[ Started: 2025-08-06 19:38:43 CEST ]
[ decoupleR v2.9.7 for BioC-3.22 from https://github.com/saezlab/decoupleR@devel (930b765 2025-02-15 00:00:59) ]

[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: 'cosmosR'
trying URL 'https://bioconductor.org/packages/3.22/bioc/src/contrib/cosmosR_1.17.0.tar.gz'
Content type 'application/x-gzip' length 3532462 bytes (3.4 MB)
==================================================
downloaded 3.4 MB

* installing *source* package ‘cosmosR’ ...
** this is package ‘cosmosR’ version ‘1.17.0’
** package ‘cosmosR’ 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 (cosmosR)

The downloaded source packages are in
	‘/tmp/RtmprRVKOu/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 40 packages ahead of CRAN: XVector, SparseArray, S4Arrays, IRanges, S4Vectors, MatrixGenerics, BiocGenerics, UCSC.utils, GenomeInfoDb, DelayedArray, Biobase, GenomicRanges, Biostrings, KEGGREST, AnnotationDbi, graph, annotate, sparseMatrixStats, assorthead, beachmat, ScaledMatrix, BiocParallel, Rhdf5lib, rhdf5filters, rhdf5, h5mread, BiocFileCache, SummarizedExperiment, SingleCellExperiment, GSEABase, DelayedMatrixStats, BiocSingular, HDF5Array, SpatialExperiment, OmnipathR, BiocStyle, AUCell, fgsea, viper, GSVA
[ Finished: 2025-08-06 19:38:56 CEST ]