[ Started: 2024-10-19 12:19:09 CEST ]
[ CARNIVAL v2.7.2 for BioC-3.20 from https://github.com/saezlab/CARNIVAL@master (2b8887a 2023-12-06 13:18:32) ]

[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: 'dir.expiry', 'wppi'
trying URL 'https://bioconductor.org/packages/3.20/bioc/src/contrib/dir.expiry_1.13.1.tar.gz'
Content type 'application/x-gzip' length 308469 bytes (301 KB)
==================================================
downloaded 301 KB

trying URL 'https://bioconductor.org/packages/3.20/bioc/src/contrib/wppi_1.13.0.tar.gz'
Content type 'application/x-gzip' length 662271 bytes (646 KB)
==================================================
downloaded 646 KB

* installing *source* package ‘dir.expiry’ ...
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (dir.expiry)
* installing *source* package ‘wppi’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
[2024-10-19 12:19:18] [INFO]    [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`.
[2024-10-19 12:19:18] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-19 12:19:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-19 12:19:18] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2024-10-19 12:19:18] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-10-19 12:19:18] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2024-10-19 12:19:18] [TRACE]   [OmnipathR] Contains 1 files.
[2024-10-19 12:19:18] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-10-19 12:19:18] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-19 12:19:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-19 12:19:18] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2024-10-19 12:19:18] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2024-10-19 12:19:18] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-10-19 12:19:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-19 12:19:18] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-10-19 12:19:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-19 12:19:18] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-10-19 12:19:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-19 12:19:18] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-10-19 12:19:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-19 12:19:18] [TRACE]   [OmnipathR] Cache locked: FALSE
Note: wrong number of arguments to '/' 
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
[2024-10-19 12:19:20] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-19 12:19:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-19 12:19:20] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2024-10-19 12:19:20] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-10-19 12:19:20] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2024-10-19 12:19:20] [TRACE]   [OmnipathR] Contains 1 files.
[2024-10-19 12:19:20] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-10-19 12:19:20] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-19 12:19:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-19 12:19:20] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2024-10-19 12:19:20] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2024-10-19 12:19:20] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-10-19 12:19:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-19 12:19:20] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-10-19 12:19:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-19 12:19:20] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-10-19 12:19:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-19 12:19:20] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-10-19 12:19:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-19 12:19:20] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2024-10-19 12:19:23] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-19 12:19:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-19 12:19:23] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2024-10-19 12:19:23] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-10-19 12:19:23] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2024-10-19 12:19:23] [TRACE]   [OmnipathR] Contains 1 files.
[2024-10-19 12:19:23] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-10-19 12:19:23] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-19 12:19:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-19 12:19:23] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2024-10-19 12:19:23] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2024-10-19 12:19:23] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-10-19 12:19:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-19 12:19:23] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-10-19 12:19:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-19 12:19:23] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-10-19 12:19:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-19 12:19:23] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-10-19 12:19:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-19 12:19:23] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package keeps a record of temporary installation path
* DONE (wppi)

The downloaded source packages are in
	‘/tmp/RtmpLmGdAH/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' 

Skipping 1 packages ahead of CRAN: BiocStyle
[ Finished: 2024-10-19 12:19:29 CEST ]