[ Started: 2023-04-06 18:27:41 CEST ] [ decoupleR v2.3.3 for BioC-3.17 from https://github.com/saezlab/decoupleR@master ] [1] "Libraries: " "/home/omnipath/local/R/4.3-3.17" [3] "/home/omnipath/local/R/4.3" "/opt/R-devel/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 Under development (unstable) (2023-03-16 r83996) Old packages: 'rhdf5' trying URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/rhdf5_2.43.3.tar.gz' Content type 'application/x-gzip' length 1248859 bytes (1.2 MB) ================================================== downloaded 1.2 MB * 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-devel/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-devel/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-devel/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-devel/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-devel/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-devel/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-devel/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-devel/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-devel/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-devel/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-devel/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-devel/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-devel/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-devel/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-devel/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-devel/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-devel/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-devel/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-devel/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-devel/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-devel/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-devel/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-devel/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-devel/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-devel/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-devel/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-devel/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) The downloaded source packages are in ‘/tmp/RtmpcrdhE9/downloaded_packages’ Bioconductor version 3.17 (BiocManager 1.30.20), R Under development (unstable) (2023-03-16 r83996) Warning message: package(s) not installed when version(s) same as or greater than current; use `force = TRUE` to re-install: 'BiocCheck' OmnipathR (ab0e87310... -> f23a107b3...) [GitHub] Skipping 51 packages not available: matrixStats, RCurl, crayon, png, RSQLite, httr, xtable, DBI, XML, Rcpp, cpp11, BH, snow, futile.logger, rsvd, irlba, BiocManager, yaml, rmarkdown, knitr, bookdown, shiny, R.utils, mixtools, data.table, fastmatch, cowplot, ggplot2, e1071, patchwork, ggrepel, Seurat, testthat, pheatmap, sessioninfo, roxygen2, RefManageR, pkgdown, covr, ranger, glmnet, withr, tidyselect, tidyr, tibble, stringr, rlang, purrr, magrittr, dplyr, broom Downloading GitHub repo saezlab/OmnipathR@HEAD Skipping 26 packages not available: yaml, xml2, withr, tidyselect, tidyr, tibble, stringr, rvest, rmarkdown, rlang, readxl, readr, rappdirs, purrr, progress, magrittr, logger, later, jsonlite, igraph, httr, dplyr, digest, curl, crayon, checkmate ── R CMD build ───────────────────────────────────────────────────────────────── * checking for file ‘/tmp/RtmpcrdhE9/remotes47d824c809988/saezlab-OmnipathR-f23a107/DESCRIPTION’ ... OK * preparing ‘OmnipathR’: * checking DESCRIPTION meta-information ... OK * checking for LF line-endings in source and make files and shell scripts * checking for empty or unneeded directories * looking to see if a ‘data/datalist’ file should be added * building ‘OmnipathR_3.7.12.tar.gz’ * installing *source* package ‘OmnipathR’ ... ** 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 [2023-04-06 18:28:05] [INFO] [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`. [2023-04-06 18:28:05] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-04-06 18:28:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-06 18:28:05] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2023-04-06 18:28:05] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2023-04-06 18:28:05] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2023-04-06 18:28:05] [TRACE] [OmnipathR] Contains 1 files. [2023-04-06 18:28:05] [TRACE] [OmnipathR] Cache is locked: FALSE. [2023-04-06 18:28:05] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-04-06 18:28:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-06 18:28:05] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2023-04-06 18:28:05] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`. [2023-04-06 18:28:05] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.17/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8). [2023-04-06 18:28:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-06 18:28:05] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.17/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2023-04-06 18:28:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-06 18:28:05] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.17/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8). [2023-04-06 18:28:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-06 18:28:05] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.17/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2023-04-06 18:28:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-06 18:28:05] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2023-04-06 18:28:06] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-04-06 18:28:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-06 18:28:06] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2023-04-06 18:28:06] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2023-04-06 18:28:06] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2023-04-06 18:28:06] [TRACE] [OmnipathR] Contains 1 files. [2023-04-06 18:28:06] [TRACE] [OmnipathR] Cache is locked: FALSE. [2023-04-06 18:28:06] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-04-06 18:28:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-06 18:28:06] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2023-04-06 18:28:06] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`. [2023-04-06 18:28:06] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.17/OmnipathR/db/db_def.json` (encoding: UTF-8). [2023-04-06 18:28:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-06 18:28:06] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.17/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2023-04-06 18:28:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-06 18:28:06] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.17/OmnipathR/internal/urls.json` (encoding: UTF-8). [2023-04-06 18:28:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-06 18:28:06] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.17/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2023-04-06 18:28:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-06 18:28:06] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package keeps a record of temporary installation path * DONE (OmnipathR) [ Finished: 2023-04-06 18:28:06 CEST ]