[ Started: 2023-04-25 00:09:18 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-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 4.3.0 (2023-04-21)
Old packages: 'BiocCheck', 'edgeR', 'limma'
trying URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/BiocCheck_1.35.20.tar.gz'
Content type 'application/x-gzip' length 4373079 bytes (4.2 MB)
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downloaded 4.2 MB

trying URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/edgeR_3.41.9.tar.gz'
Content type 'application/x-gzip' length 1814928 bytes (1.7 MB)
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downloaded 1.7 MB

trying URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/limma_3.55.10.tar.gz'
Content type 'application/x-gzip' length 1514989 bytes (1.4 MB)
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downloaded 1.4 MB

* installing *source* package ‘BiocCheck’ ...
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (BiocCheck)
* 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-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/4.3-3.17/00LOCK-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)
* installing *source* package ‘edgeR’ ...
** using staged installation
** 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’
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -c R_add_prior_count.cpp -o R_add_prior_count.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -c R_ave_log_cpm.cpp -o R_ave_log_cpm.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -c R_calculate_cpm.cpp -o R_calculate_cpm.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -c R_check_poisson_bound.cpp -o R_check_poisson_bound.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -c R_compute_apl.cpp -o R_compute_apl.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -c R_compute_nbdev.cpp -o R_compute_nbdev.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -c R_exact_test_by_deviance.cpp -o R_exact_test_by_deviance.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -c R_fit_levenberg.cpp -o R_fit_levenberg.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -c R_fit_one_group.cpp -o R_fit_one_group.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -c R_get_one_way_fitted.cpp -o R_get_one_way_fitted.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -c R_initialize_levenberg.cpp -o R_initialize_levenberg.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -c R_loess_by_col.cpp -o R_loess_by_col.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -c R_maximize_interpolant.cpp -o R_maximize_interpolant.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -c R_process_hairpin_reads.c -o R_process_hairpin_reads.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -c R_simple_good_turing.cpp -o R_simple_good_turing.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -c add_prior.cpp -o add_prior.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -c adj_coxreid.cpp -o adj_coxreid.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -c fmm_spline.c -o fmm_spline.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -c glm_levenberg.cpp -o glm_levenberg.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -c glm_one_group.cpp -o glm_one_group.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -c init.cpp -o init.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -c interpolator.cpp -o interpolator.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -c nbdev.cpp -o nbdev.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -c objects.cpp -o objects.o
g++ -std=gnu++17 -shared -L/usr/local/lib -o edgeR.so R_add_prior_count.o R_ave_log_cpm.o R_calculate_cpm.o R_check_poisson_bound.o R_compute_apl.o R_compute_nbdev.o R_exact_test_by_deviance.o R_fit_levenberg.o R_fit_one_group.o R_get_one_way_fitted.o R_initialize_levenberg.o R_loess_by_col.o R_maximize_interpolant.o R_process_hairpin_reads.o R_simple_good_turing.o add_prior.o adj_coxreid.o fmm_spline.o glm_levenberg.o glm_one_group.o init.o interpolator.o nbdev.o objects.o -llapack -L/opt/R-devel/lib/R/lib -lRblas -lgfortran -lm -lquadmath
installing to /home/omnipath/local/R/4.3-3.17/00LOCK-edgeR/00new/edgeR/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 (edgeR)

The downloaded source packages are in
	‘/tmp/RtmpIdYQ4r/downloaded_packages’
Bioconductor version 3.17 (BiocManager 1.30.20), R 4.3.0 (2023-04-21)
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: 2023-04-25 00:10:59 CEST ]