[ Started: 2024-03-20 23:51:32 CET ]
[ decoupleR v2.9.1 for BioC-3.18 from https://github.com/saezlab/decoupleR@master ]

[1] "Libraries: "                     "/home/omnipath/local/R/4.3-3.18"
[3] "/home/omnipath/local/R/4.3"      "/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 3.18 (BiocManager 1.30.22), R 4.3.3 (2024-02-29)
'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 1.30.22), 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' 
OmnipathR (eda87b858... -> d4618a868...) [GitHub]
Skipping 35 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, BiocStyle, AUCell, fgsea, viper, GSVA
Downloading GitHub repo saezlab/OmnipathR@HEAD

── R CMD build ─────────────────────────────────────────────────────────────────
* checking for file ‘/tmp/RtmpdEgWJv/remotes9b6c26f96fd57/saezlab-OmnipathR-d4618a8/DESCRIPTION’ ... OK
* preparing ‘OmnipathR’:
* checking DESCRIPTION meta-information ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* looking to see if a ‘data/datalist’ file should be added
* building ‘OmnipathR_3.11.5.tar.gz’

* installing *source* package ‘OmnipathR’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
Warning: OmnipathR.Rd: docType ‘_PACKAGE’ is unrecognized
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
[2024-03-20 23:51:56] [INFO]    [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`.
[2024-03-20 23:51:56] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-20 23:51:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-20 23:51:56] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2024-03-20 23:51:56] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-03-20 23:51:56] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2024-03-20 23:51:56] [TRACE]   [OmnipathR] Contains 1 files.
[2024-03-20 23:51:56] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-03-20 23:51:56] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-20 23:51:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-20 23:51:56] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2024-03-20 23:51:56] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2024-03-20 23:51:56] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-03-20 23:51:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-20 23:51:56] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-03-20 23:51:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-20 23:51:56] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-03-20 23:51:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-20 23:51:56] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-03-20 23:51:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-20 23:51:56] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2024-03-20 23:51:57] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-20 23:51:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-20 23:51:57] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2024-03-20 23:51:57] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-03-20 23:51:57] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2024-03-20 23:51:57] [TRACE]   [OmnipathR] Contains 1 files.
[2024-03-20 23:51:57] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-03-20 23:51:57] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-20 23:51:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-20 23:51:57] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2024-03-20 23:51:57] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2024-03-20 23:51:57] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-03-20 23:51:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-20 23:51:57] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-03-20 23:51:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-20 23:51:57] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-03-20 23:51:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-20 23:51:57] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-03-20 23:51:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-20 23:51:57] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package keeps a record of temporary installation path
* DONE (OmnipathR)
[ Finished: 2024-03-20 23:51:57 CET ]