[ Started: 2023-04-15 00:38:42 CEST ]
[ liana v0.1.12 for BioC-3.17 from https://github.com/saezlab/liana@master ]

[1] "Libraries: "                     "/home/omnipath/local/R/4.3-3.17"
[3] "/home/omnipath/local/R/4.3"      "/opt/R-beta/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 beta (2023-04-08
  r84203)
Bioconductor version 3.17 (BiocManager 1.30.20), R 4.3.0 beta (2023-04-08
  r84203)
Warning message:
package(s) not installed when version(s) same as or greater than current; use
  `force = TRUE` to re-install: 'BiocCheck' 
CellChat  (NA    -> 3c6e8d602...) [GitHub]
decoupleR (2.5.0 -> 006d5be59...) [GitHub]
Skipping 79 packages not available: matrixStats, RCurl, crayon, png, DT, shiny, filelock, DBI, dbplyr, dplyr, yaml, httr, curl, RSQLite, rappdirs, BiocManager, Rcpp, cpp11, BH, snow, futile.logger, irlba, reticulate, assertthat, rsvd, RcppHNSW, igraph, locfit, withr, tidyselect, tidyr, tibble, stringr, rlang, purrr, magrittr, broom, rmarkdown, knitr, bookdown, doParallel, foreach, digest, GlobalOptions, RColorBrewer, clue, colorspace, GetoptLong, circlize, ggrastr, ggrepel, pheatmap, uwot, RcppML, Rtsne, viridis, ggbeeswarm, ggplot2, dqrng, statmod, xml2, rvest, readxl, readr, progress, logger, later, jsonlite, checkmate, devtools, tidyverse, future, furrr, entropy, Seurat, sessioninfo, testthat, markdown, SeuratObject
Downloading GitHub repo sqjin/CellChat@HEAD

Skipping 36 packages not available: RcppEigen, Rcpp, BiocNeighbors, ggnetwork, ggpubr, plyr, colorspace, patchwork, magrittr, BiocGenerics, shape, FNN, reshape2, forcats, sna, scales, reticulate, RSpectra, ComplexHeatmap, cowplot, RColorBrewer, circlize, ggrepel, Rtsne, expm, svglite, stringr, ggalluvial, NMF, irlba, pbapply, future.apply, future, ggplot2, igraph, dplyr
── R CMD build ─────────────────────────────────────────────────────────────────
* checking for file ‘/tmp/RtmpNUFyOk/remotes2e72a68a96bb7/sqjin-CellChat-3c6e8d6/DESCRIPTION’ ... OK
* preparing ‘CellChat’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘CellChat_1.6.1.tar.gz’

ERROR: dependency ‘ggpubr’ is not available for package ‘CellChat’
* removing ‘/home/omnipath/local/R/4.3-3.17/CellChat’
Downloading GitHub repo sqjin/CellChat@HEAD

Skipping 36 packages not available: RcppEigen, Rcpp, BiocNeighbors, ggnetwork, ggpubr, plyr, colorspace, patchwork, magrittr, BiocGenerics, shape, FNN, reshape2, forcats, sna, scales, reticulate, RSpectra, ComplexHeatmap, cowplot, RColorBrewer, circlize, ggrepel, Rtsne, expm, svglite, stringr, ggalluvial, NMF, irlba, pbapply, future.apply, future, ggplot2, igraph, dplyr
── R CMD build ─────────────────────────────────────────────────────────────────
* checking for file ‘/tmp/RtmpNUFyOk/remotes2e72a3dfdfe83/sqjin-CellChat-3c6e8d6/DESCRIPTION’ ... OK
* preparing ‘CellChat’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘CellChat_1.6.1.tar.gz’

ERROR: dependency ‘ggpubr’ is not available for package ‘CellChat’
* removing ‘/home/omnipath/local/R/4.3-3.17/CellChat’
Downloading GitHub repo saezlab/decoupleR@HEAD

Skipping 10 packages not available: withr, tidyselect, tidyr, tibble, stringr, rlang, purrr, magrittr, dplyr, broom
── R CMD build ─────────────────────────────────────────────────────────────────
* checking for file ‘/tmp/RtmpNUFyOk/remotes2e72a10a36ee/saezlab-decoupleR-006d5be/DESCRIPTION’ ... OK
* preparing ‘decoupleR’:
* checking DESCRIPTION meta-information ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
Omitted ‘LazyData’ from DESCRIPTION
* building ‘decoupleR_2.3.3.tar.gz’

* 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)
Warning messages:
1: In i.p(...) :
  installation of package ‘/tmp/RtmpNUFyOk/file2e72a216faa8a/CellChat_1.6.1.tar.gz’ had non-zero exit status
2: In i.p(...) :
  installation of package ‘/tmp/RtmpNUFyOk/file2e72a59f62dfa/CellChat_1.6.1.tar.gz’ had non-zero exit status
[ Finished: 2023-04-15 00:39:07 CEST ]