[ Started: 2023-04-10 23:25:42 CEST ] [ CARNIVAL v2.7.2 for BioC-3.16 from https://github.com/saezlab/CARNIVAL@master ] [1] "Libraries: " "/home/omnipath/local/R/4.2-3.16" [3] "/home/omnipath/local/R/4.2" "/usr/lib/R/library" Warning: unable to access index for repository https://cran.uni-muenster.de/src/contrib: cannot open URL 'https://cran.uni-muenster.de/src/contrib/PACKAGES' Warning: unable to access index for repository https://cran.uni-muenster.de/src/contrib: cannot open URL 'https://cran.uni-muenster.de/src/contrib/PACKAGES' 'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details. Replacement repositories: CRAN: https://cloud.r-project.org Bioconductor version 3.16 (BiocManager 1.30.20), R 4.2.3 (2023-03-15) Old packages: 'beachmat', 'rhdf5' trying URL 'https://bioconductor.org/packages/3.16/bioc/src/contrib/beachmat_2.14.2.tar.gz' Content type 'application/x-gzip' length 1302937 bytes (1.2 MB) ================================================== downloaded 1.2 MB trying URL 'https://bioconductor.org/packages/3.16/bioc/src/contrib/rhdf5_2.42.1.tar.gz' Content type 'application/x-gzip' length 1240854 bytes (1.2 MB) ================================================== downloaded 1.2 MB * installing *source* package ‘beachmat’ ... ** using staged installation ** libs g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c fragment_sparse_rows.cpp -o fragment_sparse_rows.o g++ -std=gnu++11 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o beachmat.so RcppExports.o fragment_sparse_rows.o -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.2-3.16/00LOCK-beachmat/00new/beachmat/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 (beachmat) * installing *source* package ‘rhdf5’ ... ** using staged installation configure: creating ./config.status config.status: creating src/external_filters.h ** libs gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rhdf5lib/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c H5.c -o H5.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rhdf5lib/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c H5A.c -o H5A.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rhdf5lib/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c H5D.c -o H5D.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rhdf5lib/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c H5E.c -o H5E.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rhdf5lib/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c H5F.c -o H5F.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rhdf5lib/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c H5G.c -o H5G.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rhdf5lib/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c H5I.c -o H5I.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rhdf5lib/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c H5L.c -o H5L.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rhdf5lib/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c H5O.c -o H5O.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rhdf5lib/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c H5P.c -o H5P.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rhdf5lib/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c H5R.c -o H5R.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rhdf5lib/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c H5S.c -o H5S.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rhdf5lib/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c H5S_extras.c -o H5S_extras.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rhdf5lib/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c H5T.c -o H5T.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rhdf5lib/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c H5Z.c -o H5Z.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rhdf5lib/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c H5constants.c -o H5constants.o g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rhdf5lib/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c HandleList.cpp -o HandleList.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rhdf5lib/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c HandleListWrap.c -o HandleListWrap.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rhdf5lib/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c bit64conversion.c -o bit64conversion.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rhdf5lib/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c external_filters.c -o external_filters.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rhdf5lib/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c h5dump.c -o h5dump.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rhdf5lib/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c h5ls.c -o h5ls.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rhdf5lib/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c h5testLock.c -o h5testLock.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rhdf5lib/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c h5writeDataFrame.c -o h5writeDataFrame.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rhdf5lib/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c printdatatype.c -o printdatatype.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rhdf5lib/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c utils.c -o utils.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rhdf5lib/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c wrap.c -o wrap.o g++ -std=gnu++14 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o rhdf5.so H5.o H5A.o H5D.o H5E.o H5F.o H5G.o H5I.o H5L.o H5O.o H5P.o H5R.o H5S.o H5S_extras.o H5T.o H5Z.o H5constants.o HandleList.o HandleListWrap.o bit64conversion.o external_filters.o h5dump.o h5ls.o h5testLock.o h5writeDataFrame.o printdatatype.o utils.o wrap.o /home/omnipath/local/R/4.2-3.16/Rhdf5lib/lib/libhdf5.a -lcrypto -lcurl -lsz -laec -lz -ldl -lm -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.2-3.16/00LOCK-rhdf5/00new/rhdf5/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 (rhdf5) The downloaded source packages are in ‘/tmp/RtmpGmYxO7/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 3.16 (BiocManager 1.30.20), R 4.2.3 (2023-03-15) Warning message: package(s) not installed when version(s) same as or greater than current; use `force = TRUE` to re-install: 'BiocCheck' Skipping 17 packages not available: BiocManager, yaml, rmarkdown, knitr, bookdown, sessioninfo, testthat, covr, RefManageR, rjson, tidyr, tibble, dplyr, igraph, lpSolve, stringr, readr [ Finished: 2023-04-10 23:26:16 CEST ]