMineR’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c disjonctif.c -o disjonctif.o gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c init.c -o init.o gcc -std=gnu2x -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -o FactoMineR.so disjonctif.o init.o -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.5-3.21/00LOCK-FactoMineR/00new/FactoMineR/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/home/omnipath/local/R/4.5-3.21/mvtnorm/libs/mvtnorm.so': libRblas.so: cannot open shared object file: No such file or directory Calls: ... namespaceImport -> loadNamespace -> library.dynam -> dyn.load Execution halted ERROR: lazy loading failed for package ‘FactoMineR’ * removing ‘/home/omnipath/local/R/4.5-3.21/FactoMineR’ * restoring previous ‘/home/omnipath/local/R/4.5-3.21/FactoMineR’ The downloaded source packages are in ‘/tmp/RtmpLq5Rny/downloaded_packages’ Warning message: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, : installation of package ‘FactoMineR’ had non-zero exit status 'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details. Replacement repositories: CRAN: https://cloud.r-project.org Bioconductor version 3.21 (BiocManager 1.30.26), R 4.5.1 (2025-06-13) Old packages: 'enrichplot', 'FactoMineR', 'ggtree', 'wppi' trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/enrichplot_1.28.4.tar.gz' trying URL 'https://cloud.r-project.org/src/contrib/FactoMineR_2.12.tar.gz' trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/ggtree_3.16.3.tar.gz' trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/wppi_1.16.0.tar.gz' * installing *source* package ‘FactoMineR’ ... ** this is package ‘FactoMineR’ version ‘2.12’ ** package ‘FactoMineR’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c disjonctif.c -o disjonctif.o gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c init.c -o init.o gcc -std=gnu2x -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -o FactoMineR.so disjonctif.o init.o -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.5-3.21/00LOCK-FactoMineR/00new/FactoMineR/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/home/omnipath/local/R/4.5-3.21/mvtnorm/libs/mvtnorm.so': libRblas.so: cannot open shared object file: No such file or directory Calls: ... namespaceImport -> loadNamespace -> library.dynam -> dyn.load Execution halted ERROR: lazy loading failed for package ‘FactoMineR’ * removing ‘/home/omnipath/local/R/4.5-3.21/FactoMineR’ * restoring previous ‘/home/omnipath/local/R/4.5-3.21/FactoMineR’ * installing *source* package ‘ggtree’ ... ** this is package ‘ggtree’ version ‘3.16.3’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/home/omnipath/local/R/4.5-3.21/ape/libs/ape.so': libRblas.so: cannot open shared object file: No such file or directory Calls: ... asNamespace -> loadNamespace -> library.dynam -> dyn.load Execution halted ERROR: lazy loading failed for package ‘ggtree’ * removing ‘/home/omnipath/local/R/4.5-3.21/ggtree’ * restoring previous ‘/home/omnipath/local/R/4.5-3.21/ggtree’ * installing *source* package ‘wppi’ ... ** this is package ‘wppi’ version ‘1.16.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/home/omnipath/local/R/4.5-3.21/igraph/libs/igraph.so': libRblas.so: cannot open shared object file: No such file or directory Calls: ... asNamespace -> loadNamespace -> library.dynam -> dyn.load Execution halted ERROR: lazy loading failed for package ‘wppi’ * removing ‘/home/omnipath/local/R/4.5-3.21/wppi’ * restoring previous ‘/home/omnipath/local/R/4.5-3.21/wppi’ * installing *source* package ‘enrichplot’ ... ** this is package ‘enrichplot’ version ‘1.28.4’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/home/omnipath/local/R/4.5-3.21/igraph/libs/igraph.so': libRblas.so: cannot open shared object file: No such file or directory Calls: ... asNamespace -> loadNamespace -> library.dynam -> dyn.load Execution halted ERROR: lazy loading failed for package ‘enrichplot’ * removing ‘/home/omnipath/local/R/4.5-3.21/enrichplot’ * restoring previous ‘/home/omnipath/local/R/4.5-3.21/enrichplot’ The downloaded source packages are in ‘/tmp/RtmpLq5Rny/downloaded_packages’ Warning messages: 1: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, : installation of package ‘FactoMineR’ had non-zero exit status 2: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, : installation of package ‘ggtree’ had non-zero exit status 3: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, : installation of package ‘wppi’ had non-zero exit status 4: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, : installation of package ‘enrichplot’ had non-zero exit status 'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details. Replacement repositories: CRAN: https://cloud.r-project.org Bioconductor version 3.21 (BiocManager 1.30.26), R 4.5.1 (2025-06-13) Old packages: 'enrichplot', 'FactoMineR', 'ggtree', 'wppi' trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/enrichplot_1.28.4.tar.gz' trying URL 'https://cloud.r-project.org/src/contrib/FactoMineR_2.12.tar.gz' trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/ggtree_3.16.3.tar.gz' trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/wppi_1.16.0.tar.gz' * installing *source* package ‘FactoMineR’ ... ** this is package ‘FactoMineR’ version ‘2.12’ ** package ‘FactoMineR’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c disjonctif.c -o disjonctif.o gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c init.c -o init.o gcc -std=gnu2x -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -o FactoMineR.so disjonctif.o init.o -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.5-3.21/00LOCK-FactoMineR/00new/FactoMineR/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/home/omnipath/local/R/4.5-3.21/mvtnorm/libs/mvtnorm.so': libRblas.so: cannot open shared object file: No such file or directory Calls: ... namespaceImport -> loadNamespace -> library.dynam -> dyn.load Execution halted ERROR: lazy loading failed for package ‘FactoMineR’ * removing ‘/home/omnipath/local/R/4.5-3.21/FactoMineR’ * restoring previous ‘/home/omnipath/local/R/4.5-3.21/FactoMineR’ * installing *source* package ‘ggtree’ ... ** this is package ‘ggtree’ version ‘3.16.3’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/home/omnipath/local/R/4.5-3.21/ape/libs/ape.so': libRblas.so: cannot open shared object file: No such file or directory Calls: ... asNamespace -> loadNamespace -> library.dynam -> dyn.load Execution halted ERROR: lazy loading failed for package ‘ggtree’ * removing ‘/home/omnipath/local/R/4.5-3.21/ggtree’ * restoring previous ‘/home/omnipath/local/R/4.5-3.21/ggtree’ * installing *source* package ‘wppi’ ... ** this is package ‘wppi’ version ‘1.16.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/home/omnipath/local/R/4.5-3.21/igraph/libs/igraph.so': libRblas.so: cannot open shared object file: No such file or directory Calls: ... asNamespace -> loadNamespace -> library.dynam -> dyn.load Execution halted ERROR: lazy loading failed for package ‘wppi’ * removing ‘/home/omnipath/local/R/4.5-3.21/wppi’ * restoring previous ‘/home/omnipath/local/R/4.5-3.21/wppi’ * installing *source* package ‘enrichplot’ ... ** this is package ‘enrichplot’ version ‘1.28.4’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/home/omnipath/local/R/4.5-3.21/igraph/libs/igraph.so': libRblas.so: cannot open shared object file: No such file or directory Calls: ... asNamespace -> loadNamespace -> library.dynam -> dyn.load Execution halted ERROR: lazy loading failed for package ‘enrichplot’ * removing ‘/home/omnipath/local/R/4.5-3.21/enrichplot’ * restoring previous ‘/home/omnipath/local/R/4.5-3.21/enrichplot’ The downloaded source packages are in ‘/tmp/RtmpLq5Rny/downloaded_packages’ Warning messages: 1: package(s) not installed when version(s) same as or greater than current; use `force = TRUE` to re-install: 'BiocCheck' 2: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, : installation of package ‘FactoMineR’ had non-zero exit status 3: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, : installation of package ‘ggtree’ had non-zero exit status 4: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, : installation of package ‘wppi’ had non-zero exit status 5: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, : installation of package ‘enrichplot’ had non-zero exit status [ Finished: 2025-08-11 07:44:42 CEST ]