[ Started: 2026-10-20 17:32:15 CEST ]
[ CARNIVAL v2.5.1 for BioC-3.24 from https://github.com/saezlab/CARNIVAL@dev (81a0120 2022-03-17 09:59:10) ]
[ R version 4.6.1 Patched (2026-10-12 r90666) -- "Happy Hop" at /opt/R-4.6-patched/bin ]

[1] "Libraries: "                      "/home/omnipath/local/R/4.6-3.24" 
[3] "/home/omnipath/local/R/4.6"       "/opt/R-4.6-patched/lib/R/library"
Bioconductor version 3.24 (BiocManager 1.30.27), R 4.6.1 Patched (2026-10-12
  r90666)
Old packages: 'edgeR'
trying URL 'https://bioconductor.org/packages/3.24/bioc/src/contrib/edgeR_4.99.10.tar.gz'
Content type 'application/gzip' length 3146016 bytes (3.0 MB)
==================================================
downloaded 3.0 MB

* installing *source* package ‘edgeR’ ...
** this is package ‘edgeR’ version ‘4.99.10’
** package ‘edgeR’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
using Fortran compiler: ‘GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
gcc -std=gnu2x -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fpic  -g -O2  -c R_exports.c -o R_exports.o
gcc -std=gnu2x -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fpic  -g -O2  -c R_process_hairpin_reads.c -o R_process_hairpin_reads.o
gcc -std=gnu2x -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fpic  -g -O2  -c add_prior_count.c -o add_prior_count.o
gcc -std=gnu2x -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fpic  -g -O2  -c binomial.c -o binomial.o
gcc -std=gnu2x -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fpic  -g -O2  -c compute_apl.c -o compute_apl.o
gcc -std=gnu2x -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fpic  -g -O2  -c compute_cpm.c -o compute_cpm.o
gcc -std=gnu2x -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fpic  -g -O2  -c compute_nbdev.c -o compute_nbdev.o
gcc -std=gnu2x -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fpic  -g -O2  -c coxreid.c -o coxreid.o
gcc -std=gnu2x -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fpic  -g -O2  -c diffsplice.c -o diffsplice.o
gcc -std=gnu2x -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fpic  -g -O2  -c exact_test_by_dev.c -o exact_test_by_dev.o
gcc -std=gnu2x -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fpic  -g -O2  -c ftest.c -o ftest.o
gcc -std=gnu2x -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fpic  -g -O2  -c glm.c -o glm.o
gcc -std=gnu2x -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fpic  -g -O2  -c good_turing.c -o good_turing.o
gcc -std=gnu2x -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fpic  -g -O2  -c init.c -o init.o
gcc -std=gnu2x -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fpic  -g -O2  -c interpolator.c -o interpolator.o
gcc -std=gnu2x -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fpic  -g -O2  -c loess_by_col.c -o loess_by_col.o
gfortran  -fpic  -g -O2  -c lowess.f -o lowess.o
gcc -std=gnu2x -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fpic  -g -O2  -c object.c -o object.o
gcc -std=gnu2x -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fpic  -g -O2  -c pred_fc.c -o pred_fc.o
gcc -std=gnu2x -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fpic  -g -O2  -c ql_bin.c -o ql_bin.o
gcc -std=gnu2x -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fpic  -g -O2  -c ql_glm.c -o ql_glm.o
gcc -std=gnu2x -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fpic  -g -O2  -c ql_weights.c -o ql_weights.o
gcc -std=gnu2x -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fpic  -g -O2  -c sample_weights.c -o sample_weights.o
gfortran  -fpic  -g -O2  -c spline.f -o spline.o
gcc -std=gnu2x -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp -fpic  -g -O2  -c utils.c -o utils.o
gcc -std=gnu2x -shared -L/opt/R-4.6-patched/lib/R/lib -L/usr/local/lib -o edgeR.so R_exports.o R_process_hairpin_reads.o add_prior_count.o binomial.o compute_apl.o compute_cpm.o compute_nbdev.o coxreid.o diffsplice.o exact_test_by_dev.o ftest.o glm.o good_turing.o init.o interpolator.o loess_by_col.o lowess.o object.o pred_fc.o ql_bin.o ql_glm.o ql_weights.o sample_weights.o spline.o utils.o -fopenmp -llapack -L/opt/R-4.6-patched/lib/R/lib -lRblas -lgfortran -lm -lquadmath -lgfortran -lm -lquadmath -L/opt/R-4.6-patched/lib/R/lib -lR
installing to /home/omnipath/local/R/4.6-3.24/00LOCK-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/RtmpG2Qc87/downloaded_packages’
Bioconductor version 3.24 (BiocManager 1.30.27), R 4.6.1 Patched (2026-10-12
  r90666)
Warning message:
package(s) not installed when version(s) same as or greater than current; use
  `force = TRUE` to re-install: 'BiocCheck' 

[ Finished: 2026-10-20 17:32:37 CEST ]