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This page was generated on 2025-10-22 12:05 -0400 (Wed, 22 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4890
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4680
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4625
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4642
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 1499/2355HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OmnipathR 3.17.6  (landing page)
Denes Turei
Snapshot Date: 2025-10-21 13:45 -0400 (Tue, 21 Oct 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 12.7.6 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    NA  


CHECK results for OmnipathR on lconway

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.

raw results


Summary

Package: OmnipathR
Version: 3.17.6
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings OmnipathR_3.17.6.tar.gz
StartedAt: 2025-10-21 23:47:54 -0400 (Tue, 21 Oct 2025)
EndedAt: 2025-10-22 00:07:04 -0400 (Wed, 22 Oct 2025)
EllapsedTime: 1149.3 seconds
RetCode: 1
Status:   ERROR  
CheckDir: OmnipathR.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings OmnipathR_3.17.6.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/OmnipathR.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* 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 whether startup messages can be suppressed ... NOTE
[2025-10-21 23:48:32] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-21 23:48:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-21 23:48:32] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-10-21 23:48:32] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-10-21 23:48:32] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-10-21
[2025-10-21 23:48:32] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-10-21 19:13:01 UTC; unix
[2025-10-21 23:48:32] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.17.6
[2025-10-21 23:48:32] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-10-21 23:48:33] [INFO]    [OmnipathR] Session info: [version=R version 4.5.1 Patched (2025-09-10 r88807); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-10-21; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto]
[2025-10-21 23:48:33] [INFO]    [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.44 2024-06-07; ICU=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-10-21 23:48:33] [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); 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 1.1.4(2025-10-17); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.2.0(2025-10-13); 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(2025-10-21); 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)
[2025-10-21 23:48:33] [INFO]    [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: x86_64-apple-darwin22.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2025-10-21 23:48:33] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-10-21 23:48:33] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-10-21 23:48:33] [TRACE]   [OmnipathR] Contains 1 files.
[2025-10-21 23:48:33] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-10-21 23:48:33] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-21 23:48:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-21 23:48:33] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-10-21 23:48:33] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-10-21 23:48:33] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-10-21 23:48:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-21 23:48:33] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-10-21 23:48:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-21 23:48:33] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-10-21 23:48:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-21 23:48:33] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-10-21 23:48:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-21 23:48:33] [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
[2025-10-21 23:48:59] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-21 23:48:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-21 23:48:59] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-10-21 23:48:59] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-10-21 23:48:59] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-10-21
[2025-10-21 23:48:59] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-10-21 19:13:01 UTC; unix
[2025-10-21 23:48:59] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.17.6
[2025-10-21 23:48:59] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-10-21 23:48:59] [INFO]    [OmnipathR] Session info: [version=R version 4.5.1 Patched (2025-09-10 r88807); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-10-21; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto]
[2025-10-21 23:49:00] [INFO]    [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.44 2024-06-07; ICU=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-10-21 23:49:00] [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 1.1.4(2025-10-17); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.2.0(2025-10-13); 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(2025-10-21); 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)
[2025-10-21 23:49:00] [INFO]    [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: x86_64-apple-darwin22.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2025-10-21 23:49:00] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-10-21 23:49:00] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-10-21 23:49:00] [TRACE]   [OmnipathR] Contains 1 files.
[2025-10-21 23:49:00] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-10-21 23:49:00] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-21 23:49:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-21 23:49:00] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-10-21 23:49:00] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-10-21 23:49:00] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-10-21 23:49:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-21 23:49:00] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-10-21 23:49:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-21 23:49:00] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-10-21 23:49:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-21 23:49:00] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-10-21 23:49:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-21 23:49:00] [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 '/Users/biocbuild/Library/Caches/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
curated_ligrec_stats                 46.139 19.793 141.200
annotation_categories                58.858  0.452  61.109
filter_extra_attrs                   43.089 12.483  68.009
omnipath-interactions                33.384  3.107  59.775
all_uniprots                         26.400  3.075  50.456
extra_attrs_to_cols                  18.635  3.792  22.652
extra_attr_values                    17.133  3.202  27.603
nichenet_gr_network_omnipath         17.919  1.789  21.885
curated_ligand_receptor_interactions  8.302  9.542  29.622
go_annot_download                    14.079  1.803  14.770
nichenet_signaling_network_omnipath  12.634  1.182  16.160
extra_attrs                          10.704  3.045  13.870
giant_component                      12.123  1.165  16.241
has_extra_attrs                      10.025  2.908  12.929
omnipath_for_cosmos                  10.590  0.946  99.220
pivot_annotations                    10.087  1.021  19.609
filter_by_resource                    9.956  0.784  13.155
filter_intercell                      8.640  0.667  16.204
find_all_paths                        7.667  0.511   8.299
print_interactions                    6.949  0.557  11.649
enzsub_graph                          3.299  0.258   7.155
print_path_vs                         2.899  0.331   5.751
ensembl_id_mapping_table              2.601  0.551  19.057
database_summary                      2.316  0.230   5.193
kegg_conv                             1.530  0.212  11.971
metalinksdb_sqlite                    1.052  0.322  10.155
kinasephos                            1.068  0.168  17.822
kegg_picture                          1.076  0.055   6.330
kegg_rm_prefix                        0.848  0.104   5.252
kegg_link                             0.764  0.095   6.261
* 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
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/OmnipathR.Rcheck/00check.log’
for details.


Installation output

OmnipathR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL OmnipathR
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/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
[2025-10-21 15:13:14] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-21 15:13:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-21 15:13:14] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-10-21 15:13:14] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-10-21 15:13:14] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-10-21
[2025-10-21 15:13:14] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-10-21 19:13:01 UTC; unix
[2025-10-21 15:13:14] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.17.6
[2025-10-21 15:13:14] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-10-21 15:13:17] [INFO]    [OmnipathR] Session info: [version=R version 4.5.1 Patched (2025-09-10 r88807); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-10-21; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto]
[2025-10-21 15:13:17] [INFO]    [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.44 2024-06-07; ICU=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-10-21 15:13:17] [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 1.1.4(2025-10-17); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.2.0(2025-10-13); 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(2025-10-21); 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)
[2025-10-21 15:13:17] [INFO]    [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: x86_64-apple-darwin22.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2025-10-21 15:13:17] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-10-21 15:13:17] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-10-21 15:13:17] [TRACE]   [OmnipathR] Contains 1 files.
[2025-10-21 15:13:17] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-10-21 15:13:17] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-21 15:13:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-21 15:13:17] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-10-21 15:13:17] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-10-21 15:13:17] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-10-21 15:13:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-21 15:13:17] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-10-21 15:13:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-21 15:13:17] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-10-21 15:13:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-21 15:13:17] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-10-21 15:13:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-21 15:13:17] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2025-10-21 15:13:19] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-21 15:13:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-21 15:13:19] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-10-21 15:13:19] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-10-21 15:13:19] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-10-21
[2025-10-21 15:13:19] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-10-21 19:13:01 UTC; unix
[2025-10-21 15:13:19] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.17.6
[2025-10-21 15:13:19] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-10-21 15:13:20] [INFO]    [OmnipathR] Session info: [version=R version 4.5.1 Patched (2025-09-10 r88807); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-10-21; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto]
[2025-10-21 15:13:20] [INFO]    [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.44 2024-06-07; ICU=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-10-21 15:13:20] [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 1.1.4(2025-10-17); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.2.0(2025-10-13); 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(2025-10-21); 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)
[2025-10-21 15:13:20] [INFO]    [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: x86_64-apple-darwin22.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2025-10-21 15:13:20] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-10-21 15:13:20] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-10-21 15:13:20] [TRACE]   [OmnipathR] Contains 1 files.
[2025-10-21 15:13:20] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-10-21 15:13:20] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-21 15:13:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-21 15:13:20] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-10-21 15:13:20] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-10-21 15:13:20] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-10-21 15:13:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-21 15:13:20] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-10-21 15:13:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-21 15:13:21] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-10-21 15:13:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-21 15:13:21] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-10-21 15:13:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-21 15:13:21] [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 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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)
[2025-10-22 00:05:23] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-22 00:05:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-22 00:05:23] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-10-22 00:05:23] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-10-22 00:05:23] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-10-21
[2025-10-22 00:05:23] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-10-21 19:13:01 UTC; unix
[2025-10-22 00:05:23] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.17.6
[2025-10-22 00:05:23] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-10-22 00:05:24] [INFO]    [OmnipathR] Session info: [version=R version 4.5.1 Patched (2025-09-10 r88807); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=C; collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-10-22; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto]
[2025-10-22 00:05:25] [INFO]    [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.44 2024-06-07; ICU=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-10-22 00:05:25] [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); 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); 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 1.1.4(2025-10-17); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.2.0(2025-10-13); 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(2025-10-21); 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); 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); 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)
[2025-10-22 00:05:25] [INFO]    [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: x86_64-apple-darwin22.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2025-10-22 00:05:25] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-10-22 00:05:25] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-10-22 00:05:25] [TRACE]   [OmnipathR] Contains 12 files.
[2025-10-22 00:05:25] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-10-22 00:05:25] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-22 00:05:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-22 00:05:25] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-10-22 00:05:25] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-10-22 00:05:25] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-10-22 00:05:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-22 00:05:25] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-10-22 00:05:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-22 00:05:25] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-10-22 00:05:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-22 00:05:25] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-10-22 00:05:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-22 00:05:25] [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 
 49.109   6.220  85.024 

Example timings

OmnipathR.Rcheck/OmnipathR-Ex.timings

nameusersystemelapsed
OmnipathR0.0000.0000.001
all_uniprot_acs0.0190.0020.022
all_uniprots26.400 3.07550.456
ancestors0.0100.0020.012
annotated_network1.4460.1404.786
annotation_categories58.858 0.45261.109
annotation_resources0.0780.0310.794
annotations0.7190.1701.660
biomart_query1.6130.6674.730
bioplex10.0130.0050.017
bioplex20.0120.0040.017
bioplex30.0120.0040.017
bioplex_all0.0130.0040.018
bioplex_hct116_10.0120.0050.018
bma_motif_es0.8050.3501.788
bma_motif_vs0.2630.0841.007
chalmers_gem0.0130.0040.017
chalmers_gem_id_mapping_table0.0130.0040.016
chalmers_gem_id_type0.0030.0010.004
chalmers_gem_metabolites0.0130.0060.020
chalmers_gem_network0.0110.0050.016
chalmers_gem_raw0.0120.0050.016
chalmers_gem_reactions0.0110.0060.016
common_name0.1230.0320.161
complex_genes0.7820.6583.742
complex_resources0.0710.0750.766
complexes0.1940.1431.105
consensuspathdb_download0.0000.0010.003
consensuspathdb_raw_table0.0110.0070.017
cosmos_pkn0.0000.0000.001
curated_ligand_receptor_interactions 8.302 9.54229.622
curated_ligrec_stats 46.139 19.793141.200
database_summary2.3160.2305.193
descendants0.0130.0020.015
ensembl_dataset0.0600.0020.108
ensembl_id_mapping_table 2.601 0.55119.057
ensembl_id_type0.0020.0000.003
ensembl_name0.2940.0270.334
ensembl_organisms0.1620.0320.197
ensembl_organisms_raw0.1630.0330.199
ensembl_orthology000
enzsub_graph3.2990.2587.155
enzsub_resources0.0800.0080.670
enzyme_substrate1.8830.0933.640
evex_download0.0130.0020.015
evidences000
extra_attr_values17.133 3.20227.603
extra_attrs10.704 3.04513.870
extra_attrs_to_cols18.635 3.79222.652
filter_by_resource 9.956 0.78413.155
filter_extra_attrs43.08912.48368.009
filter_intercell 8.640 0.66716.204
filter_intercell_network0.0230.0040.027
find_all_paths7.6670.5118.299
from_evidences0.0000.0010.001
get_db0.0010.0000.000
get_ontology_db0.0110.0010.013
giant_component12.123 1.16516.241
go_annot_download14.079 1.80314.770
go_annot_slim0.0000.0010.001
go_ontology_download0.0120.0020.014
guide2pharma_download0.0110.0020.014
harmonizome_download0.0120.0020.014
has_extra_attrs10.025 2.90812.929
hmdb_id_mapping_table0.0110.0020.014
hmdb_id_type0.0020.0010.003
hmdb_metabolite_fields0.0000.0010.001
hmdb_protein_fields0.0000.0000.001
hmdb_table0.0110.0020.012
homologene_download0.0100.0020.012
homologene_raw0.0580.0040.063
homologene_uniprot_orthology0.0120.0020.014
hpo_download3.0390.5343.503
htridb_download0.0110.0020.013
id_translation_resources000
id_types0.0620.0130.075
inbiomap_download0.0000.0010.001
inbiomap_raw000
interaction_datasets0.7420.0921.195
interaction_graph0.4890.0341.039
interaction_resources0.0640.0090.584
interaction_types0.0820.0070.091
intercell0.8780.1161.889
intercell_categories0.6930.0981.015
intercell_consensus_filter1.5530.1643.431
intercell_generic_categories0.0910.0080.100
intercell_network0.0110.0020.014
intercell_resources0.0620.0080.583
intercell_summary0.0890.0220.111
is_ontology_id0.0010.0000.001
is_swissprot0.0600.0050.065
is_trembl0.0580.0060.064
is_uniprot0.0120.0030.014
kegg_api_templates0.0010.0020.004
kegg_conv 1.530 0.21211.971
kegg_databases0.0000.0010.000
kegg_ddi0.7000.0772.122
kegg_find0.6620.0722.783
kegg_info0.0110.0020.012
kegg_link0.7640.0956.261
kegg_list0.6540.0731.667
kegg_open0.0100.0020.013
kegg_operations0.0000.0000.001
kegg_organism_codes0.0240.0640.089
kegg_organisms0.0300.0070.037
kegg_pathway_annotations0.0000.0000.001
kegg_pathway_download0.0110.0010.013
kegg_pathway_list0.0100.0020.012
kegg_pathways_download000
kegg_picture1.0760.0556.330
kegg_process0.0220.0030.026
kegg_query0.0100.0010.011
kegg_request0.0770.0090.087
kegg_rm_prefix0.8480.1045.252
kinasephos 1.068 0.16817.822
latin_name0.2340.0090.246
load_db0.0970.0210.119
metalinksdb_sqlite 1.052 0.32210.155
metalinksdb_table0.2660.0490.321
metalinksdb_tables0.0200.0040.024
ncbi_taxid0.2520.0090.263
nichenet_build_model000
nichenet_expression_data0.0120.0020.014
nichenet_gr_network0.0290.0050.034
nichenet_gr_network_evex0.0100.0020.011
nichenet_gr_network_harmonizome0.0100.0020.012
nichenet_gr_network_htridb0.0100.0010.012
nichenet_gr_network_omnipath17.919 1.78921.885
nichenet_gr_network_pathwaycommons0.0130.0020.014
nichenet_gr_network_regnetwork0.0100.0010.012
nichenet_gr_network_remap0.0100.0020.012
nichenet_gr_network_trrust0.0120.0030.014
nichenet_ligand_activities0.0010.0010.001
nichenet_ligand_target_links0.0000.0010.001
nichenet_ligand_target_matrix0.0000.0010.001
nichenet_lr_network0.0300.0050.036
nichenet_lr_network_guide2pharma0.0110.0020.013
nichenet_lr_network_omnipath0.0340.0060.039
nichenet_lr_network_ramilowski0.0110.0020.013
nichenet_main000
nichenet_networks0.0550.0110.066
nichenet_optimization0.0000.0000.001
nichenet_remove_orphan_ligands0.0330.0050.039
nichenet_results_dir0.0000.0000.001
nichenet_signaling_network0.0350.0060.041
nichenet_signaling_network_cpdb0.0110.0020.014
nichenet_signaling_network_evex0.0090.0020.011
nichenet_signaling_network_harmonizome0.0100.0020.012
nichenet_signaling_network_inbiomap0.0000.0010.000
nichenet_signaling_network_omnipath12.634 1.18216.160
nichenet_signaling_network_pathwaycommons0.0170.0030.020
nichenet_signaling_network_vinayagam0.0150.0020.016
nichenet_test0.0010.0000.001
nichenet_workarounds0.0000.0010.001
obo_parser0.0970.0222.222
oma_code0.1260.0050.132
oma_organisms0.0760.0150.092
oma_pairwise0.0110.0020.014
oma_pairwise_genesymbols0.0110.0010.013
oma_pairwise_translated0.0090.0010.011
omnipath-interactions33.384 3.10759.775
omnipath_cache_autoclean000
omnipath_cache_clean0.0120.0030.016
omnipath_cache_clean_db0.1160.0200.135
omnipath_cache_download_ready0.5720.1250.771
omnipath_cache_filter_versions0.1040.0300.140
omnipath_cache_get0.0870.0200.108
omnipath_cache_key0.0020.0000.002
omnipath_cache_latest_or_new0.0640.0140.079
omnipath_cache_load0.5460.0442.669
omnipath_cache_move_in0.1660.0390.213
omnipath_cache_remove0.1040.0270.145
omnipath_cache_save0.1520.0300.193
omnipath_cache_search0.0010.0000.001
omnipath_cache_set_ext0.1310.0250.163
omnipath_cache_update_status0.0910.0210.113
omnipath_cache_wipe000
omnipath_config_path0.0000.0010.000
omnipath_for_cosmos10.590 0.94699.220
omnipath_load_config000
omnipath_log0.0000.0010.000
omnipath_logfile0.0020.0000.002
omnipath_msg0.0070.0010.008
omnipath_query4.1320.2494.416
omnipath_reset_config000
omnipath_save_config000
omnipath_set_cachedir0.0280.0060.034
omnipath_set_console_loglevel0.0030.0010.003
omnipath_set_logfile_loglevel0.0040.0000.005
omnipath_set_loglevel0.0020.0000.002
omnipath_show_db0.0770.0180.099
omnipath_unlock_cache_db000
only_from000
ontology_ensure_id0.0000.0010.001
ontology_ensure_name0.0000.0000.001
ontology_name_id0.0010.0000.002
organism_for0.1840.0090.195
pathwaycommons_download0.0010.0010.001
pivot_annotations10.087 1.02119.609
preppi_download0.0000.0010.001
preppi_filter000
print_bma_motif_es0.4980.0801.273
print_bma_motif_vs0.1430.0250.632
print_interactions 6.949 0.55711.649
print_path_es0.9000.0912.446
print_path_vs2.8990.3315.751
pubmed_open4.6610.2704.978
query_info0.4460.0370.707
ramilowski_download0.0010.0000.001
ramp_id_mapping_table0.0000.0010.001
ramp_id_type0.0020.0010.003
ramp_sqlite000
ramp_table000
ramp_tables0.0000.0000.001