[ Started: 2025-03-20 01:02:40 CET ]
[ cosmosR v1.9.1 for BioC-3.21 from https://github.com/saezlab/cosmosR@master (ef9d5aa 2025-03-09 13:20:11) ]

[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 1.30.25), R Under development (unstable)
  (2025-02-12 r87715)
Bioconductor version 3.21 (BiocManager 1.30.25), 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' 
limma (8f044335d... -> 80931c691...) [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/RtmpLp6TRt/file14758643df2b2b
Cloning into '/tmp/RtmpLp6TRt/file14758643df2b2b'...

── R CMD build ─────────────────────────────────────────────────────────────────
* checking for file ‘/tmp/RtmpLp6TRt/file14758643df2b2b/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_3.63.10.tar.gz’

* installing *source* package ‘limma’ ...
** this is package ‘limma’ version ‘3.63.10’
** 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: 2025-03-20 01:03:02 CET ]