[ Started: 2023-04-11 23:41:15 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 beta (2023-04-08
  r84203)
Old packages: 'fgsea', 'GSEABase', 'limma'
trying URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/fgsea_1.25.2.tar.gz'
Content type 'application/x-gzip' length 4953557 bytes (4.7 MB)
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downloaded 4.7 MB

trying URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/GSEABase_1.61.2.tar.gz'
Content type 'application/x-gzip' length 298946 bytes (291 KB)
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downloaded 291 KB

trying URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/limma_3.55.7.tar.gz'
Content type 'application/x-gzip' length 1516843 bytes (1.4 MB)
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downloaded 1.4 MB

* installing *source* package ‘fgsea’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
using C++11
g++ -std=gnu++11 -I"/opt/R-beta/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I'/home/omnipath/local/R/4.3-3.17/BH/include' -I/usr/local/include    -fpic  -g -O2  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/opt/R-beta/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I'/home/omnipath/local/R/4.3-3.17/BH/include' -I/usr/local/include    -fpic  -g -O2  -c ScoreCalculation.cpp -o ScoreCalculation.o
g++ -std=gnu++11 -I"/opt/R-beta/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I'/home/omnipath/local/R/4.3-3.17/BH/include' -I/usr/local/include    -fpic  -g -O2  -c ScoreRuler.cpp -o ScoreRuler.o
g++ -std=gnu++11 -I"/opt/R-beta/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I'/home/omnipath/local/R/4.3-3.17/BH/include' -I/usr/local/include    -fpic  -g -O2  -c esCalculation.cpp -o esCalculation.o
g++ -std=gnu++11 -I"/opt/R-beta/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I'/home/omnipath/local/R/4.3-3.17/BH/include' -I/usr/local/include    -fpic  -g -O2  -c fastGSEA.cpp -o fastGSEA.o
g++ -std=gnu++11 -I"/opt/R-beta/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I'/home/omnipath/local/R/4.3-3.17/BH/include' -I/usr/local/include    -fpic  -g -O2  -c fgseaMultilevel.cpp -o fgseaMultilevel.o
g++ -std=gnu++11 -I"/opt/R-beta/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I'/home/omnipath/local/R/4.3-3.17/BH/include' -I/usr/local/include    -fpic  -g -O2  -c fgseaMultilevelSupplement.cpp -o fgseaMultilevelSupplement.o
g++ -std=gnu++11 -I"/opt/R-beta/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I'/home/omnipath/local/R/4.3-3.17/BH/include' -I/usr/local/include    -fpic  -g -O2  -c geseca.cpp -o geseca.o
g++ -std=gnu++11 -I"/opt/R-beta/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I'/home/omnipath/local/R/4.3-3.17/BH/include' -I/usr/local/include    -fpic  -g -O2  -c util.cpp -o util.o
g++ -std=gnu++11 -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/4.3-3.17/00LOCK-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)
* installing *source* package ‘GSEABase’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning message:
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’
** 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 (GSEABase)
* installing *source* package ‘limma’ ...
** 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 init.c -o init.o
gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c normexp.c -o normexp.o
gcc -I"/opt/R-beta/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/4.3-3.17/00LOCK-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)

The downloaded source packages are in
	‘/tmp/Rtmpg3uY96/downloaded_packages’
Bioconductor version 3.17 (BiocManager 1.30.20), R 4.3.0 beta (2023-04-08
  r84203)
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: 2023-04-11 23:42:17 CEST ]