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This page was generated on 2025-10-01 12:07 -0400 (Wed, 01 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4843
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4631
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4575
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4576
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1488/2337HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OmnipathR 3.17.6  (landing page)
Denes Turei
Snapshot Date: 2025-09-30 13:45 -0400 (Tue, 30 Sep 2025)
git_url: https://git.bioconductor.org/packages/OmnipathR
git_branch: devel
git_last_commit: 69ba6ef
git_last_commit_date: 2025-09-24 06:19:47 -0400 (Wed, 24 Sep 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    ERROR  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    ERROR    OK  
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    ERROR    OK  
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    ERROR  


CHECK results for OmnipathR on taishan

To the developers/maintainers of the OmnipathR package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/OmnipathR.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: OmnipathR
Version: 3.17.6
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings OmnipathR_3.17.6.tar.gz
StartedAt: 2025-09-30 10:56:50 -0000 (Tue, 30 Sep 2025)
EndedAt: 2025-09-30 11:20:46 -0000 (Tue, 30 Sep 2025)
EllapsedTime: 1435.6 seconds
RetCode: 1
Status:   ERROR  
CheckDir: OmnipathR.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings OmnipathR_3.17.6.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/OmnipathR.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OmnipathR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OmnipathR’ version ‘3.17.6’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 35 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 ‘OmnipathR’ can be installed ... OK
* checking installed package size ... OK
* checking package 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 whether startup messages can be suppressed ... NOTE
[2025-09-30 10:57:39] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-09-30 10:57:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-30 10:57:39] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-09-30 10:57:39] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-09-30 10:57:39] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-09-29
[2025-09-30 10:57:39] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-09-29 20:39:00 UTC; unix
[2025-09-30 10:57:39] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.17.6
[2025-09-30 10:57:39] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-09-30 10:57:40] [INFO]    [OmnipathR] Session info: [version=R version 4.5.0 (2025-04-11); os=openEuler 24.03 (LTS); system=aarch64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=UTC; date=2025-09-30; pandoc=2.12 @ /home/biocbuild/bin/ (via rmarkdown); quarto=1.7.32 @ /home/biocbuild/bioconductor/quarto-1.7.32/bin/quarto]
[2025-09-30 10:57:40] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.51.0; png=1.6.47; jpeg=6.2; tiff=LIBTIFF, Version 4.7.0; tcl=8.6.14; curl=8.13.0; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.8.1; deflate=; PCRE=10.44 2024-06-07; ICU=74.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.38; readline=8.2; BLAS=/usr/lib64/libopenblas-r0.3.25.so; lapack=/usr/lib64/libopenblas-r0.3.25.so; lapack_version=3.11.0]
[2025-09-30 10:57:41] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); 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); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); 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); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.17.6(2025-09-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); 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); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.3(2025-08-20); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.2(2025-09-08); 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 0.53(2025-08-19); XML 3.99-0.19(2025-08-22); xml2 1.4.0(2025-08-20); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-09-30 10:57:41] [INFO]    [OmnipathR] CURL: version: 8.13.0; headers: 8.13.0; ssl_version: OpenSSL/3.5.0; libz_version: 1.3.1; libssh_version: libssh2/1.11.1; libidn_version: NA; host: aarch64-conda-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, mqtt, pop3, pop3s, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2025-09-30 10:57:41] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-09-30 10:57:41] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-09-30 10:57:41] [TRACE]   [OmnipathR] Contains 1 files.
[2025-09-30 10:57:41] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-09-30 10:57:41] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-09-30 10:57:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-30 10:57:41] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-09-30 10:57:41] [TRACE]   [OmnipathR] Pandoc version: `2.12`.
[2025-09-30 10:57:41] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-09-30 10:57:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-30 10:57:41] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-09-30 10:57:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-30 10:57:41] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-09-30 10:57:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-30 10:57:41] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-09-30 10:57:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-30 10:57:41] [TRACE]   [OmnipathR] Cache locked: FALSE

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
[2025-09-30 10:58:10] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-09-30 10:58:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-30 10:58:10] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-09-30 10:58:10] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-09-30 10:58:10] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-09-29
[2025-09-30 10:58:10] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-09-29 20:39:00 UTC; unix
[2025-09-30 10:58:10] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.17.6
[2025-09-30 10:58:10] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-09-30 10:58:11] [INFO]    [OmnipathR] Session info: [version=R version 4.5.0 (2025-04-11); os=openEuler 24.03 (LTS); system=aarch64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=UTC; date=2025-09-30; pandoc=2.12 @ /home/biocbuild/bin/ (via rmarkdown); quarto=1.7.32 @ /home/biocbuild/bioconductor/quarto-1.7.32/bin/quarto]
[2025-09-30 10:58:11] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.51.0; png=1.6.47; jpeg=6.2; tiff=LIBTIFF, Version 4.7.0; tcl=8.6.14; curl=8.13.0; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.8.1; deflate=; PCRE=10.44 2024-06-07; ICU=74.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.38; readline=8.2; BLAS=/usr/lib64/libopenblas-r0.3.25.so; lapack=/usr/lib64/libopenblas-r0.3.25.so; lapack_version=3.11.0]
[2025-09-30 10:58:11] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); 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); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); 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); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.17.6(2025-09-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); 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); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.3(2025-08-20); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.2(2025-09-08); 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 0.53(2025-08-19); XML 3.99-0.19(2025-08-22); xml2 1.4.0(2025-08-20); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-09-30 10:58:11] [INFO]    [OmnipathR] CURL: version: 8.13.0; headers: 8.13.0; ssl_version: OpenSSL/3.5.0; libz_version: 1.3.1; libssh_version: libssh2/1.11.1; libidn_version: NA; host: aarch64-conda-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, mqtt, pop3, pop3s, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2025-09-30 10:58:11] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-09-30 10:58:11] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-09-30 10:58:11] [TRACE]   [OmnipathR] Contains 1 files.
[2025-09-30 10:58:11] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-09-30 10:58:11] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-09-30 10:58:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-30 10:58:11] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-09-30 10:58:11] [TRACE]   [OmnipathR] Pandoc version: `2.12`.
[2025-09-30 10:58:11] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-09-30 10:58:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-30 10:58:11] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-09-30 10:58:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-30 10:58:11] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-09-30 10:58:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-30 10:58:11] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-09-30 10:58:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-30 10:58:11] [TRACE]   [OmnipathR] Cache locked: FALSE
.cosmos_pkn: no visible global function definition for
  ‘metabolite_idsc’
cosmos_ksn: no visible binding for global variable
  ‘substrate_genesymbol’
cosmos_ksn: no visible binding for global variable ‘residue_type’
cosmos_ksn: no visible binding for global variable ‘residue_offset’
cosmos_ksn: no visible binding for global variable ‘enzyme_genesymbol’
cosmos_ksn: no visible binding for global variable ‘mor’
recon3d_genes: no visible binding for global variable ‘notes’
recon3d_genes: no visible binding for global variable ‘annotation’
recon3d_genes: no visible binding for global variable
  ‘original_bigg_ids’
recon3d_metabolites: no visible binding for global variable ‘notes’
recon3d_metabolites: no visible binding for global variable
  ‘original_bigg_ids’
recon3d_metabolites: no visible binding for global variable
  ‘annotation’
recon3d_metabolites: no visible global function definition for
  ‘chalmers_gem_matlab_tibble’
recon3d_metabolites: no visible binding for global variable ‘hmdb’
recon3d_metabolites: no visible binding for global variable ‘metHMDBID’
recon3d_reactions: no visible binding for global variable ‘notes’
recon3d_reactions: no visible binding for global variable ‘metabolites’
recon3d_reactions: no visible binding for global variable
  ‘original_bigg_ids’
taxon_names_table: no visible binding for global variable
  ‘latin_name_uniprot’
taxon_names_table: no visible binding for global variable
  ‘latin_name_ensembl’
taxon_names_table: no visible binding for global variable
  ‘latin_name_oma’
taxon_names_table: no visible binding for global variable
  ‘common_name_ensembl’
taxon_names_table: no visible binding for global variable
  ‘common_name_uniprot’
Undefined global functions or variables:
  annotation chalmers_gem_matlab_tibble common_name_ensembl
  common_name_uniprot enzyme_genesymbol hmdb latin_name_ensembl
  latin_name_oma latin_name_uniprot metHMDBID metabolite_idsc
  metabolites mor notes original_bigg_ids residue_offset residue_type
  substrate_genesymbol
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘recon3d_raw’ ‘recon3d_raw_vmh’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in Rd file 'recon3d.Rd'
  ‘extra_hmdb’

Undocumented arguments in Rd file 'translate_ids_multi.Rd'
  ‘ramp’ ‘expand’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘OmnipathR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: recon3d_metabolites
> ### Title: Metabolites from Recon-3D
> ### Aliases: recon3d_metabolites recon3d_reactions recon3d_genes
> ###   recon3d_compartments
> 
> ### ** Examples
> 
> recon3d_metabolites()
Warning in readLines(con = path, encoding = encoding) :
  incomplete final line found on '/home/biocbuild/.cache/OmnipathR/be81cd1c9a119b749e4206f26272806591e8fb4c-1.gz'
Error in chalmers_gem_matlab_tibble(., "mets", "metHMDBID") : 
  could not find function "chalmers_gem_matlab_tibble"
Calls: recon3d_metabolites ... same_src.data.frame -> is.data.frame -> %>% -> unnest -> unnest
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                                        user system elapsed
annotation_categories                107.073  0.000 123.749
curated_ligrec_stats                  43.533  3.218 207.976
filter_extra_attrs                    36.457  5.491  65.664
omnipath-interactions                 35.085  2.122  92.906
all_uniprots                          32.723  2.226  55.553
extra_attrs_to_cols                   19.187  1.592  25.486
nichenet_gr_network_omnipath          19.670  0.661  25.235
extra_attr_values                     18.240  1.690  39.528
nichenet_signaling_network_omnipath   13.756  0.560  21.702
go_annot_download                     12.974  0.593  37.351
giant_component                       12.208  0.581  19.648
omnipath_for_cosmos                   11.928  0.544  35.072
extra_attrs                           10.378  1.010  17.131
has_extra_attrs                        9.839  1.278  13.520
filter_by_resource                    10.349  0.389  15.400
pivot_annotations                      9.435  0.266  31.614
curated_ligand_receptor_interactions   7.553  0.632  28.450
find_all_paths                         7.403  0.317  13.200
print_interactions                     7.278  0.267  15.031
filter_intercell                       6.943  0.300  19.297
pubmed_open                            5.095  0.106   6.917
omnipath_query                         4.685  0.170   5.073
hpo_download                           3.218  0.202  24.011
print_path_vs                          2.707  0.154   8.167
enzsub_graph                           2.714  0.098   9.110
ensembl_id_mapping_table               2.611  0.118  23.670
kegg_conv                              1.481  0.128   5.439
annotated_network                      1.467  0.090   6.292
metalinksdb_sqlite                     1.107  0.134  14.779
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 2 WARNINGs, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/OmnipathR.Rcheck/00check.log’
for details.


Installation output

OmnipathR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL OmnipathR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘OmnipathR’ ...
** this is package ‘OmnipathR’ version ‘3.17.6’
** 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
[2025-09-29 20:39:20] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-09-29 20:39:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-29 20:39:20] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-09-29 20:39:20] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-09-29 20:39:20] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-09-29
[2025-09-29 20:39:20] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-09-29 20:39:00 UTC; unix
[2025-09-29 20:39:20] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.17.6
[2025-09-29 20:39:20] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-09-29 20:39:21] [INFO]    [OmnipathR] Session info: [version=R version 4.5.0 (2025-04-11); os=openEuler 24.03 (LTS); system=aarch64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=UTC; date=2025-09-29; pandoc=2.12 @ /home/biocbuild/bin/ (via rmarkdown); quarto=1.7.32 @ /home/biocbuild/bioconductor/quarto-1.7.32/bin/quarto]
[2025-09-29 20:39:21] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.51.0; png=1.6.47; jpeg=6.2; tiff=LIBTIFF, Version 4.7.0; tcl=8.6.14; curl=8.13.0; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.8.1; deflate=; PCRE=10.44 2024-06-07; ICU=74.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.38; readline=8.2; BLAS=/usr/lib64/libopenblas-r0.3.25.so; lapack=/usr/lib64/libopenblas-r0.3.25.so; lapack_version=3.11.0]
[2025-09-29 20:39:21] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); 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); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); 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); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.17.6(2025-09-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); 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); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.3(2025-08-20); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.2(2025-09-08); 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 0.53(2025-08-19); XML 3.99-0.19(2025-08-22); xml2 1.4.0(2025-08-20); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-09-29 20:39:21] [INFO]    [OmnipathR] CURL: version: 8.13.0; headers: 8.13.0; ssl_version: OpenSSL/3.5.0; libz_version: 1.3.1; libssh_version: libssh2/1.11.1; libidn_version: NA; host: aarch64-conda-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, mqtt, pop3, pop3s, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2025-09-29 20:39:21] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-09-29 20:39:21] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-09-29 20:39:21] [TRACE]   [OmnipathR] Contains 4 files.
[2025-09-29 20:39:21] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-09-29 20:39:21] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-09-29 20:39:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-29 20:39:21] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-09-29 20:39:21] [TRACE]   [OmnipathR] Pandoc version: `2.12`.
[2025-09-29 20:39:21] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-09-29 20:39:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-29 20:39:21] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-09-29 20:39:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-29 20:39:21] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-09-29 20:39:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-29 20:39:21] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-09-29 20:39:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-29 20:39:21] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2025-09-29 20:39:24] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-09-29 20:39:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-29 20:39:24] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-09-29 20:39:24] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-09-29 20:39:24] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-09-29
[2025-09-29 20:39:24] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-09-29 20:39:00 UTC; unix
[2025-09-29 20:39:24] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.17.6
[2025-09-29 20:39:24] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-09-29 20:39:24] [INFO]    [OmnipathR] Session info: [version=R version 4.5.0 (2025-04-11); os=openEuler 24.03 (LTS); system=aarch64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=UTC; date=2025-09-29; pandoc=2.12 @ /home/biocbuild/bin/ (via rmarkdown); quarto=1.7.32 @ /home/biocbuild/bioconductor/quarto-1.7.32/bin/quarto]
[2025-09-29 20:39:24] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.51.0; png=1.6.47; jpeg=6.2; tiff=LIBTIFF, Version 4.7.0; tcl=8.6.14; curl=8.13.0; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.8.1; deflate=; PCRE=10.44 2024-06-07; ICU=74.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.38; readline=8.2; BLAS=/usr/lib64/libopenblas-r0.3.25.so; lapack=/usr/lib64/libopenblas-r0.3.25.so; lapack_version=3.11.0]
[2025-09-29 20:39:25] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); 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); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); 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); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.17.6(2025-09-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); 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); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.3(2025-08-20); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.2(2025-09-08); 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 0.53(2025-08-19); XML 3.99-0.19(2025-08-22); xml2 1.4.0(2025-08-20); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-09-29 20:39:25] [INFO]    [OmnipathR] CURL: version: 8.13.0; headers: 8.13.0; ssl_version: OpenSSL/3.5.0; libz_version: 1.3.1; libssh_version: libssh2/1.11.1; libidn_version: NA; host: aarch64-conda-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, mqtt, pop3, pop3s, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2025-09-29 20:39:25] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-09-29 20:39:25] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-09-29 20:39:25] [TRACE]   [OmnipathR] Contains 1 files.
[2025-09-29 20:39:25] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-09-29 20:39:25] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-09-29 20:39:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-29 20:39:25] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-09-29 20:39:25] [TRACE]   [OmnipathR] Pandoc version: `2.12`.
[2025-09-29 20:39:25] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-09-29 20:39:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-29 20:39:25] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-09-29 20:39:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-29 20:39:25] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-09-29 20:39:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-29 20:39:25] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-09-29 20:39:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-29 20:39:25] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package keeps a record of temporary installation path
* DONE (OmnipathR)

Tests output

OmnipathR.Rcheck/tests/testthat.Rout


R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> #!/usr/bin/env Rscript
> 
> #
> #  This file is part of the `OmnipathR` R package
> #
> #  Copyright
> #  2018-2024
> #  Saez Lab, Uniklinik RWTH Aachen, Heidelberg University
> #
> #  File author(s): Alberto Valdeolivas
> #                  Dénes Türei (turei.denes@gmail.com)
> #                  Attila Gábor
> #
> #  Distributed under the MIT (Expat) License.
> #  See accompanying file `LICENSE` or find a copy at
> #      https://directory.fsf.org/wiki/License:Expat
> #
> #  Website: https://r.omnipathdb.org/
> #  Git repo: https://github.com/saezlab/OmnipathR
> #
> 
> 
> library(testthat)
> library(OmnipathR)
[2025-09-30 11:18:30] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-09-30 11:18:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-30 11:18:30] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-09-30 11:18:30] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-09-30 11:18:30] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-09-29
[2025-09-30 11:18:30] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-09-29 20:39:00 UTC; unix
[2025-09-30 11:18:30] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.17.6
[2025-09-30 11:18:30] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-09-30 11:18:32] [INFO]    [OmnipathR] Session info: [version=R version 4.5.0 (2025-04-11); os=openEuler 24.03 (LTS); system=aarch64, linux-gnu; ui=X11; language=C; collate=C; ctype=en_US.UTF-8; tz=UTC; date=2025-09-30; pandoc=2.12 @ /home/biocbuild/bin/ (via rmarkdown); quarto=1.7.32 @ /home/biocbuild/bioconductor/quarto-1.7.32/bin/quarto]
[2025-09-30 11:18:32] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.51.0; png=1.6.47; jpeg=6.2; tiff=LIBTIFF, Version 4.7.0; tcl=8.6.14; curl=8.13.0; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.8.1; deflate=; PCRE=10.44 2024-06-07; ICU=74.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.38; readline=8.2; BLAS=/usr/lib64/libopenblas-r0.3.25.so; lapack=/usr/lib64/libopenblas-r0.3.25.so; lapack_version=3.11.0]
[2025-09-30 11:18:33] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); brio 1.1.5(2024-04-24); 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); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); 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); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.17.6(2025-09-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); 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); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.3(2025-08-20); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.2(2025-09-08); testthat 3.2.3(2025-01-13); 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); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-09-30 11:18:33] [INFO]    [OmnipathR] CURL: version: 8.13.0; headers: 8.13.0; ssl_version: OpenSSL/3.5.0; libz_version: 1.3.1; libssh_version: libssh2/1.11.1; libidn_version: NA; host: aarch64-conda-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, mqtt, pop3, pop3s, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2025-09-30 11:18:33] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-09-30 11:18:33] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-09-30 11:18:33] [TRACE]   [OmnipathR] Contains 12 files.
[2025-09-30 11:18:33] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-09-30 11:18:33] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-09-30 11:18:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-30 11:18:33] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-09-30 11:18:33] [TRACE]   [OmnipathR] Pandoc version: `2.12`.
[2025-09-30 11:18:33] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-09-30 11:18:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-30 11:18:33] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-09-30 11:18:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-30 11:18:33] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-09-30 11:18:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-30 11:18:33] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-09-30 11:18:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-30 11:18:33] [TRACE]   [OmnipathR] Cache locked: FALSE
> 
> test_check('OmnipathR')
[ FAIL 0 | WARN 12 | SKIP 0 | PASS 38 ]

[ FAIL 0 | WARN 12 | SKIP 0 | PASS 38 ]
> 
> proc.time()
   user  system elapsed 
 57.786   3.469 122.998 

Example timings

OmnipathR.Rcheck/OmnipathR-Ex.timings

nameusersystemelapsed
OmnipathR000
all_uniprot_acs0.0250.0000.025
all_uniprots32.723 2.22655.553
ancestors0.0130.0000.025
annotated_network1.4670.0906.292
annotation_categories107.073 0.000123.749
annotation_resources0.0860.0001.164
annotations0.7050.0002.897
biomart_query1.2720.0572.995
bioplex10.0110.0000.011
bioplex20.0110.0000.011
bioplex30.0110.0000.011
bioplex_all0.0110.0000.011
bioplex_hct116_10.0110.0000.012
bma_motif_es0.7530.0732.920
bma_motif_vs0.2580.0171.515
chalmers_gem0.0130.0000.013
chalmers_gem_id_mapping_table0.0130.0000.012
chalmers_gem_id_type0.0000.0020.002
chalmers_gem_metabolites0.0130.0000.013
chalmers_gem_network0.0140.0000.013
chalmers_gem_raw0.0060.0080.014
chalmers_gem_reactions0.0140.0000.014
common_name0.1660.0080.175
complex_genes0.7830.0303.499
complex_resources0.0830.0001.175
complexes0.2160.0141.499
consensuspathdb_download000
consensuspathdb_raw_table0.0450.0040.100
cosmos_pkn000
curated_ligand_receptor_interactions 7.553 0.63228.450
curated_ligrec_stats 43.533 3.218207.976
database_summary2.0070.1354.371
descendants0.0140.0000.029
ensembl_dataset0.0600.0000.118
ensembl_id_mapping_table 2.611 0.11823.670
ensembl_id_type0.0030.0000.003
ensembl_name0.3570.0050.727
ensembl_organisms0.1660.0090.344
ensembl_organisms_raw0.1540.0140.334
ensembl_orthology0.0000.0000.005
enzsub_graph2.7140.0989.110
enzsub_resources0.1040.0061.290
enzyme_substrate1.5080.0544.159
evex_download0.0130.0010.025
evidences000
extra_attr_values18.240 1.69039.528
extra_attrs10.378 1.01017.131
extra_attrs_to_cols19.187 1.59225.486
filter_by_resource10.349 0.38915.400
filter_extra_attrs36.457 5.49165.664
filter_intercell 6.943 0.30019.297
filter_intercell_network0.0280.0010.062
find_all_paths 7.403 0.31713.200
from_evidences0.0010.0000.001
get_db0.0000.0010.000
get_ontology_db0.0100.0030.013
giant_component12.208 0.58119.648
go_annot_download12.974 0.59337.351
go_annot_slim0.0010.0000.000
go_ontology_download0.0140.0000.014
guide2pharma_download0.0090.0040.013
harmonizome_download0.0100.0040.013
has_extra_attrs 9.839 1.27813.520
hmdb_id_mapping_table0.0130.0000.013
hmdb_id_type0.0030.0000.003
hmdb_metabolite_fields0.0000.0000.001
hmdb_protein_fields000
hmdb_table0.0130.0000.013
homologene_download0.0130.0000.014
homologene_raw0.0680.0000.069
homologene_uniprot_orthology0.0130.0000.013
hpo_download 3.218 0.20224.011
htridb_download0.0090.0040.012
id_translation_resources000
id_types0.0420.0220.063
inbiomap_download0.0000.0000.001
inbiomap_raw000
interaction_datasets0.8010.0421.787
interaction_graph0.4950.0201.939
interaction_resources0.0920.0021.177
interaction_types0.0940.0050.284
intercell0.8720.0672.269
intercell_categories0.7320.0421.778
intercell_consensus_filter1.4750.0573.856
intercell_generic_categories0.0950.0080.104
intercell_network0.0090.0050.013
intercell_resources0.0830.0011.188
intercell_summary0.0910.0080.099
is_ontology_id000
is_swissprot0.0650.0130.078
is_trembl0.0700.0080.079
is_uniprot0.0120.0040.016
kegg_api_templates0.0010.0000.001
kegg_conv1.4810.1285.439
kegg_databases000
kegg_ddi0.6850.0401.691
kegg_find0.6500.0402.127
kegg_info0.0120.0000.012
kegg_link0.7210.0412.780
kegg_list0.6590.0271.481
kegg_open0.0130.0010.027
kegg_operations000
kegg_organism_codes0.0190.0040.029
kegg_organisms0.0200.0080.029
kegg_pathway_annotations000
kegg_pathway_download0.0090.0030.012
kegg_pathway_list0.0070.0040.012
kegg_pathways_download000
kegg_picture0.9570.0372.556
kegg_process0.0210.0040.026
kegg_query0.010.000.01
kegg_request0.0820.0000.127
kegg_rm_prefix0.7540.0694.362
kinasephos1.0250.1094.488
latin_name0.2890.0150.306
load_db0.0950.0170.113
metalinksdb_sqlite 1.107 0.13414.779
metalinksdb_table0.2770.0170.393
metalinksdb_tables0.0180.0040.024
ncbi_taxid0.2890.0030.293
nichenet_build_model0.0000.0000.001
nichenet_expression_data0.0150.0000.015
nichenet_gr_network0.0340.0040.039
nichenet_gr_network_evex0.0120.0000.012
nichenet_gr_network_harmonizome0.0130.0000.013
nichenet_gr_network_htridb0.0120.0000.012
nichenet_gr_network_omnipath19.670 0.66125.235
nichenet_gr_network_pathwaycommons0.0130.0010.031
nichenet_gr_network_regnetwork0.0140.0000.026
nichenet_gr_network_remap0.0100.0040.030
nichenet_gr_network_trrust0.0110.0050.027
nichenet_ligand_activities0.0010.0000.001
nichenet_ligand_target_links000
nichenet_ligand_target_matrix000
nichenet_lr_network0.040.000.04
nichenet_lr_network_guide2pharma0.0140.0000.013
nichenet_lr_network_omnipath0.0320.0080.039
nichenet_lr_network_ramilowski0.0130.0000.013
nichenet_main000
nichenet_networks0.0640.0000.064
nichenet_optimization0.0000.0000.001
nichenet_remove_orphan_ligands0.0370.0000.037
nichenet_results_dir000
nichenet_signaling_network0.0390.0000.039
nichenet_signaling_network_cpdb0.0130.0000.013
nichenet_signaling_network_evex0.0130.0000.014
nichenet_signaling_network_harmonizome0.0130.0000.013
nichenet_signaling_network_inbiomap0.0010.0000.000
nichenet_signaling_network_omnipath13.756 0.56021.702
nichenet_signaling_network_pathwaycommons0.3510.0030.467
nichenet_signaling_network_vinayagam0.0120.0000.012
nichenet_test000
nichenet_workarounds000
obo_parser0.1110.0070.849
oma_code0.1430.0090.306
oma_organisms0.0850.0040.177
oma_pairwise0.0090.0040.024
oma_pairwise_genesymbols0.0120.0000.025
oma_pairwise_translated0.0120.0000.023
omnipath-interactions35.085 2.12292.906
omnipath_cache_autoclean000
omnipath_cache_clean0.0140.0000.015
omnipath_cache_clean_db0.1360.0120.149
omnipath_cache_download_ready0.6800.0760.868
omnipath_cache_filter_versions0.1280.0180.203
omnipath_cache_get0.1170.0160.143
omnipath_cache_key0.0020.0000.002
omnipath_cache_latest_or_new0.0670.0210.096
omnipath_cache_load0.5440.0704.195
omnipath_cache_move_in0.2150.0080.251
omnipath_cache_remove0.1380.0020.235
omnipath_cache_save0.2010.0300.402
omnipath_cache_search0.0010.0000.000
omnipath_cache_set_ext0.1000.0130.152
omnipath_cache_update_status0.1900.0080.206
omnipath_cache_wipe000
omnipath_config_path0.0010.0000.010
omnipath_for_cosmos11.928 0.54435.072
omnipath_load_config0.0010.0000.000
omnipath_log000
omnipath_logfile0.0010.0000.001
omnipath_msg0.0030.0040.007
omnipath_query4.6850.1705.073
omnipath_reset_config000
omnipath_save_config000
omnipath_set_cachedir0.0300.0050.034
omnipath_set_console_loglevel0.0040.0000.005
omnipath_set_logfile_loglevel0.0050.0000.004
omnipath_set_loglevel0.0000.0020.003
omnipath_show_db0.0580.0300.089
omnipath_unlock_cache_db000
only_from000
ontology_ensure_id0.0010.0000.001
ontology_ensure_name0.0010.0000.001
ontology_name_id0.0020.0000.002
organism_for0.2010.0040.204
pathwaycommons_download0.0010.0000.001
pivot_annotations 9.435 0.26631.614
preppi_download0.0010.0000.001
preppi_filter0.0010.0010.001
print_bma_motif_es0.5220.0232.490
print_bma_motif_vs0.2060.0021.435
print_interactions 7.278 0.26715.031
print_path_es0.8650.0392.960
print_path_vs2.7070.1548.167
pubmed_open5.0950.1066.917
query_info0.4120.0021.106
ramilowski_download0.0000.0000.001
ramp_id_mapping_table000
ramp_id_type0.0030.0000.002
ramp_sqlite0.0010.0000.001
ramp_table0.0010.0000.001
ramp_tables0.0000.0010.001