[ Started: 2023-04-28 23:58:30 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-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) 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' CellChat (NA -> 3c6e8d602...) [GitHub] OmnipathR (3.8.0 -> 75189a8b9...) [GitHub] decoupleR (2.6.0 -> 3d343dd61...) [GitHub] basilisk.... (1.12.0 -> 7ee521309...) [GitHub] basilisk (1.12.0 -> 6b6ba9fd8...) [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/Rtmp4UawQY/remotes27494858dfb724/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/Rtmp4UawQY/remotes2749486fda803e/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/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/Rtmp4UawQY/remotes2749485d6d403d/saezlab-OmnipathR-75189a8/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_3.9.1.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 [2023-04-28 23:58:57] [INFO] [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`. [2023-04-28 23:58:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-04-28 23:58:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-28 23:58:57] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2023-04-28 23:58:57] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2023-04-28 23:58:57] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2023-04-28 23:58:57] [TRACE] [OmnipathR] Contains 1 files. [2023-04-28 23:58:57] [TRACE] [OmnipathR] Cache is locked: FALSE. [2023-04-28 23:58:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-04-28 23:58:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-28 23:58:57] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2023-04-28 23:58:57] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`. [2023-04-28 23:58:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.17/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8). [2023-04-28 23:58:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-28 23:58:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.17/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2023-04-28 23:58:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-28 23:58:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.17/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8). [2023-04-28 23:58:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-28 23:58:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.17/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2023-04-28 23:58:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-28 23:58:57] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2023-04-28 23:58:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-04-28 23:58:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-28 23:58:58] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2023-04-28 23:58:58] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2023-04-28 23:58:58] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2023-04-28 23:58:58] [TRACE] [OmnipathR] Contains 1 files. [2023-04-28 23:58:58] [TRACE] [OmnipathR] Cache is locked: FALSE. [2023-04-28 23:58:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-04-28 23:58:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-28 23:58:58] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2023-04-28 23:58:58] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`. [2023-04-28 23:58:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.17/OmnipathR/db/db_def.json` (encoding: UTF-8). [2023-04-28 23:58:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-28 23:58:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.17/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2023-04-28 23:58:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-28 23:58:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.17/OmnipathR/internal/urls.json` (encoding: UTF-8). [2023-04-28 23:58:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-28 23:58:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.17/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2023-04-28 23:58:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-28 23:58:58] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package keeps a record of temporary installation path * DONE (OmnipathR) 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/Rtmp4UawQY/remotes27494825cc4f5f/saezlab-decoupleR-3d343dd/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_2.5.0.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) Downloading GitHub repo LTLA/basilisk.utils@HEAD Skipping 1 packages not available: filelock ── R CMD build ───────────────────────────────────────────────────────────────── * checking for file ‘/tmp/Rtmp4UawQY/remotes2749481c581644/LTLA-basilisk.utils-7ee5213/DESCRIPTION’ ... OK * preparing ‘basilisk.utils’: * checking DESCRIPTION meta-information ... OK * checking for LF line-endings in source and make files and shell scripts * checking for empty or unneeded directories * building ‘basilisk.utils_1.11.2.tar.gz’ * 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) Downloading GitHub repo LTLA/basilisk@HEAD Skipping 2 packages not available: filelock, reticulate ── R CMD build ───────────────────────────────────────────────────────────────── * checking for file ‘/tmp/Rtmp4UawQY/remotes2749485f702bef/LTLA-basilisk-6b6ba9f/DESCRIPTION’ ... OK * preparing ‘basilisk’: * checking DESCRIPTION meta-information ... OK * checking for LF line-endings in source and make files and shell scripts * checking for empty or unneeded directories * building ‘basilisk_1.11.3.tar.gz’ * 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) Warning messages: 1: In i.p(...) : installation of package ‘/tmp/Rtmp4UawQY/file274948576a1513/CellChat_1.6.1.tar.gz’ had non-zero exit status 2: In i.p(...) : installation of package ‘/tmp/Rtmp4UawQY/file274948437f6553/CellChat_1.6.1.tar.gz’ had non-zero exit status [ Finished: 2023-04-28 23:59:12 CEST ]