[ Started: 2025-10-09 11:24:17 CEST ]
[ cosmosR v1.9.1 for BioC-3.22 from https://github.com/saezlab/cosmosR@master (5a38475 2025-07-06 10:04:33) ]

[1] "Libraries: "                     "/home/omnipath/local/R/4.5-3.22"
[3] "/home/omnipath/local/R/4.5"      "/usr/lib/R/library"             
'getOption("repos")' replaces Bioconductor standard repositories, see
'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
    CRAN: https://cloud.r-project.org
Bioconductor version 3.22 (BiocManager 1.30.26), R 4.5.1 (2025-06-13)
Old packages: 'CellNOptR', 'statmod'
trying URL 'https://bioconductor.org/packages/3.22/bioc/src/contrib/CellNOptR_1.55.0.tar.gz'
trying URL 'https://cloud.r-project.org/src/contrib/statmod_1.5.1.tar.gz'
* installing *source* package ‘CellNOptR’ ...
** this is package ‘CellNOptR’ version ‘1.55.0’
** package ‘CellNOptR’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG      -I./include  -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c simulatorT1.c -o simulatorT1.o
gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG      -I./include  -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c simulatorTN.c -o simulatorTN.o
gcc -std=gnu2x -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -o CellNOptR.so simulatorT1.o simulatorTN.o -L/usr/lib/R/lib -lR
installing to /home/omnipath/local/R/4.5-3.22/00LOCK-CellNOptR/00new/CellNOptR/libs
** R
** data
** 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 (CellNOptR)
* installing *source* package ‘statmod’ ...
** this is package ‘statmod’ version ‘1.5.1’
** package ‘statmod’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
using Fortran compiler: ‘GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG       -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c expectedDeviance.c -o expectedDeviance.o
gfortran  -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0  -c gaussq2.f -o gaussq2.o
gcc -std=gnu2x -I"/usr/share/R/include" -DNDEBUG       -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c init.c -o init.o
gcc -std=gnu2x -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -o statmod.so expectedDeviance.o gaussq2.o init.o -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR
installing to /home/omnipath/local/R/4.5-3.22/00LOCK-statmod/00new/statmod/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** 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 (statmod)

The downloaded source packages are in
	‘/tmp/RtmpTJAq0a/downloaded_packages’
'getOption("repos")' replaces Bioconductor standard repositories, see
'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
    CRAN: https://cloud.r-project.org
Bioconductor version 3.22 (BiocManager 1.30.26), R 4.5.1 (2025-06-13)
Warning message:
package(s) not installed when version(s) same as or greater than current; use
  `force = TRUE` to re-install: 'BiocCheck' 

Skipping 23 packages ahead of CRAN: BiocParallel, statmod, BiocGenerics, GenomeInfoDbData, UCSC.utils, GenomeInfoDb, XVector, Biostrings, KEGGREST, S4Vectors, IRanges, Biobase, AnnotationDbi, fgsea, marray, graph, annotate, decoupleR, bcellViper, piano, GSEABase, dorothea, CARNIVAL
[ Finished: 2025-10-09 11:24:40 CEST ]