[ Started: 2023-04-30 00:34:51 CEST ]
[ mistyR v1.8.0 for BioC-3.16 from https://github.com/saezlab/mistyR@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'
Bioconductor version '3.16' is out-of-date; the current release version '3.17'
  is available with R version '4.3'; see https://bioconductor.org/install
'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)
Old packages: 'ggbeeswarm'
trying URL 'https://cloud.r-project.org/src/contrib/ggbeeswarm_0.7.2.tar.gz'
Content type 'application/x-gzip' length 1718982 bytes (1.6 MB)
==================================================
downloaded 1.6 MB

* installing *source* package ‘ggbeeswarm’ ...
** package ‘ggbeeswarm’ 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 (ggbeeswarm)

The downloaded source packages are in
	‘/tmp/Rtmpus1f9F/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 3.16 (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' 

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: 2023-04-30 00:35:02 CEST ]