[ Started: 2025-07-13 20:24:11 CEST ]
[ progeny v1.17.3 for BioC-3.22 from https://github.com/saezlab/progeny@master (cad6be0 2023-01-30 11:01:10) ]

[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: 'mistyR'
trying URL 'https://bioconductor.org/packages/3.22/bioc/src/contrib/mistyR_1.17.0.tar.gz'
Content type 'application/x-gzip' length 3127302 bytes (3.0 MB)
==================================================
downloaded 3.0 MB

* installing *source* package ‘mistyR’ ...
** this is package ‘mistyR’ version ‘1.17.0’
** package ‘mistyR’ successfully unpacked and MD5 sums checked
** using staged installation
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (mistyR)

The downloaded source packages are in
	‘/tmp/RtmpW6cswI/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' 
DESeq2  (NA -> 1.48.1) [CRAN]
biomaRt (NA -> 2.64.0) [CRAN]
airway  (NA -> 1.28.0) [CRAN]
Skipping 22 packages ahead of CRAN: BiocGenerics, XVector, UCSC.utils, SparseArray, DelayedArray, S4Arrays, GenomeInfoDb, IRanges, S4Vectors, Biobase, GenomicRanges, MatrixGenerics, Biostrings, KEGGREST, BiocParallel, SummarizedExperiment, BiocFileCache, httr2, AnnotationDbi, BiocStyle, SingleCellExperiment, decoupleR
Installing 3 packages: DESeq2, biomaRt, airway
trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/DESeq2_1.48.1.tar.gz'
trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/biomaRt_2.64.0.tar.gz'
trying URL 'https://bioconductor.org/packages/3.21/data/experiment/src/contrib/airway_1.28.0.tar.gz'
* installing *source* package ‘DESeq2’ ...
** this is package ‘DESeq2’ version ‘1.48.1’
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.5-3.22/Rcpp/include' -I'/home/omnipath/local/R/4.5-3.22/RcppArmadillo/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 DESeq2.cpp -o DESeq2.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.5-3.22/Rcpp/include' -I'/home/omnipath/local/R/4.5-3.22/RcppArmadillo/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 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -o DESeq2.so DESeq2.o RcppExports.o -llapack -lblas -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR
installing to /home/omnipath/local/R/4.5-3.22/00LOCK-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 ‘2.64.0’
** 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 ‘1.28.0’
** 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/RtmpW6cswI/downloaded_packages’
[ Finished: 2025-07-13 20:25:20 CEST ]