[ Started: 2024-03-29 12:25:35 CET ]
[ CARNIVAL v2.7.2 for BioC-3.19 from https://github.com/saezlab/CARNIVAL@master (2b8887a 2023-12-06 13:18:32) ]

[1] "Libraries: "                     "/home/omnipath/local/R/4.4-3.19"
[3] "/home/omnipath/local/R/4.4"      "/opt/R-devel/lib/R/library"     
trying URL 'https://cran.uni-muenster.de/src/contrib/bslib_0.7.0.tar.gz'
Content type 'application/x-gzip' length 5125401 bytes (4.9 MB)
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downloaded 4.9 MB

trying URL 'https://cran.uni-muenster.de/src/contrib/future.apply_1.11.2.tar.gz'
Content type 'application/x-gzip' length 63881 bytes (62 KB)
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downloaded 62 KB

trying URL 'https://cran.uni-muenster.de/src/contrib/gh_1.4.1.tar.gz'
Content type 'application/x-gzip' length 46164 bytes (45 KB)
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downloaded 45 KB

* installing *source* package ‘bslib’ ...
** package ‘bslib’ 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
** 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 (bslib)
* installing *source* package ‘future.apply’ ...
** package ‘future.apply’ 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (future.apply)
* installing *source* package ‘gh’ ...
** package ‘gh’ 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 (gh)

The downloaded source packages are in
	‘/tmp/RtmpfUXya5/downloaded_packages’
Bioconductor version 3.19 (BiocManager 1.30.22), R Under development (unstable)
  (2024-03-23 r86179)
Old packages: 'BiocFileCache', 'iml', 'SingleCellExperiment', 'wppi'
trying URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/BiocFileCache_2.11.2.tar.gz'
Content type 'application/x-gzip' length 299525 bytes (292 KB)
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downloaded 292 KB

trying URL 'https://cloud.r-project.org/src/contrib/iml_0.11.2.tar.gz'
Content type 'application/x-gzip' length 176756 bytes (172 KB)
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downloaded 172 KB

trying URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/SingleCellExperiment_1.25.1.tar.gz'
Content type 'application/x-gzip' length 985365 bytes (962 KB)
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downloaded 962 KB

trying URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/wppi_1.11.0.tar.gz'
Content type 'application/x-gzip' length 662120 bytes (646 KB)
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downloaded 646 KB

* installing *source* package ‘BiocFileCache’ ...
** 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 (BiocFileCache)
* installing *source* package ‘iml’ ...
** package ‘iml’ 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 (iml)
* installing *source* package ‘SingleCellExperiment’ ...
** 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 (SingleCellExperiment)
* installing *source* package ‘wppi’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
[2024-03-29 12:26:18] [INFO]    [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`.
[2024-03-29 12:26:18] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-29 12:26:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-29 12:26:18] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2024-03-29 12:26:18] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-03-29 12:26:18] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2024-03-29 12:26:18] [TRACE]   [OmnipathR] Contains 1 files.
[2024-03-29 12:26:18] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-03-29 12:26:18] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-29 12:26:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-29 12:26:18] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2024-03-29 12:26:18] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2024-03-29 12:26:18] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-03-29 12:26:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-29 12:26:18] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-03-29 12:26:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-29 12:26:18] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-03-29 12:26:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-29 12:26:18] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-03-29 12:26:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-29 12:26:18] [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
[2024-03-29 12:26:20] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-29 12:26:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-29 12:26:20] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2024-03-29 12:26:20] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-03-29 12:26:20] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2024-03-29 12:26:20] [TRACE]   [OmnipathR] Contains 1 files.
[2024-03-29 12:26:20] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-03-29 12:26:20] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-29 12:26:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-29 12:26:20] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2024-03-29 12:26:20] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2024-03-29 12:26:20] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-03-29 12:26:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-29 12:26:20] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-03-29 12:26:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-29 12:26:20] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-03-29 12:26:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-29 12:26:20] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-03-29 12:26:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-29 12:26:20] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2024-03-29 12:26:22] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-29 12:26:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-29 12:26:22] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2024-03-29 12:26:22] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-03-29 12:26:22] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2024-03-29 12:26:22] [TRACE]   [OmnipathR] Contains 1 files.
[2024-03-29 12:26:22] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-03-29 12:26:22] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-29 12:26:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-29 12:26:22] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2024-03-29 12:26:22] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2024-03-29 12:26:22] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-03-29 12:26:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-29 12:26:22] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-03-29 12:26:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-29 12:26:22] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-03-29 12:26:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-29 12:26:22] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-03-29 12:26:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-29 12:26:22] [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/RtmpfUXya5/downloaded_packages’
Bioconductor version 3.19 (BiocManager 1.30.22), R Under development (unstable)
  (2024-03-23 r86179)
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: 2024-03-29 12:26:25 CET ]