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### Running command:
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###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:decoupleR.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings decoupleR_2.15.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/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 ‘2.15.0’
* 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 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 ... OK
* 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
[2025-07-20 21:36:57] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-20 21:36:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-20 21:36:57] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-07-20 21:36:57] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-07-20 21:36:57] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-07-20
[2025-07-20 21:36:57] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-07-20 19:10:14 UTC; unix
[2025-07-20 21:36:57] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.17.4
[2025-07-20 21:36:57] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-07-20 21:36:57] [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); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-07-20; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2025-07-20 21:36:57] [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=/home/biocbuild/bbs-3.22-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-07-20 21:36:57] [INFO]    [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); annotate 1.87.0(2025-07-20); AnnotationDbi 1.71.0(2025-07-20); AUCell 1.31.0(2025-07-20); backports 1.5.0(2024-05-23); beachmat 2.25.2(2025-07-20); Biobase 2.69.0(2025-07-20); BiocGenerics 0.55.0(2025-07-20); BiocParallel 1.43.4(2025-07-20); BiocSingular 1.25.0(2025-07-20); Biostrings 2.77.2(2025-07-20); 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 2.3.2(2024-07-29); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); codetools 0.2-20(2024-03-31); crayon 1.5.3(2024-06-20); curl 6.4.0(2025-06-22); data.table 1.17.8(2025-07-10); DBI 1.2.3(2024-06-02); decoupleR 2.15.0(2025-07-20); DelayedArray 0.35.2(2025-07-20); DelayedMatrixStats 1.31.0(2025-07-20); 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(2025-07-20); glue 1.8.0(2024-09-30); graph 1.87.0(2025-07-20); GSEABase 1.71.0(2025-07-20); GSVA 2.3.1(2025-07-20); h5mread 1.1.1(2025-07-20); HDF5Array 1.37.0(2025-07-20); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.0(2025-07-13); igraph 2.1.4(2025-01-23); IRanges 2.43.0(2025-07-20); irlba 2.3.5.1(2022-10-03); jsonlite 2.0.0(2025-03-27); KEGGREST 1.49.1(2025-07-20); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); 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(2025-07-20); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); OmnipathR 3.17.4(2025-07-20); parallelly 1.45.0(2025-06-02); 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); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.3.3(2025-05-29); ps 1.9.1(2025-04-12); 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 2.53.3(2025-07-20); rhdf5filters 1.21.0(2025-07-20); Rhdf5lib 1.31.0(2025-07-20); rjson 0.2.23(2024-09-16); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.4.2(2025-07-18); rsvd 1.0.5(2021-04-16); rvest 1.0.4(2024-02-12); S4Arrays 1.9.1(2025-07-20); S4Vectors 0.47.0(2025-07-20); ScaledMatrix 1.17.0(2025-07-20); Seqinfo 0.99.1(2025-07-20); sessioninfo 1.2.3(2025-02-05); SingleCellExperiment 1.31.1(2025-07-20); SparseArray 1.9.1(2025-07-20); sparseMatrixStats 1.21.0(2025-07-20); SpatialExperiment 1.19.1(2025-07-20); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); SummarizedExperiment 1.39.1(2025-07-20); 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); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); xtable 1.8-4(2019-04-21); XVector 0.49.0(2025-07-20); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-07-20 21:36:57] [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
[2025-07-20 21:36:57] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-07-20 21:36:57] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-07-20 21:36:57] [TRACE]   [OmnipathR] Contains 9 files.
[2025-07-20 21:36:57] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-07-20 21:36:57] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-20 21:36:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-20 21:36:57] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-07-20 21:36:57] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-07-20 21:36:57] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-07-20 21:36:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-20 21:36:57] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-07-20 21:36:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-20 21:36:57] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-07-20 21:36:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-20 21:36:57] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-07-20 21:36:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-20 21:36:57] [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’ ‘GeneSetCollection’

Non-topic package-anchored link(s) in Rd file 'pipe.Rd':
  ‘[magrittr:pipe]{%>%}’

See section 'Cross-references' in the 'Writing R Extensions' manual.

Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  run_gsva.Rd: GSVA::gsva, GeneSetCollection
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system  elapsed
get_collectri 28.949  2.943  103.982
run_fgsea     22.211  0.523   22.749
get_dorothea  21.198  1.479  170.653
get_progeny    9.472  2.010 1323.095
run_aucell     9.409  1.664   11.122
get_resource   1.041  0.086   14.472
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’