[ Started: 2026-10-13 19:37:27 CEST ]
[ progeny v1.17.3 for BioC-3.24 from https://github.com/saezlab/progeny@master (cad6be0 2023-01-30 11:01:10) ]
[ 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: 'GSVA'
trying URL 'https://bioconductor.org/packages/3.24/bioc/src/contrib/GSVA_2.7.23.tar.gz'
Content type 'application/gzip' length 6215084 bytes (5.9 MB)
==================================================
downloaded 5.9 MB

* installing *source* package ‘GSVA’ ...
** this is package ‘GSVA’ version ‘2.7.23’
** package ‘GSVA’ 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’
gcc -std=gnu2x -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.6-3.24/cli/include' -I/usr/local/include    -fpic  -g -O2  -c average.c -o average.o
gcc -std=gnu2x -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.6-3.24/cli/include' -I/usr/local/include    -fpic  -g -O2  -c ecdfvals.c -o ecdfvals.o
gcc -std=gnu2x -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.6-3.24/cli/include' -I/usr/local/include    -fpic  -g -O2  -c kcdfvals.c -o kcdfvals.o
gcc -std=gnu2x -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.6-3.24/cli/include' -I/usr/local/include    -fpic  -g -O2  -c kernel_estimation.c -o kernel_estimation.o
gcc -std=gnu2x -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.6-3.24/cli/include' -I/usr/local/include    -fpic  -g -O2  -c ks_test.c -o ks_test.o
gcc -std=gnu2x -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.6-3.24/cli/include' -I/usr/local/include    -fpic  -g -O2  -c register_cmethods.c -o register_cmethods.o
gcc -std=gnu2x -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.6-3.24/cli/include' -I/usr/local/include    -fpic  -g -O2  -c row_rngs_nzrngs.c -o row_rngs_nzrngs.o
gcc -std=gnu2x -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.6-3.24/cli/include' -I/usr/local/include    -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 GSVA.so average.o ecdfvals.o kcdfvals.o kernel_estimation.o ks_test.o register_cmethods.o row_rngs_nzrngs.o utils.o -L/opt/R-4.6-patched/lib/R/lib -lR
installing to /home/omnipath/local/R/4.6-3.24/00LOCK-GSVA/00new/GSVA/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 (GSVA)

The downloaded source packages are in
	‘/tmp/Rtmp8z6KDw/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' 
DESeq2  (NA -> 1.53.6) [CRAN]
biomaRt (NA -> 2.69.3) [CRAN]
airway  (NA -> 1.33.2) [CRAN]
Installing 3 packages: DESeq2, biomaRt, airway
trying URL 'https://bioconductor.org/packages/3.24/bioc/src/contrib/DESeq2_1.53.6.tar.gz'
trying URL 'https://bioconductor.org/packages/3.24/bioc/src/contrib/biomaRt_2.69.3.tar.gz'
trying URL 'https://bioconductor.org/packages/3.24/data/experiment/src/contrib/airway_1.33.2.tar.gz'
* installing *source* package ‘DESeq2’ ...
** this is package ‘DESeq2’ version ‘1.53.6’
** package ‘DESeq2’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
g++ -std=gnu++20 -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.6-3.24/Rcpp/include' -I'/home/omnipath/local/R/4.6-3.24/RcppArmadillo/include' -I/usr/local/include    -fpic  -g -O2   -c DESeq2.cpp -o DESeq2.o
g++ -std=gnu++20 -I"/opt/R-4.6-patched/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.6-3.24/Rcpp/include' -I'/home/omnipath/local/R/4.6-3.24/RcppArmadillo/include' -I/usr/local/include    -fpic  -g -O2   -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++20 -shared -L/opt/R-4.6-patched/lib/R/lib -L/usr/local/lib -o DESeq2.so DESeq2.o RcppExports.o -llapack -L/opt/R-4.6-patched/lib/R/lib -lRblas -lgfortran -lm -lquadmath -L/opt/R-4.6-patched/lib/R/lib -lR
installing to /home/omnipath/local/R/4.6-3.24/00LOCK-DESeq2/00new/DESeq2/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 (DESeq2)
* installing *source* package ‘biomaRt’ ...
** this is package ‘biomaRt’ version ‘2.69.3’
** package ‘biomaRt’ successfully unpacked and MD5 sums checked
** 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 (biomaRt)
* installing *source* package ‘airway’ ...
** this is package ‘airway’ version ‘1.33.2’
** using staged installation
** data
** inst
** 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 (airway)

The downloaded source packages are in
	‘/tmp/Rtmp8z6KDw/downloaded_packages’
[ Finished: 2026-10-13 19:39:14 CEST ]