[ Started: 2025-07-24 19:30:26 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/RtmpafPfwA/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: 'AnnotationHub', 'BiocFileCache', 'enrichplot', 'ExperimentHub', 'FactoMineR', 'GenomeInfoDb', 'ggtree', 'parallelly', 'SparseArray', 'wppi' trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/AnnotationHub_3.16.1.tar.gz' trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/BiocFileCache_2.16.1.tar.gz' trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/enrichplot_1.28.4.tar.gz' trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/ExperimentHub_2.16.1.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/GenomeInfoDb_1.44.1.tar.gz' trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/ggtree_3.16.3.tar.gz' trying URL 'https://cloud.r-project.org/src/contrib/parallelly_1.45.1.tar.gz' trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/SparseArray_1.8.1.tar.gz' trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/wppi_1.16.0.tar.gz' * installing *source* package ‘BiocFileCache’ ... ** this is package ‘BiocFileCache’ version ‘2.16.1’ ** using staged installation ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BiocFileCache) * 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 ‘GenomeInfoDb’ ... ** this is package ‘GenomeInfoDb’ version ‘1.44.1’ ** using staged installation ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (GenomeInfoDb) * 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 ‘parallelly’ ... ** this is package ‘parallelly’ version ‘1.45.1’ ** package ‘parallelly’ 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 000.init.c -o 000.init.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 calc-serialized-size.c -o calc-serialized-size.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 test_tcp_port.c -o test_tcp_port.o gcc -std=gnu2x -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -o parallelly.so 000.init.o calc-serialized-size.o test_tcp_port.o -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.5-3.21/00LOCK-parallelly/00new/parallelly/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 (parallelly) * installing *source* package ‘SparseArray’ ... ** this is package ‘SparseArray’ version ‘1.8.1’ ** 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 -I'/home/omnipath/local/R/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/XVector/include' -fopenmp -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 ExtendableJaggedArray.c -o ExtendableJaggedArray.o gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/XVector/include' -fopenmp -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 IRanges_stubs.c -o IRanges_stubs.o gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/XVector/include' -fopenmp -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 OPBufTree.c -o OPBufTree.o gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/XVector/include' -fopenmp -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 R_init_SparseArray.c -o R_init_SparseArray.o gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/XVector/include' -fopenmp -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 Rvector_summarization.c -o Rvector_summarization.o gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/XVector/include' -fopenmp -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 Rvector_utils.c -o Rvector_utils.o gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/XVector/include' -fopenmp -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 S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/XVector/include' -fopenmp -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 SBT_utils.c -o SBT_utils.o gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/XVector/include' -fopenmp -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 SVT_SparseArray_class.c -o SVT_SparseArray_class.o gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/XVector/include' -fopenmp -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 SparseArray_Arith_methods.c -o SparseArray_Arith_methods.o gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/XVector/include' -fopenmp -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 SparseArray_Compare_methods.c -o SparseArray_Compare_methods.o gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/XVector/include' -fopenmp -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 SparseArray_Complex_methods.c -o SparseArray_Complex_methods.o gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/XVector/include' -fopenmp -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 SparseArray_Logic_methods.c -o SparseArray_Logic_methods.o gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/XVector/include' -fopenmp -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 SparseArray_Math_methods.c -o SparseArray_Math_methods.o gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/XVector/include' -fopenmp -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 SparseArray_abind.c -o SparseArray_abind.o gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/XVector/include' -fopenmp -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 SparseArray_aperm.c -o SparseArray_aperm.o gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/XVector/include' -fopenmp -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 SparseArray_dim_tuning.c -o SparseArray_dim_tuning.o gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/XVector/include' -fopenmp -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 SparseArray_matrixStats.c -o SparseArray_matrixStats.o gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/XVector/include' -fopenmp -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 SparseArray_misc_methods.c -o SparseArray_misc_methods.o gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/XVector/include' -fopenmp -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 SparseArray_subassignment.c -o SparseArray_subassignment.o gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/XVector/include' -fopenmp -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 SparseArray_subassignment_OLD.c -o SparseArray_subassignment_OLD.o gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/XVector/include' -fopenmp -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 SparseArray_subsetting.c -o SparseArray_subsetting.o gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/XVector/include' -fopenmp -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 SparseArray_summarization.c -o SparseArray_summarization.o gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/XVector/include' -fopenmp -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 SparseMatrix_mult.c -o SparseMatrix_mult.o gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/XVector/include' -fopenmp -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 SparseVec.c -o SparseVec.o gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/XVector/include' -fopenmp -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 SparseVec_Arith.c -o SparseVec_Arith.o gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/XVector/include' -fopenmp -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 SparseVec_Compare.c -o SparseVec_Compare.o gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/XVector/include' -fopenmp -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 SparseVec_Logic.c -o SparseVec_Logic.o gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/XVector/include' -fopenmp -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 SparseVec_Math.c -o SparseVec_Math.o gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/XVector/include' -fopenmp -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 SparseVec_dotprod.c -o SparseVec_dotprod.o gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/XVector/include' -fopenmp -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 XVector_stubs.c -o XVector_stubs.o gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/XVector/include' -fopenmp -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 argcheck_utils.c -o argcheck_utils.o gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/XVector/include' -fopenmp -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 coerceVector2.c -o coerceVector2.o gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/XVector/include' -fopenmp -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 leaf_utils.c -o leaf_utils.o gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/XVector/include' -fopenmp -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 randomSparseArray.c -o randomSparseArray.o gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/XVector/include' -fopenmp -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 readSparseCSV.c -o readSparseCSV.o gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/XVector/include' -fopenmp -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 rowsum_methods.c -o rowsum_methods.o gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/XVector/include' -fopenmp -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 sparseMatrix_utils.c -o sparseMatrix_utils.o gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/XVector/include' -fopenmp -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 test.c -o test.o gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/S4Vectors/include' -I'/home/omnipath/local/R/4.5-3.21/IRanges/include' -I'/home/omnipath/local/R/4.5-3.21/XVector/include' -fopenmp -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 thread_control.c -o thread_control.o gcc -std=gnu2x -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -o SparseArray.so ExtendableJaggedArray.o IRanges_stubs.o OPBufTree.o R_init_SparseArray.o Rvector_summarization.o Rvector_utils.o S4Vectors_stubs.o SBT_utils.o SVT_SparseArray_class.o SparseArray_Arith_methods.o SparseArray_Compare_methods.o SparseArray_Complex_methods.o SparseArray_Logic_methods.o SparseArray_Math_methods.o SparseArray_abind.o SparseArray_aperm.o SparseArray_dim_tuning.o SparseArray_matrixStats.o SparseArray_misc_methods.o SparseArray_subassignment.o SparseArray_subassignment_OLD.o SparseArray_subsetting.o SparseArray_summarization.o SparseMatrix_mult.o SparseVec.o SparseVec_Arith.o SparseVec_Compare.o SparseVec_Logic.o SparseVec_Math.o SparseVec_dotprod.o XVector_stubs.o argcheck_utils.o coerceVector2.o leaf_utils.o randomSparseArray.o readSparseCSV.o rowsum_methods.o sparseMatrix_utils.o test.o thread_control.o -fopenmp -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.5-3.21/00LOCK-SparseArray/00new/SparseArray/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 (SparseArray) * 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 ‘AnnotationHub’ ... ** this is package ‘AnnotationHub’ version ‘3.16.1’ ** using staged installation ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (AnnotationHub) * 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’ * installing *source* package ‘ExperimentHub’ ... ** this is package ‘ExperimentHub’ version ‘2.16.1’ ** 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 (ExperimentHub) The downloaded source packages are in ‘/tmp/RtmpafPfwA/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/RtmpafPfwA/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: 2025-07-24 19:31:54 CEST ]