[ Started: 2025-07-13 03:19:18 CEST ] [ MetaProViz v3.0.1 for BioC-3.21 from https://github.com/saezlab/MetaProViz@development (c0029b6 2025-07-12 14:10:31) ] [1] "Libraries: " "/home/omnipath/local/R/4.5-3.21" [3] "/home/omnipath/local/R/4.5" "/opt/R-devel/lib/R/library" Bioconductor version 3.21 (BiocManager 1.30.26), R Under development (unstable) (2025-02-12 r87715) Old packages: 'decoupleR' trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/decoupleR_2.14.0.tar.gz' Content type 'application/x-gzip' length 5246125 bytes (5.0 MB) ================================================== downloaded 5.0 MB * installing *source* package ‘decoupleR’ ... ** this is package ‘decoupleR’ version ‘2.14.0’ ** 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 (decoupleR) The downloaded source packages are in ‘/tmp/Rtmp6QjECT/downloaded_packages’ Bioconductor version 3.21 (BiocManager 1.30.26), R Under development (unstable) (2025-02-12 r87715) Warning message: package(s) not installed when version(s) same as or greater than current; use `force = TRUE` to re-install: 'BiocCheck' cosmosR (1.16.0 -> 5a38475ce...) [GitHub] NA (NA -> 14d0e4322...) [Git] Downloading git repo https://git.bioconductor.org/packages/limma.git '/usr/bin/git' clone --depth 1 --no-hardlinks https://git.bioconductor.org/packages/limma.git /tmp/Rtmp6QjECT/file30aeec2185f225 Cloning into '/tmp/Rtmp6QjECT/file30aeec2185f225'... ── R CMD build ───────────────────────────────────────────────────────────────── * checking for file ‘/tmp/Rtmp6QjECT/file30aeec2185f225/DESCRIPTION’ ... OK * preparing ‘limma’: * checking DESCRIPTION meta-information ... OK * cleaning src * checking for LF line-endings in source and make files and shell scripts * checking for empty or unneeded directories * building ‘limma_3.65.1.tar.gz’ * installing *source* package ‘limma’ ... ** this is package ‘limma’ version ‘3.65.1’ ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c init.c -o init.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c normexp.c -o normexp.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c weighted_lowess.c -o weighted_lowess.o gcc -shared -L/usr/local/lib -o limma.so init.o normexp.o weighted_lowess.o installing to /home/omnipath/local/R/4.5-3.21/00LOCK-limma/00new/limma/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 (limma) Skipping 1 packages ahead of CRAN: rprojroot Downloading GitHub repo saezlab/cosmosR@HEAD ── R CMD build ───────────────────────────────────────────────────────────────── * checking for file ‘/tmp/Rtmp6QjECT/remotes30aeec6eb8e84d/saezlab-cosmosR-5a38475/DESCRIPTION’ ... OK * preparing ‘cosmosR’: * 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 ‘cosmosR_1.9.1.tar.gz’ Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: ‘cosmosR/vignettes/net_compr_MOON_files/figure-markdown_strict/extract_subnetwork_from_scored_MOON_network_1.png’ * installing *source* package ‘cosmosR’ ... ** this is package ‘cosmosR’ version ‘1.9.1’ ** using staged installation ** R ** data ** 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 (cosmosR) Downloading git repo https://git.bioconductor.org/packages/limma.git '/usr/bin/git' clone --depth 1 --no-hardlinks https://git.bioconductor.org/packages/limma.git /tmp/Rtmp6QjECT/file30aeec1963ca38 Cloning into '/tmp/Rtmp6QjECT/file30aeec1963ca38'... ── R CMD build ───────────────────────────────────────────────────────────────── * checking for file ‘/tmp/Rtmp6QjECT/file30aeec1963ca38/DESCRIPTION’ ... OK * preparing ‘limma’: * checking DESCRIPTION meta-information ... OK * cleaning src * checking for LF line-endings in source and make files and shell scripts * checking for empty or unneeded directories * building ‘limma_3.65.1.tar.gz’ * installing *source* package ‘limma’ ... ** this is package ‘limma’ version ‘3.65.1’ ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c init.c -o init.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c normexp.c -o normexp.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c weighted_lowess.c -o weighted_lowess.o gcc -shared -L/usr/local/lib -o limma.so init.o normexp.o weighted_lowess.o installing to /home/omnipath/local/R/4.5-3.21/00LOCK-limma/00new/limma/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 (limma) [ Finished: 2025-07-13 03:20:16 CEST ]