[ Started: 2025-08-26 09:46:09 CEST ] [ decoupleR v2.9.7 for BioC-3.22 from https://github.com/saezlab/decoupleR@devel (930b765 2025-02-15 00:00:59) ] * using log directory ‘/mnt/disk0/build/bioc-check/decoupler/bioc-3.22/2025-08-26_0943/decoupleR/decoupleR.Rcheck’ * using R version 4.5.1 (2025-06-13) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 * running under: Ubuntu 24.04.2 LTS * using session charset: UTF-8 * checking for file ‘decoupleR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘decoupleR’ version ‘2.9.7’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘decoupleR’ can be installed ... OK * checking installed package size ... INFO installed size is 8.5Mb sub-directories of 1Mb or more: doc 6.2Mb extdata 1.5Mb * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking dependencies in R code ... NOTE [2025-08-26 09:46:35] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-26 09:46:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-26 09:46:35] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2025-08-26 09:46:35] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-08-26 07:09:50 UTC; omnipath [2025-08-26 09:46:35] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2025-08-26 09:46:35] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-08-26 07:09:53 UTC; unix [2025-08-26 09:46:35] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.4 [2025-08-26 09:46:35] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2025-08-26 09:46:35] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2025-08-26; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2025-08-26 09:46:35] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/usr/lib/x86_64-linux-gnu/blas/libblas.so.3.12.0; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2025-08-26 09:46:35] [INFO] [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); annotate 1.87.0(2025-04-15); AnnotationDbi 1.71.1(2025-07-29); AUCell 1.31.0(2025-04-15); backports 1.5.0(2024-05-23); beachmat 2.25.5(2025-08-20); Biobase 2.69.0(2025-04-15); BiocGenerics 0.55.1(2025-07-28); BiocParallel 1.43.4(2025-06-16); BiocSingular 1.25.0(2025-04-15); Biostrings 2.77.2(2025-06-22); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); cli 3.6.5(2025-04-23); codetools 0.2-20(2024-03-31); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); data.table 1.17.8(2025-07-10); DBI 1.2.3(2024-06-02); decoupleR 2.9.7(2025-08-26); DelayedArray 0.35.2(2025-06-18); DelayedMatrixStats 1.31.0(2025-04-15); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.4(2025-06-18); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); GenomicRanges 1.61.1(2025-06-22); glue 1.8.0(2024-09-30); graph 1.87.0(2025-04-15); GSEABase 1.71.0(2025-04-15); GSVA 2.3.1(2025-04-24); h5mread 1.1.1(2025-05-18); HDF5Array 1.37.0(2025-04-15); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.1.4(2025-01-23); IRanges 2.43.0(2025-04-15); irlba 2.3.5.1(2022-10-03); jsonlite 2.0.0(2025-03-27); KEGGREST 1.49.1(2025-06-18); knitr 1.50(2025-03-16); later 1.4.3(2025-08-20); lattice 0.22-7(2025-04-02); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magick 2.8.7(2025-06-06); magrittr 2.0.3(2022-03-30); Matrix 1.7-3(2025-03-11); MatrixGenerics 1.21.0(2025-04-15); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); OmnipathR 3.17.4(2025-08-26); parallelly 1.45.1(2025-07-24); pillar 1.11.0(2025-07-04); pkgconfig 2.0.3(2019-09-22); png 0.1-8(2022-11-29); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rhdf5 2.53.4(2025-08-06); rhdf5filters 1.21.0(2025-04-15); Rhdf5lib 1.31.0(2025-04-15); rjson 0.2.23(2024-09-16); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.4.3(2025-08-20); rsvd 1.0.5(2021-04-16); rvest 1.0.4(2024-02-12); S4Arrays 1.9.1(2025-05-29); S4Vectors 0.47.0(2025-04-15); ScaledMatrix 1.17.0(2025-04-15); Seqinfo 0.99.2(2025-07-22); sessioninfo 1.2.3(2025-02-05); SingleCellExperiment 1.31.1(2025-06-27); SparseArray 1.9.1(2025-07-18); sparseMatrixStats 1.21.0(2025-04-15); SpatialExperiment 1.19.1(2025-05-08); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); SummarizedExperiment 1.39.1(2025-06-22); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); withr 3.0.2(2024-10-28); xfun 0.53(2025-08-19); XML 3.99-0.19(2025-08-22); xml2 1.4.0(2025-08-20); xtable 1.8-4(2019-04-21); XVector 0.49.0(2025-04-15); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13) [2025-08-26 09:46:35] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2025-08-26 09:46:35] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-08-26 09:46:35] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2025-08-26 09:46:35] [TRACE] [OmnipathR] Contains 7 files. [2025-08-26 09:46:35] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-08-26 09:46:35] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-26 09:46:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-26 09:46:35] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2025-08-26 09:46:35] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2025-08-26 09:46:35] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.22/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-08-26 09:46:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-26 09:46:35] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.22/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-08-26 09:46:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-26 09:46:35] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.22/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-08-26 09:46:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-26 09:46:35] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.22/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-08-26 09:46:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-26 09:46:35] [TRACE] [OmnipathR] Cache locked: FALSE * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... WARNING Missing link(s) in Rd file 'run_gsva.Rd': ‘GSVA::gsva’ ‘GeneIdentifierType-class’ ‘GeneIdentifierType’ ‘ExpressionSet’ ‘SummarizedExperiment’ ‘SingleCellExperiment’ See section 'Cross-references' in the 'Writing R Extensions' manual. * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 1 NOTE See ‘/mnt/disk0/build/bioc-check/decoupler/bioc-3.22/2025-08-26_0943/decoupleR/decoupleR.Rcheck/00check.log’ for details. [ Finished: 2025-08-26 09:54:26 CEST ]