[ Started: 2024-11-01 13:29:20 CET ]
[ MetaProViz v2.1.1 for BioC-3.20 from https://github.com/saezlab/MetaProViz@development (94d345c 2024-10-31 14:07:21) ]

[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 1.30.25), R 4.4.1 (2024-06-14)
Old packages: 'decoupleR', 'OmnipathR'
trying URL 'https://bioconductor.org/packages/3.20/bioc/src/contrib/decoupleR_2.12.0.tar.gz'
Content type 'application/x-gzip' length 5238810 bytes (5.0 MB)
==================================================
downloaded 5.0 MB

trying URL 'https://bioconductor.org/packages/3.20/bioc/src/contrib/OmnipathR_3.14.0.tar.gz'
Content type 'application/x-gzip' length 3715601 bytes (3.5 MB)
==================================================
downloaded 3.5 MB

* installing *source* package ‘decoupleR’ ...
** package ‘decoupleR’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** 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 (decoupleR)
* installing *source* package ‘OmnipathR’ ...
** package ‘OmnipathR’ successfully unpacked and MD5 sums checked
** 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
[2024-11-01 13:29:39] [INFO]    [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`.
[2024-11-01 13:29:39] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-01 13:29:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-01 13:29:39] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2024-11-01 13:29:39] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-11-01 13:29:39] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2024-11-01 13:29:39] [TRACE]   [OmnipathR] Contains 1 files.
[2024-11-01 13:29:39] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-11-01 13:29:39] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-01 13:29:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-01 13:29:39] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2024-11-01 13:29:39] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2024-11-01 13:29:39] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-11-01 13:29:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-01 13:29:39] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-11-01 13:29:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-01 13:29:39] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-11-01 13:29:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-01 13:29:39] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-11-01 13:29:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-01 13:29:39] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2024-11-01 13:29:40] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-01 13:29:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-01 13:29:40] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2024-11-01 13:29:40] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-11-01 13:29:40] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2024-11-01 13:29:40] [TRACE]   [OmnipathR] Contains 1 files.
[2024-11-01 13:29:40] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-11-01 13:29:40] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-01 13:29:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-01 13:29:40] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2024-11-01 13:29:40] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2024-11-01 13:29:40] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-11-01 13:29:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-01 13:29:41] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-11-01 13:29:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-01 13:29:41] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-11-01 13:29:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-01 13:29:41] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-11-01 13:29:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-01 13:29:41] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package keeps a record of temporary installation path
* DONE (OmnipathR)

The downloaded source packages are in
	‘/tmp/RtmplMmBKr/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 1.30.25), 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' 
Error: Command failed (128)
In addition: Warning message:
In system(full, intern = TRUE, ignore.stderr = quiet) :
  running command ''/usr/bin/git' ls-remote https://code.bioconductor.org/packages/limma.git  2>/dev/null' had status 128
Execution halted
[ Finished: 2024-11-01 13:29:47 CET ]