[ Started: 2023-02-02 01:05:15 CET ]
[ decoupleR v2.3.3 for BioC-3.16 from https://github.com/saezlab/decoupleR@master ]

[1] "Libraries: "                     "/home/omnipath/local/R/4.2-3.16"
[3] "/home/omnipath/local/R/4.2"      "/usr/lib/R/library"             
'getOption("repos")' replaces Bioconductor standard repositories, see
'?repositories' for details

replacement repositories:
    CRAN: https://cloud.r-project.org

Bioconductor version 3.16 (BiocManager 1.30.19), R 4.2.2 Patched (2022-11-10
  r83330)
OmnipathR (edf276bb6... -> e05772468...) [GitHub]
Skipping 4 packages ahead of CRAN: future, tinytex, sourcetools, e1071
Downloading GitHub repo saezlab/OmnipathR@HEAD

Skipping 1 packages ahead of CRAN: tinytex
── R CMD build ─────────────────────────────────────────────────────────────────
* checking for file ‘/tmp/RtmpQ64RSs/remotes3569adf177126/saezlab-OmnipathR-e057724/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_3.7.1.tar.gz’

* installing *source* package ‘OmnipathR’ ...
** 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
[2023-02-02 01:05:32] [INFO]    [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`.
[2023-02-02 01:05:32] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-02-02 01:05:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-02-02 01:05:32] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2023-02-02 01:05:32] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-02-02 01:05:32] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2023-02-02 01:05:32] [TRACE]   [OmnipathR] Contains 1 files.
[2023-02-02 01:05:32] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-02-02 01:05:32] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-02-02 01:05:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-02-02 01:05:32] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2023-02-02 01:05:32] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2023-02-02 01:05:32] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.2-3.16/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-02-02 01:05:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-02-02 01:05:32] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.2-3.16/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-02-02 01:05:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-02-02 01:05:32] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.2-3.16/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-02-02 01:05:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-02-02 01:05:32] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.2-3.16/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-02-02 01:05:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-02-02 01:05:32] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2023-02-02 01:05:33] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-02-02 01:05:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-02-02 01:05:33] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2023-02-02 01:05:33] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-02-02 01:05:33] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2023-02-02 01:05:33] [TRACE]   [OmnipathR] Contains 1 files.
[2023-02-02 01:05:33] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-02-02 01:05:33] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-02-02 01:05:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-02-02 01:05:33] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2023-02-02 01:05:33] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2023-02-02 01:05:33] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.2-3.16/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-02-02 01:05:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-02-02 01:05:33] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.2-3.16/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-02-02 01:05:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-02-02 01:05:33] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.2-3.16/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-02-02 01:05:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-02-02 01:05:33] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.2-3.16/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-02-02 01:05:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-02-02 01:05:33] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package keeps a record of temporary installation path
* DONE (OmnipathR)
[ Finished: 2023-02-02 01:05:33 CET ]