[ Started: 2023-04-15 00:25:37 CEST ]
[ decoupleR v2.3.3 for BioC-3.16 from https://github.com/saezlab/decoupleR@master ]

[1] "Libraries: "                     "/home/omnipath/local/R/4.2-3.16"
[3] "/home/omnipath/local/R/4.2"      "/usr/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'
'getOption("repos")' replaces Bioconductor standard repositories, see
'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
    CRAN: https://cloud.r-project.org
Bioconductor version 3.16 (BiocManager 1.30.20), R 4.2.3 (2023-03-15)
'getOption("repos")' replaces Bioconductor standard repositories, see
'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
    CRAN: https://cloud.r-project.org
Bioconductor version 3.16 (BiocManager 1.30.20), R 4.2.3 (2023-03-15)
Warning message:
package(s) not installed when version(s) same as or greater than current; use
  `force = TRUE` to re-install: 'BiocCheck' 
OmnipathR (889c06226... -> 678281244...) [GitHub]
Skipping 64 packages not available: RCurl, matrixStats, cpp11, BH, snow, futile.logger, Rcpp, rsvd, irlba, crayon, png, RSQLite, httr, xtable, DBI, XML, yaml, xml2, withr, tidyselect, tidyr, tibble, stringr, rvest, rmarkdown, rlang, readxl, readr, rappdirs, purrr, progress, magrittr, logger, later, jsonlite, igraph, dplyr, digest, curl, checkmate, BiocManager, knitr, bookdown, shiny, R.utils, mixtools, data.table, fastmatch, cowplot, ggplot2, e1071, patchwork, ggrepel, Seurat, testthat, pheatmap, sessioninfo, roxygen2, RefManageR, pkgdown, covr, ranger, glmnet, broom
Downloading GitHub repo saezlab/OmnipathR@HEAD

Skipping 26 packages not available: yaml, xml2, withr, tidyselect, tidyr, tibble, stringr, rvest, rmarkdown, rlang, readxl, readr, rappdirs, purrr, progress, magrittr, logger, later, jsonlite, igraph, httr, dplyr, digest, curl, crayon, checkmate
── R CMD build ─────────────────────────────────────────────────────────────────
* checking for file ‘/tmp/Rtmpx4uP1n/remotes2aff526fcb0d0/saezlab-OmnipathR-6782812/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_3.7.19.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
[2023-04-15 00:25:54] [INFO]    [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`.
[2023-04-15 00:25:54] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-15 00:25:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-15 00:25:54] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2023-04-15 00:25:54] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-04-15 00:25:54] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2023-04-15 00:25:54] [TRACE]   [OmnipathR] Contains 1 files.
[2023-04-15 00:25:54] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-04-15 00:25:54] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-15 00:25:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-15 00:25:54] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2023-04-15 00:25:54] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2023-04-15 00:25:54] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.2-3.16/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-04-15 00:25:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-15 00:25:54] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.2-3.16/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-04-15 00:25:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-15 00:25:54] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.2-3.16/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-04-15 00:25:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-15 00:25:54] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.2-3.16/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-04-15 00:25:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-15 00:25:54] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2023-04-15 00:25:55] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-15 00:25:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-15 00:25:55] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2023-04-15 00:25:55] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-04-15 00:25:55] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2023-04-15 00:25:55] [TRACE]   [OmnipathR] Contains 1 files.
[2023-04-15 00:25:55] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-04-15 00:25:55] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-15 00:25:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-15 00:25:55] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2023-04-15 00:25:55] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2023-04-15 00:25:55] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.2-3.16/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-04-15 00:25:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-15 00:25:55] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.2-3.16/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-04-15 00:25:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-15 00:25:55] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.2-3.16/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-04-15 00:25:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-15 00:25:55] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.2-3.16/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-04-15 00:25:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-15 00:25:55] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package keeps a record of temporary installation path
* DONE (OmnipathR)
[ Finished: 2023-04-15 00:25:55 CEST ]