[ Started: 2024-05-10 16:11:03 CEST ]
[ decoupleR v2.9.7 for BioC-3.18 from https://github.com/saezlab/decoupleR@master (8716d1a 2024-04-11 16:27:42) ]

[1] "Libraries: "                     "/home/omnipath/local/R/4.3-3.18"
[3] "/home/omnipath/local/R/4.3"      "/usr/lib/R/library"             
Bioconductor version '3.18' is out-of-date; the current release version '3.19'
  is available with R version '4.4'; see https://bioconductor.org/install
'getOption("repos")' replaces Bioconductor standard repositories, see
'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
    CRAN: https://cloud.r-project.org
Bioconductor version 3.18 (BiocManager 1.30.23), R 4.3.3 (2024-02-29)
Old packages: 'cosmosR'
trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/cosmosR_1.10.0.tar.gz'
Content type 'application/x-gzip' length 3527925 bytes (3.4 MB)
==================================================
downloaded 3.4 MB

* installing *source* package ‘cosmosR’ ...
** 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/RtmpMJLuwc/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 3.18 (BiocManager 1.30.23), R 4.3.3 (2024-02-29)
Warning message:
package(s) not installed when version(s) same as or greater than current; use
  `force = TRUE` to re-install: 'BiocCheck' 

Skipping 36 packages ahead of CRAN: S4Arrays, IRanges, S4Vectors, MatrixGenerics, BiocGenerics, GenomeInfoDbData, zlibbioc, XVector, GenomeInfoDb, DelayedArray, Biobase, GenomicRanges, Biostrings, KEGGREST, AnnotationDbi, graph, annotate, sparseMatrixStats, beachmat, ScaledMatrix, BiocParallel, Rhdf5lib, rhdf5filters, rhdf5, SummarizedExperiment, GSEABase, DelayedMatrixStats, BiocSingular, HDF5Array, SingleCellExperiment, OmnipathR, BiocStyle, AUCell, fgsea, viper, GSVA
[ Finished: 2024-05-10 16:11:22 CEST ]