[ Started: 2025-08-04 19:36:37 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: 'beachmat', 'BiocStyle', 'CellNOptR'
trying URL 'https://bioconductor.org/packages/3.22/bioc/src/contrib/beachmat_2.25.4.tar.gz'
trying URL 'https://bioconductor.org/packages/3.22/bioc/src/contrib/BiocStyle_2.37.1.tar.gz'
trying URL 'https://bioconductor.org/packages/3.22/bioc/src/contrib/CellNOptR_1.55.0.tar.gz'
* installing *source* package ‘beachmat’ ...
** this is package ‘beachmat’ version ‘2.25.4’
** package ‘beachmat’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
using C++17
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I'/home/omnipath/local/R/4.5-3.22/Rcpp/include' -I'/home/omnipath/local/R/4.5-3.22/assorthead/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 RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I'/home/omnipath/local/R/4.5-3.22/Rcpp/include' -I'/home/omnipath/local/R/4.5-3.22/assorthead/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 constant_matrix.cpp -o constant_matrix.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I'/home/omnipath/local/R/4.5-3.22/Rcpp/include' -I'/home/omnipath/local/R/4.5-3.22/assorthead/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 delayed_isometric_binary.cpp -o delayed_isometric_binary.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I'/home/omnipath/local/R/4.5-3.22/Rcpp/include' -I'/home/omnipath/local/R/4.5-3.22/assorthead/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 delayed_isometric_math.cpp -o delayed_isometric_math.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I'/home/omnipath/local/R/4.5-3.22/Rcpp/include' -I'/home/omnipath/local/R/4.5-3.22/assorthead/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 delayed_isometric_unary.cpp -o delayed_isometric_unary.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I'/home/omnipath/local/R/4.5-3.22/Rcpp/include' -I'/home/omnipath/local/R/4.5-3.22/assorthead/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 delayed_other.cpp -o delayed_other.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I'/home/omnipath/local/R/4.5-3.22/Rcpp/include' -I'/home/omnipath/local/R/4.5-3.22/assorthead/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 dense_matrix.cpp -o dense_matrix.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I'/home/omnipath/local/R/4.5-3.22/Rcpp/include' -I'/home/omnipath/local/R/4.5-3.22/assorthead/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 fragment_sparse_rows.cpp -o fragment_sparse_rows.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I'/home/omnipath/local/R/4.5-3.22/Rcpp/include' -I'/home/omnipath/local/R/4.5-3.22/assorthead/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 get_executor.cpp -o get_executor.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I'/home/omnipath/local/R/4.5-3.22/Rcpp/include' -I'/home/omnipath/local/R/4.5-3.22/assorthead/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 na_cast.cpp -o na_cast.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I'/home/omnipath/local/R/4.5-3.22/Rcpp/include' -I'/home/omnipath/local/R/4.5-3.22/assorthead/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 sparse_matrix.cpp -o sparse_matrix.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I'/home/omnipath/local/R/4.5-3.22/Rcpp/include' -I'/home/omnipath/local/R/4.5-3.22/assorthead/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 tatami_utils.cpp -o tatami_utils.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I'/home/omnipath/local/R/4.5-3.22/Rcpp/include' -I'/home/omnipath/local/R/4.5-3.22/assorthead/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 unknown_matrix.cpp -o unknown_matrix.o
g++ -std=gnu++17 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -o beachmat.so RcppExports.o constant_matrix.o delayed_isometric_binary.o delayed_isometric_math.o delayed_isometric_unary.o delayed_other.o dense_matrix.o fragment_sparse_rows.o get_executor.o na_cast.o sparse_matrix.o tatami_utils.o unknown_matrix.o -L/usr/lib/R/lib -lR
installing to /home/omnipath/local/R/4.5-3.22/00LOCK-beachmat/00new/beachmat/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 (beachmat)
* installing *source* package ‘BiocStyle’ ...
** this is package ‘BiocStyle’ version ‘2.37.1’
** package ‘BiocStyle’ successfully unpacked and MD5 sums checked
** 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 (BiocStyle)
* 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)

The downloaded source packages are in
	‘/tmp/Rtmp6D9A2k/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 21 packages ahead of CRAN: BiocParallel, BiocGenerics, UCSC.utils, GenomeInfoDb, XVector, Biostrings, KEGGREST, S4Vectors, IRanges, Biobase, AnnotationDbi, fgsea, marray, graph, annotate, decoupleR, bcellViper, piano, GSEABase, dorothea, CARNIVAL
[ Finished: 2025-08-04 19:38:32 CEST ]