[ Started: 2024-10-25 12:19:11 CEST ] [ CARNIVAL v2.7.2 for BioC-3.20 from https://github.com/saezlab/CARNIVAL@master (2b8887a 2023-12-06 13:18:32) ] [1] "Libraries: " "/home/omnipath/local/R/4.4-3.20" [3] "/home/omnipath/local/R/4.4" "/usr/lib/R/library" 'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details. Replacement repositories: CRAN: https://cloud.r-project.org Bioconductor version 3.20 (BiocManager 1.30.25), R 4.4.1 (2024-06-14) Old packages: 'MatrixGenerics', 'wppi' trying URL 'https://bioconductor.org/packages/3.20/bioc/src/contrib/MatrixGenerics_1.17.1.tar.gz' Content type 'application/x-gzip' length 31797 bytes (31 KB) ================================================== downloaded 31 KB trying URL 'https://bioconductor.org/packages/3.20/bioc/src/contrib/wppi_1.13.0.tar.gz' Content type 'application/x-gzip' length 662273 bytes (646 KB) ================================================== downloaded 646 KB * installing *source* package ‘MatrixGenerics’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘rowAlls’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colAlls’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowAnyNAs’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colAnyNAs’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowAnys’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colAnys’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowAvgsPerColSet’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colAvgsPerRowSet’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowCollapse’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colCollapse’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowCounts’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colCounts’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowCummaxs’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colCummaxs’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowCummins’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colCummins’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowCumprods’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colCumprods’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowCumsums’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colCumsums’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowDiffs’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colDiffs’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowIQRDiffs’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colIQRDiffs’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowIQRs’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colIQRs’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowLogSumExps’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colLogSumExps’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowMadDiffs’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colMadDiffs’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowMads’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colMads’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowMaxs’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colMaxs’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowMeans2’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colMeans2’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowMedians’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colMedians’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowMins’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colMins’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowOrderStats’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colOrderStats’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowProds’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colProds’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowQuantiles’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colQuantiles’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowRanges’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colRanges’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowRanks’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colRanks’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowSdDiffs’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colSdDiffs’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowSds’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colSds’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowSums2’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colSums2’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowTabulates’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colTabulates’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowVarDiffs’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colVarDiffs’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowVars’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colVars’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowWeightedMads’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colWeightedMads’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowWeightedMeans’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colWeightedMeans’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowWeightedMedians’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colWeightedMedians’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowWeightedSds’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colWeightedSds’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowWeightedVars’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colWeightedVars’ in package ‘MatrixGenerics’ ** help *** installing help indices ** building package indices ** 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 (MatrixGenerics) * installing *source* package ‘wppi’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading [2024-10-25 12:19:20] [INFO] [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`. [2024-10-25 12:19:20] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-10-25 12:19:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-25 12:19:20] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2024-10-25 12:19:20] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-10-25 12:19:20] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2024-10-25 12:19:20] [TRACE] [OmnipathR] Contains 1 files. [2024-10-25 12:19:20] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-10-25 12:19:20] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-10-25 12:19:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-25 12:19:20] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2024-10-25 12:19:20] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2024-10-25 12:19:20] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-10-25 12:19:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-25 12:19:20] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-10-25 12:19:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-25 12:19:20] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-10-25 12:19:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-25 12:19:20] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-10-25 12:19:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-25 12:19:20] [TRACE] [OmnipathR] Cache locked: FALSE Note: wrong number of arguments to '/' ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location [2024-10-25 12:19:23] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-10-25 12:19:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-25 12:19:23] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2024-10-25 12:19:23] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-10-25 12:19:23] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2024-10-25 12:19:23] [TRACE] [OmnipathR] Contains 1 files. [2024-10-25 12:19:23] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-10-25 12:19:23] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-10-25 12:19:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-25 12:19:23] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2024-10-25 12:19:23] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2024-10-25 12:19:23] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-10-25 12:19:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-25 12:19:23] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-10-25 12:19:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-25 12:19:23] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-10-25 12:19:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-25 12:19:23] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-10-25 12:19:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-25 12:19:23] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2024-10-25 12:19:25] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-10-25 12:19:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-25 12:19:25] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2024-10-25 12:19:25] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-10-25 12:19:25] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2024-10-25 12:19:25] [TRACE] [OmnipathR] Contains 1 files. [2024-10-25 12:19:25] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-10-25 12:19:25] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-10-25 12:19:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-25 12:19:25] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2024-10-25 12:19:25] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2024-10-25 12:19:25] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-10-25 12:19:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-25 12:19:25] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-10-25 12:19:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-25 12:19:25] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-10-25 12:19:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-25 12:19:25] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-10-25 12:19:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-25 12:19:25] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package keeps a record of temporary installation path * DONE (wppi) The downloaded source packages are in ‘/tmp/RtmpYRlcNa/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 3.20 (BiocManager 1.30.25), R 4.4.1 (2024-06-14) Warning message: package(s) not installed when version(s) same as or greater than current; use `force = TRUE` to re-install: 'BiocCheck' Skipping 1 packages ahead of CRAN: BiocStyle [ Finished: 2024-10-25 12:19:31 CEST ]