[ Started: 2025-02-13 21:14:25 CET ]
[ progeny v1.17.3 for BioC-3.21 from https://github.com/saezlab/progeny@master (cad6be0 2023-01-30 11:01:10) ]

[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)
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' 
DESeq2  (NA -> 1.47.3) [CRAN]
biomaRt (NA -> 2.63.1) [CRAN]
airway  (NA -> 1.27.0) [CRAN]
Skipping 1 packages ahead of CRAN: cli
Installing 3 packages: DESeq2, biomaRt, airway
trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/DESeq2_1.47.3.tar.gz'
trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/biomaRt_2.63.1.tar.gz'
trying URL 'https://bioconductor.org/packages/3.21/data/experiment/src/contrib/airway_1.27.0.tar.gz'
* installing *source* package ‘DESeq2’ ...
** this is package ‘DESeq2’ version ‘1.47.3’
** 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/RcppArmadillo/include' -I/usr/local/include    -fpic  -g -O2   -c DESeq2.cpp -o DESeq2.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/RcppArmadillo/include' -I/usr/local/include    -fpic  -g -O2   -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -shared -L/usr/local/lib -o DESeq2.so DESeq2.o RcppExports.o -llapack -L/opt/R-devel/lib/R/lib -lRblas -lgfortran -lm -lquadmath
installing to /home/omnipath/local/R/4.5-3.21/00LOCK-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 ‘2.63.1’
** 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 (biomaRt)
* installing *source* package ‘airway’ ...
** this is package ‘airway’ version ‘1.27.0’
** 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/Rtmp7ilQto/downloaded_packages’
[ Finished: 2025-02-13 21:15:28 CET ]