[ Started: 2023-04-19 00:19:01 CEST ] [ CARNIVAL v2.7.2 for BioC-3.17 from https://github.com/saezlab/CARNIVAL@master ] [1] "Libraries: " "/home/omnipath/local/R/4.3-3.17" [3] "/home/omnipath/local/R/4.3" "/opt/R-beta/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' Bioconductor version 3.17 (BiocManager 1.30.20), R 4.3.0 RC (2023-04-13 r84266) Old packages: 'fontawesome', 'GSVA', 'processx', 'ps', 'rhdf5', 'tinytex' trying URL 'https://cloud.r-project.org/src/contrib/fontawesome_0.5.1.tar.gz' Content type 'application/x-gzip' length 1276983 bytes (1.2 MB) ================================================== downloaded 1.2 MB trying URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/GSVA_1.47.3.tar.gz' Content type 'application/x-gzip' length 2268069 bytes (2.2 MB) ================================================== downloaded 2.2 MB trying URL 'https://cloud.r-project.org/src/contrib/processx_3.8.1.tar.gz' Content type 'application/x-gzip' length 164170 bytes (160 KB) ================================================== downloaded 160 KB trying URL 'https://cloud.r-project.org/src/contrib/ps_1.7.5.tar.gz' Content type 'application/x-gzip' length 129213 bytes (126 KB) ================================================== downloaded 126 KB trying URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/rhdf5_2.43.5.tar.gz' Content type 'application/x-gzip' length 1249815 bytes (1.2 MB) ================================================== downloaded 1.2 MB trying URL 'https://cloud.r-project.org/src/contrib/tinytex_0.45.tar.gz' Content type 'application/x-gzip' length 33082 bytes (32 KB) ================================================== downloaded 32 KB * installing *source* package ‘fontawesome’ ... ** package ‘fontawesome’ 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 ** 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 (fontawesome) * installing *source* package ‘GSVA’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’ gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c kernel_estimation.c -o kernel_estimation.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c ks_test.c -o ks_test.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c register_cmethods.c -o register_cmethods.o gcc -shared -L/usr/local/lib -o GSVA.so kernel_estimation.o ks_test.o register_cmethods.o installing to /home/omnipath/local/R/4.3-3.17/00LOCK-GSVA/00new/GSVA/libs ** R ** inst ** byte-compile and prepare package for lazy loading Warning: replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘AnnotationDbi’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘AnnotationDbi’ ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location Warning: replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘AnnotationDbi’ ** testing if installed package keeps a record of temporary installation path * DONE (GSVA) * installing *source* package ‘ps’ ... ** package ‘ps’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’ gcc -g -O2 -L/usr/local/lib -Wall px.c -o px gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c init.c -o init.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c api-common.c -o api-common.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c common.c -o common.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c extra.c -o extra.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c dummy.c -o dummy.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c error-codes.c -o error-codes.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c posix.c -o posix.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c api-posix.c -o api-posix.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c linux.c -o linux.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c api-linux.c -o api-linux.o gcc -shared -L/usr/local/lib -o ps.so init.o api-common.o common.o extra.o dummy.o error-codes.o posix.o api-posix.o linux.o api-linux.o installing via 'install.libs.R' to /home/omnipath/local/R/4.3-3.17/00LOCK-ps/00new/ps ** R ** 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 ** 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 (ps) * installing *source* package ‘rhdf5’ ... ** using staged installation configure: creating ./config.status config.status: creating src/external_filters.h ** libs using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’ using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’ gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c H5.c -o H5.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c H5A.c -o H5A.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c H5D.c -o H5D.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c H5E.c -o H5E.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c H5F.c -o H5F.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c H5G.c -o H5G.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c H5I.c -o H5I.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c H5L.c -o H5L.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c H5O.c -o H5O.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c H5P.c -o H5P.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c H5R.c -o H5R.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c H5S.c -o H5S.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c H5S_extras.c -o H5S_extras.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c H5T.c -o H5T.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c H5Z.c -o H5Z.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c H5constants.c -o H5constants.o g++ -std=gnu++17 -I"/opt/R-beta/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c HandleList.cpp -o HandleList.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c HandleListWrap.c -o HandleListWrap.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c bit64conversion.c -o bit64conversion.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c external_filters.c -o external_filters.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c h5dump.c -o h5dump.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c h5ls.c -o h5ls.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c h5testLock.c -o h5testLock.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c h5writeDataFrame.c -o h5writeDataFrame.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c printdatatype.c -o printdatatype.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c utils.c -o utils.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c wrap.c -o wrap.o g++ -std=gnu++17 -shared -L/usr/local/lib -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/4.3-3.17/Rhdf5lib/lib/libhdf5.a -lcrypto -lcurl -lsz -laec -lz -ldl -lm installing to /home/omnipath/local/R/4.3-3.17/00LOCK-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) * installing *source* package ‘tinytex’ ... ** package ‘tinytex’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** 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 (tinytex) * installing *source* package ‘processx’ ... ** package ‘processx’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’ gcc -g -O2 -L/usr/local/lib -Wall tools/px.c -o tools/px gcc -g -O2 -L/usr/local/lib -I../inst/include -Wall tools/sock.c -o tools/sock gcc -g -O2 -L/usr/local/lib supervisor/supervisor.c \ supervisor/utils.c -o supervisor/supervisor gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c base64.c -o base64.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c client.c -o client.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c errors.c -o errors.o gcc -shared -L/usr/local/lib -o client.so base64.o client.o errors.o \ if [ -n "" ]; then \ echo Removing libR.so dependency from client.so; \ patchelf --remove-needed libR.so client.so; \ fi gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c init.c -o init.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c poll.c -o poll.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c processx-connection.c -o processx-connection.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c processx-vector.c -o processx-vector.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c create-time.c -o create-time.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c unix/childlist.c -o unix/childlist.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c unix/connection.c -o unix/connection.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c unix/processx.c -o unix/processx.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c unix/sigchld.c -o unix/sigchld.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c unix/utils.c -o unix/utils.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c unix/named_pipe.c -o unix/named_pipe.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c cleancall.c -o cleancall.o gcc -shared -L/usr/local/lib -o processx.so init.o poll.o errors.o processx-connection.o processx-vector.o create-time.o base64.o unix/childlist.o unix/connection.o unix/processx.o unix/sigchld.o unix/utils.o unix/named_pipe.o cleancall.o installing via 'install.libs.R' to /home/omnipath/local/R/4.3-3.17/00LOCK-processx/00new/processx ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** 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 (processx) The downloaded source packages are in ‘/tmp/RtmpRMlYez/downloaded_packages’ Bioconductor version 3.17 (BiocManager 1.30.20), R 4.3.0 RC (2023-04-13 r84266) 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: 2023-04-19 00:19:51 CEST ]