[ Started: 2024-08-18 01:00:59 CEST ]
[ wppi v1.6.0 for BioC-3.20 from https://github.com/AnaGalhoz37/wppi@main (9b574a4 2022-11-02 08:18:02) ]

[1] "Libraries: "                     "/home/omnipath/local/R/4.4-3.20"
[3] "/home/omnipath/local/R/4.4"      "/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 3.20 (BiocManager 1.30.23), R 4.4.1 (2024-06-14)
Old packages: 'progeny'
trying URL 'https://bioconductor.org/packages/3.20/bioc/src/contrib/progeny_1.27.0.tar.gz'
Content type 'application/x-gzip' length 10609361 bytes (10.1 MB)
==================================================
downloaded 10.1 MB

* installing *source* package ‘progeny’ ...
** package ‘progeny’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (progeny)

The downloaded source packages are in
	‘/tmp/RtmpaqGKEU/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 3.20 (BiocManager 1.30.23), R 4.4.1 (2024-06-14)
Warning message:
package(s) not installed when version(s) same as or greater than current; use
  `force = TRUE` to re-install: 'BiocCheck' 
OmnipathR (2f92123f6... -> 652f5c798...) [GitHub]
Skipping 1 packages ahead of CRAN: rmarkdown
Downloading GitHub repo saezlab/OmnipathR@HEAD

Skipping 1 packages ahead of CRAN: rmarkdown
── R CMD build ─────────────────────────────────────────────────────────────────
* checking for file ‘/tmp/RtmpaqGKEU/remotes12eeb21e059042/saezlab-OmnipathR-652f5c7/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_3.13.15.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
[2024-08-18 01:01:27] [INFO]    [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`.
[2024-08-18 01:01:27] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-18 01:01:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-08-18 01:01:27] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2024-08-18 01:01:27] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-08-18 01:01:27] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2024-08-18 01:01:27] [TRACE]   [OmnipathR] Contains 1 files.
[2024-08-18 01:01:27] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-08-18 01:01:27] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-18 01:01:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-08-18 01:01:27] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2024-08-18 01:01:27] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2024-08-18 01:01:27] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-08-18 01:01:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-08-18 01:01:27] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-08-18 01:01:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-08-18 01:01:27] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-08-18 01:01:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-08-18 01:01:27] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-08-18 01:01:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-08-18 01:01:27] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2024-08-18 01:01:28] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-18 01:01:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-08-18 01:01:28] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2024-08-18 01:01:28] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-08-18 01:01:29] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2024-08-18 01:01:29] [TRACE]   [OmnipathR] Contains 1 files.
[2024-08-18 01:01:29] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-08-18 01:01:29] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-18 01:01:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-08-18 01:01:29] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2024-08-18 01:01:29] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2024-08-18 01:01:29] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-08-18 01:01:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-08-18 01:01:29] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-08-18 01:01:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-08-18 01:01:29] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-08-18 01:01:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-08-18 01:01:29] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-08-18 01:01:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-08-18 01:01:29] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package keeps a record of temporary installation path
* DONE (OmnipathR)
[ Finished: 2024-08-18 01:01:29 CEST ]