[ Started: 2023-04-27 01:12:03 CEST ]
[ mistyR v1.7.2 for BioC-3.17 from https://github.com/saezlab/mistyR@devel ]

[1] "Libraries: "                     "/home/omnipath/local/R/4.3-3.17"
[3] "/home/omnipath/local/R/4.3"      "/opt/R-devel/lib/R/library"     
Warning: unable to access index for repository https://cran.uni-muenster.de/src/contrib:
  cannot open URL 'https://cran.uni-muenster.de/src/contrib/PACKAGES'
Warning: unable to access index for repository https://cran.uni-muenster.de/src/contrib:
  cannot open URL 'https://cran.uni-muenster.de/src/contrib/PACKAGES'
Bioconductor version 3.17 (BiocManager 1.30.20), R 4.3.0 (2023-04-21)
Old packages: 'basilisk', 'basilisk.utils', 'decoupleR', 'OmnipathR'
trying URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/basilisk_1.12.0.tar.gz'
Content type 'application/x-gzip' length 267174 bytes (260 KB)
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downloaded 260 KB

trying URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/basilisk.utils_1.12.0.tar.gz'
Content type 'application/x-gzip' length 240019 bytes (234 KB)
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downloaded 234 KB

trying URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/decoupleR_2.6.0.tar.gz'
Content type 'application/x-gzip' length 4329686 bytes (4.1 MB)
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downloaded 4.1 MB

trying URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/OmnipathR_3.8.0.tar.gz'
Content type 'application/x-gzip' length 3363813 bytes (3.2 MB)
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* installing *source* package ‘basilisk.utils’ ...
** 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 (basilisk.utils)
* installing *source* package ‘decoupleR’ ...
** 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’ ...
** 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
[2023-04-27 01:12:19] [INFO]    [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`.
[2023-04-27 01:12:19] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-27 01:12:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-27 01:12:19] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2023-04-27 01:12:19] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-04-27 01:12:19] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2023-04-27 01:12:19] [TRACE]   [OmnipathR] Contains 1 files.
[2023-04-27 01:12:19] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-04-27 01:12:19] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-27 01:12:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-27 01:12:19] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2023-04-27 01:12:19] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2023-04-27 01:12:19] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.17/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-04-27 01:12:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-27 01:12:19] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.17/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-04-27 01:12:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-27 01:12:19] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.17/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-04-27 01:12:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-27 01:12:19] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.17/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-04-27 01:12:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-27 01:12:19] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2023-04-27 01:12:20] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-27 01:12:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-27 01:12:20] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2023-04-27 01:12:20] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-04-27 01:12:20] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2023-04-27 01:12:20] [TRACE]   [OmnipathR] Contains 1 files.
[2023-04-27 01:12:20] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-04-27 01:12:20] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-27 01:12:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-27 01:12:20] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2023-04-27 01:12:20] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2023-04-27 01:12:20] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.17/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-04-27 01:12:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-27 01:12:20] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.17/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-04-27 01:12:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-27 01:12:20] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.17/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-04-27 01:12:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-27 01:12:20] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.17/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-04-27 01:12:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-27 01:12:20] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package keeps a record of temporary installation path
* DONE (OmnipathR)
* installing *source* package ‘basilisk’ ...
** using non-staged installation via StagedInstall field
** 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
* DONE (basilisk)

The downloaded source packages are in
	‘/tmp/RtmpVpKnqx/downloaded_packages’
Bioconductor version 3.17 (BiocManager 1.30.20), R 4.3.0 (2023-04-21)
Warning message:
package(s) not installed when version(s) same as or greater than current; use
  `force = TRUE` to re-install: 'BiocCheck' 

Skipping 35 packages not available: BiocManager, yaml, rmarkdown, knitr, bookdown, xgboost, testthat, RSNNS, kernlab, iml, igraph, future, earth, covr, withr, tidyselect, tidyr, tibble, stringr, R.utils, rlist, rlang, ridge, readr, ranger, purrr, ggplot2, furrr, filelock, dplyr, distances, digest, deldir, caret, assertthat
[ Finished: 2023-04-27 01:12:25 CEST ]