[ Started: 2025-03-19 01:20:33 CET ]
[ mistyR v1.10.0 for BioC-3.21 from https://github.com/saezlab/mistyR@master (8bb8ba9 2024-03-25 14:10:38) ]

[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)
Old packages: 'cosmosR', 'fgsea'
trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/cosmosR_1.15.0.tar.gz'
trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/fgsea_1.33.2.tar.gz'
* installing *source* package ‘cosmosR’ ...
** this is package ‘cosmosR’ version ‘1.15.0’
** 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)
* installing *source* package ‘fgsea’ ...
** this is package ‘fgsea’ version ‘1.33.2’
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.5-3.21/Rcpp/include' -I'/home/omnipath/local/R/4.5-3.21/BH/include' -I/usr/local/include    -fpic  -g -O2   -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.5-3.21/Rcpp/include' -I'/home/omnipath/local/R/4.5-3.21/BH/include' -I/usr/local/include    -fpic  -g -O2   -c ScoreCalculation.cpp -o ScoreCalculation.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.5-3.21/Rcpp/include' -I'/home/omnipath/local/R/4.5-3.21/BH/include' -I/usr/local/include    -fpic  -g -O2   -c ScoreRuler.cpp -o ScoreRuler.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.5-3.21/Rcpp/include' -I'/home/omnipath/local/R/4.5-3.21/BH/include' -I/usr/local/include    -fpic  -g -O2   -c esCalculation.cpp -o esCalculation.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.5-3.21/Rcpp/include' -I'/home/omnipath/local/R/4.5-3.21/BH/include' -I/usr/local/include    -fpic  -g -O2   -c fastGSEA.cpp -o fastGSEA.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.5-3.21/Rcpp/include' -I'/home/omnipath/local/R/4.5-3.21/BH/include' -I/usr/local/include    -fpic  -g -O2   -c fgseaMultilevel.cpp -o fgseaMultilevel.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.5-3.21/Rcpp/include' -I'/home/omnipath/local/R/4.5-3.21/BH/include' -I/usr/local/include    -fpic  -g -O2   -c fgseaMultilevelSupplement.cpp -o fgseaMultilevelSupplement.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.5-3.21/Rcpp/include' -I'/home/omnipath/local/R/4.5-3.21/BH/include' -I/usr/local/include    -fpic  -g -O2   -c geseca.cpp -o geseca.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.5-3.21/Rcpp/include' -I'/home/omnipath/local/R/4.5-3.21/BH/include' -I/usr/local/include    -fpic  -g -O2   -c util.cpp -o util.o
g++ -std=gnu++17 -shared -L/usr/local/lib -o fgsea.so RcppExports.o ScoreCalculation.o ScoreRuler.o esCalculation.o fastGSEA.o fgseaMultilevel.o fgseaMultilevelSupplement.o geseca.o util.o
installing to /home/omnipath/local/R/4.5-3.21/00LOCK-fgsea/00new/fgsea/libs
** R
** data
*** moving datasets to lazyload DB
** 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 (fgsea)

The downloaded source packages are in
	‘/tmp/RtmpTZMFgP/downloaded_packages’
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' 

[ Finished: 2025-03-19 01:21:11 CET ]