[ Started: 2024-03-21 21:46:06 CET ]
[ decoupleR v2.9.1 for BioC-3.19 from https://github.com/saezlab/decoupleR@master ]

[1] "Libraries: "                     "/home/omnipath/local/R/4.4-3.19"
[3] "/home/omnipath/local/R/4.4"      "/opt/R-devel/lib/R/library"     
Bioconductor version 3.19 (BiocManager 1.30.22), R Under development (unstable)
  (2024-03-20 r86162)
Bioconductor version 3.19 (BiocManager 1.30.22), R Under development (unstable)
  (2024-03-20 r86162)
Warning message:
package(s) not installed when version(s) same as or greater than current; use
  `force = TRUE` to re-install: 'BiocCheck' 
OmnipathR (6646f0e8b... -> 23bec2044...) [GitHub]
Skipping 36 packages ahead of CRAN: zlibbioc, XVector, SparseArray, S4Arrays, IRanges, S4Vectors, MatrixGenerics, BiocGenerics, GenomeInfoDb, DelayedArray, Biobase, GenomicRanges, Biostrings, KEGGREST, AnnotationDbi, graph, annotate, sparseMatrixStats, beachmat, ScaledMatrix, BiocParallel, Rhdf5lib, rhdf5filters, rhdf5, SummarizedExperiment, spatstat.explore, GSEABase, DelayedMatrixStats, BiocSingular, HDF5Array, SingleCellExperiment, BiocStyle, AUCell, fgsea, viper, GSVA
Downloading GitHub repo saezlab/OmnipathR@HEAD

── R CMD build ─────────────────────────────────────────────────────────────────
* checking for file ‘/tmp/RtmpCs0Dbk/remotes7f752385b81dd/saezlab-OmnipathR-23bec20/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_3.11.7.tar.gz’

* installing *source* package ‘OmnipathR’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
Warning: OmnipathR.Rd:3: docType ‘_PACKAGE’ is unrecognized
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
[2024-03-21 21:46:25] [INFO]    [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`.
[2024-03-21 21:46:25] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-21 21:46:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-21 21:46:25] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2024-03-21 21:46:25] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-03-21 21:46:25] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2024-03-21 21:46:25] [TRACE]   [OmnipathR] Contains 1 files.
[2024-03-21 21:46:25] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-03-21 21:46:25] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-21 21:46:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-21 21:46:25] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2024-03-21 21:46:25] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2024-03-21 21:46:25] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-03-21 21:46:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-21 21:46:25] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-03-21 21:46:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-21 21:46:25] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-03-21 21:46:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-21 21:46:25] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-03-21 21:46:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-21 21:46:25] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2024-03-21 21:46:26] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-21 21:46:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-21 21:46:26] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2024-03-21 21:46:26] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-03-21 21:46:26] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2024-03-21 21:46:26] [TRACE]   [OmnipathR] Contains 1 files.
[2024-03-21 21:46:26] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-03-21 21:46:26] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-21 21:46:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-21 21:46:26] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2024-03-21 21:46:26] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2024-03-21 21:46:26] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-03-21 21:46:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-21 21:46:26] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-03-21 21:46:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-21 21:46:26] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-03-21 21:46:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-21 21:46:26] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-03-21 21:46:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-21 21:46:26] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package keeps a record of temporary installation path
* DONE (OmnipathR)
[ Finished: 2024-03-21 21:46:26 CET ]