Back to Multiple platform build/check report for BioC 3.22:   simplified   long
ABCDEFGHIJKLMN[O]PQRSTUVWXYZ

This page was generated on 2025-09-26 12:06 -0400 (Fri, 26 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4831
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4619
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4563
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4563
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 1486/2334HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OmnipathR 3.17.6  (landing page)
Denes Turei
Snapshot Date: 2025-09-25 13:45 -0400 (Thu, 25 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    TIMEOUT  skipped


CHECK results for OmnipathR on kjohnson3

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: 2025-09-25 20:46:03 -0400 (Thu, 25 Sep 2025)
EndedAt: 2025-09-25 20:55:48 -0400 (Thu, 25 Sep 2025)
EllapsedTime: 584.9 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: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.7
* 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
[2025-09-25 20:46:16] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-09-25 20:46:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-25 20:46:16] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-09-25 20:46:16] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-09-25 20:46:16] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-09-25
[2025-09-25 20:46:16] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-09-25 19:06:29 UTC; unix
[2025-09-25 20:46:16] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.17.6
[2025-09-25 20:46:16] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-09-25 20:46:16] [INFO]    [OmnipathR] Session info: [version=R version 4.5.1 Patched (2025-09-10 r88807); os=macOS Ventura 13.7.7; system=aarch64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-09-25; pandoc=3.1.12.3 @ /opt/homebrew/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2025-09-25 20:46:16] [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=70.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-09-25 20:46:16] [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(2025-09-25); 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 2.29(2024-11-04); 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)
[2025-09-25 20:46:16] [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: aarch64-apple-darwin23.6.0; 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
[2025-09-25 20:46:16] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-09-25 20:46:16] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-09-25 20:46:16] [TRACE]   [OmnipathR] Contains 1 files.
[2025-09-25 20:46:16] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-09-25 20:46:16] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-09-25 20:46:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-25 20:46:16] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-09-25 20:46:16] [TRACE]   [OmnipathR] Pandoc version: `3.1.12.3`.
[2025-09-25 20:46:16] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-09-25 20:46:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-25 20:46:16] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-09-25 20:46:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-25 20:46:16] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-09-25 20:46:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-25 20:46:16] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-09-25 20:46:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-25 20:46:16] [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
[2025-09-25 20:46:24] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-09-25 20:46:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-25 20:46:24] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-09-25 20:46:24] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-09-25 20:46:24] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-09-25
[2025-09-25 20:46:24] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-09-25 19:06:29 UTC; unix
[2025-09-25 20:46:24] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.17.6
[2025-09-25 20:46:24] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-09-25 20:46:24] [INFO]    [OmnipathR] Session info: [version=R version 4.5.1 Patched (2025-09-10 r88807); os=macOS Ventura 13.7.7; system=aarch64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-09-25; pandoc=3.1.12.3 @ /opt/homebrew/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2025-09-25 20:46:24] [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=70.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-09-25 20:46:24] [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(2025-09-25); 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 2.29(2024-11-04); 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)
[2025-09-25 20:46:24] [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: aarch64-apple-darwin23.6.0; 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
[2025-09-25 20:46:24] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-09-25 20:46:24] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-09-25 20:46:24] [TRACE]   [OmnipathR] Contains 1 files.
[2025-09-25 20:46:24] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-09-25 20:46:24] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-09-25 20:46:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-25 20:46:24] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-09-25 20:46:24] [TRACE]   [OmnipathR] Pandoc version: `3.1.12.3`.
[2025-09-25 20:46:24] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-09-25 20:46:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-25 20:46:24] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-09-25 20:46:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-25 20:46:24] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-09-25 20:46:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-25 20:46:24] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-09-25 20:46:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-25 20:46:24] [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
annotation_categories                37.318  0.041  39.026
curated_ligrec_stats                 14.007  1.974  83.548
omnipath-interactions                11.344  1.089  45.677
filter_extra_attrs                    8.235  2.924  12.605
go_annot_download                     8.283  0.582  13.041
all_uniprots                          6.737  0.688  23.612
extra_attrs_to_cols                   5.322  1.432   6.919
nichenet_gr_network_omnipath          5.534  0.624   8.798
giant_component                       5.170  0.469  10.794
extra_attr_values                     4.461  0.896   9.847
nichenet_signaling_network_omnipath   4.132  0.448   8.625
pivot_annotations                     4.243  0.291  19.536
omnipath_for_cosmos                   3.922  0.278  23.500
has_extra_attrs                       2.752  0.724   5.335
filter_by_resource                    3.187  0.198   5.800
filter_intercell                      2.983  0.196   7.653
curated_ligand_receptor_interactions  2.491  0.387  12.594
print_interactions                    2.681  0.183   8.048
ensembl_id_mapping_table              1.460  0.289  20.028
kegg_conv                             0.549  0.071  10.698
metalinksdb_sqlite                    0.367  0.112  10.094
kinasephos                            0.409  0.066  18.742
kegg_picture                          0.437  0.017   5.038
kegg_link                             0.254  0.038   5.762
* 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-arm64/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
[2025-09-25 15:06:34] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-09-25 15:06:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-25 15:06:34] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-09-25 15:06:34] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-09-25 15:06:34] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-09-25
[2025-09-25 15:06:34] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-09-25 19:06:29 UTC; unix
[2025-09-25 15:06:34] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.17.6
[2025-09-25 15:06:34] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-09-25 15:06:34] [INFO]    [OmnipathR] Session info: [version=R version 4.5.1 Patched (2025-09-10 r88807); os=macOS Ventura 13.7.7; system=aarch64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-09-25; pandoc=3.1.12.3 @ /opt/homebrew/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2025-09-25 15:06:34] [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=70.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-09-25 15:06:34] [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(2025-09-25); 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 2.29(2024-11-04); 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)
[2025-09-25 15:06:34] [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: aarch64-apple-darwin23.6.0; 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
[2025-09-25 15:06:34] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-09-25 15:06:34] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-09-25 15:06:34] [TRACE]   [OmnipathR] Contains 1 files.
[2025-09-25 15:06:34] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-09-25 15:06:34] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-09-25 15:06:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-25 15:06:34] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-09-25 15:06:34] [TRACE]   [OmnipathR] Pandoc version: `3.1.12.3`.
[2025-09-25 15:06:34] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-09-25 15:06:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-25 15:06:34] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-09-25 15:06:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-25 15:06:34] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-09-25 15:06:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-25 15:06:34] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-09-25 15:06:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-25 15:06:34] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2025-09-25 15:06:35] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-09-25 15:06:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-25 15:06:35] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-09-25 15:06:35] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-09-25 15:06:35] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-09-25
[2025-09-25 15:06:35] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-09-25 19:06:29 UTC; unix
[2025-09-25 15:06:35] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.17.6
[2025-09-25 15:06:35] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-09-25 15:06:35] [INFO]    [OmnipathR] Session info: [version=R version 4.5.1 Patched (2025-09-10 r88807); os=macOS Ventura 13.7.7; system=aarch64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-09-25; pandoc=3.1.12.3 @ /opt/homebrew/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2025-09-25 15:06:35] [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=70.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-09-25 15:06:35] [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(2025-09-25); 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 2.29(2024-11-04); 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)
[2025-09-25 15:06:35] [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: aarch64-apple-darwin23.6.0; 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
[2025-09-25 15:06:35] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-09-25 15:06:35] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-09-25 15:06:35] [TRACE]   [OmnipathR] Contains 1 files.
[2025-09-25 15:06:35] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-09-25 15:06:35] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-09-25 15:06:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-25 15:06:35] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-09-25 15:06:35] [TRACE]   [OmnipathR] Pandoc version: `3.1.12.3`.
[2025-09-25 15:06:35] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-09-25 15:06:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-25 15:06:35] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-09-25 15:06:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-25 15:06:35] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-09-25 15:06:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-25 15:06:35] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-09-25 15:06:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-25 15:06:35] [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: aarch64-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)
[2025-09-25 20:54:51] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-09-25 20:54:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-25 20:54:51] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-09-25 20:54:51] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-09-25 20:54:51] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-09-25
[2025-09-25 20:54:51] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-09-25 19:06:29 UTC; unix
[2025-09-25 20:54:51] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.17.6
[2025-09-25 20:54:51] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-09-25 20:54:52] [INFO]    [OmnipathR] Session info: [version=R version 4.5.1 Patched (2025-09-10 r88807); os=macOS Ventura 13.7.7; system=aarch64, darwin20; ui=X11; language=C; collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-09-25; pandoc=3.1.12.3 @ /opt/homebrew/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2025-09-25 20:54:52] [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=70.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-09-25 20:54:52] [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 1.1.3(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(2025-09-25); 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 2.29(2024-11-04); 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)
[2025-09-25 20:54:52] [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: aarch64-apple-darwin23.6.0; 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
[2025-09-25 20:54:52] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-09-25 20:54:52] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-09-25 20:54:52] [TRACE]   [OmnipathR] Contains 12 files.
[2025-09-25 20:54:52] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-09-25 20:54:52] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-09-25 20:54:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-25 20:54:52] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-09-25 20:54:52] [TRACE]   [OmnipathR] Pandoc version: `3.1.12.3`.
[2025-09-25 20:54:52] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-09-25 20:54:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-25 20:54:52] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-09-25 20:54:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-25 20:54:52] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-09-25 20:54:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-25 20:54:52] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-09-25 20:54:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-25 20:54:52] [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 
 14.988   1.862  50.499 

Example timings

OmnipathR.Rcheck/OmnipathR-Ex.timings

nameusersystemelapsed
OmnipathR000
all_uniprot_acs0.0040.0010.006
all_uniprots 6.737 0.68823.612
ancestors0.0020.0000.003
annotated_network0.5340.0533.704
annotation_categories37.318 0.04139.026
annotation_resources0.0210.0040.549
annotations0.2330.0211.170
biomart_query0.570.073.48
bioplex10.0030.0010.003
bioplex20.0020.0010.003
bioplex30.0020.0010.003
bioplex_all0.0020.0000.003
bioplex_hct116_10.0030.0000.004
bma_motif_es0.2380.0311.164
bma_motif_vs0.0660.0110.636
chalmers_gem0.0030.0010.004
chalmers_gem_id_mapping_table0.0030.0000.003
chalmers_gem_id_type0.0000.0010.001
chalmers_gem_metabolites0.0020.0000.003
chalmers_gem_network0.0030.0010.003
chalmers_gem_raw0.0020.0000.003
chalmers_gem_reactions0.0030.0000.003
common_name0.0430.0030.045
complex_genes0.2840.0282.073
complex_resources0.0210.0030.481
complexes0.0650.0080.668
consensuspathdb_download0.0000.0010.000
consensuspathdb_raw_table0.0020.0000.003
cosmos_pkn000
curated_ligand_receptor_interactions 2.491 0.38712.594
curated_ligrec_stats14.007 1.97483.548
database_summary0.8730.1063.307
descendants0.0030.0000.005
ensembl_dataset0.0200.0010.021
ensembl_id_mapping_table 1.460 0.28920.028
ensembl_id_type0.0010.0010.001
ensembl_name0.1130.0060.143
ensembl_organisms0.0400.0080.105
ensembl_organisms_raw0.0360.0070.069
ensembl_orthology0.0000.0000.001
enzsub_graph0.9930.0723.141
enzsub_resources0.0200.0040.582
enzyme_substrate0.3950.0230.947
evex_download0.0030.0010.004
evidences000
extra_attr_values4.4610.8969.847
extra_attrs2.8290.8103.777
extra_attrs_to_cols5.3221.4326.919
filter_by_resource3.1870.1985.800
filter_extra_attrs 8.235 2.92412.605
filter_intercell2.9830.1967.653
filter_intercell_network0.0050.0010.006
find_all_paths2.4360.1482.736
from_evidences000
get_db000
get_ontology_db0.0030.0010.004
giant_component 5.170 0.46910.794
go_annot_download 8.283 0.58213.041
go_annot_slim000
go_ontology_download0.0030.0010.014
guide2pharma_download0.0040.0010.040
harmonizome_download0.0040.0010.021
has_extra_attrs2.7520.7245.335
hmdb_id_mapping_table0.0030.0000.003
hmdb_id_type0.0010.0000.001
hmdb_metabolite_fields000
hmdb_protein_fields000
hmdb_table0.0030.0010.003
homologene_download0.0020.0000.002
homologene_raw0.0220.0010.022
homologene_uniprot_orthology0.0030.0010.003
hpo_download1.3060.1402.182
htridb_download0.0040.0010.004
id_translation_resources000
id_types0.0160.0050.027
inbiomap_download000
inbiomap_raw000
interaction_datasets0.2790.0350.763
interaction_graph0.1680.0180.791
interaction_resources0.0260.0060.625
interaction_types0.0250.0030.032
intercell0.3350.0551.500
intercell_categories0.2400.0400.711
intercell_consensus_filter0.6150.0723.222
intercell_generic_categories0.0280.0040.031
intercell_network0.0030.0010.004
intercell_resources0.0200.0030.581
intercell_summary0.0270.0120.039
is_ontology_id000
is_swissprot0.0210.0030.024
is_trembl0.0210.0030.024
is_uniprot0.0030.0010.004
kegg_api_templates0.0000.0020.002
kegg_conv 0.549 0.07110.698
kegg_databases000
kegg_ddi0.2340.0301.600
kegg_find0.2090.0291.770
kegg_info0.0020.0010.003
kegg_link0.2540.0385.762
kegg_list0.2090.0231.742
kegg_open0.0020.0000.003
kegg_operations000
kegg_organism_codes0.0070.0240.032
kegg_organisms0.0060.0030.010
kegg_pathway_annotations000
kegg_pathway_download0.0030.0000.003
kegg_pathway_list0.0030.0000.003
kegg_pathways_download000
kegg_picture0.4370.0175.038
kegg_process0.0050.0010.005
kegg_query0.0020.0000.002
kegg_request0.0200.0020.023
kegg_rm_prefix0.2610.0324.660
kinasephos 0.409 0.06618.742
latin_name0.0870.0050.091
load_db0.0210.0100.033
metalinksdb_sqlite 0.367 0.11210.094
metalinksdb_table0.0760.0120.088
metalinksdb_tables0.0060.0010.007
ncbi_taxid0.0880.0060.096
nichenet_build_model000
nichenet_expression_data0.0030.0010.004
nichenet_gr_network0.0090.0020.014
nichenet_gr_network_evex0.0030.0000.003
nichenet_gr_network_harmonizome0.0030.0010.003
nichenet_gr_network_htridb0.0020.0010.002
nichenet_gr_network_omnipath5.5340.6248.798
nichenet_gr_network_pathwaycommons0.0030.0010.003
nichenet_gr_network_regnetwork0.0030.0000.003
nichenet_gr_network_remap0.0020.0010.003
nichenet_gr_network_trrust0.0020.0000.002
nichenet_ligand_activities000
nichenet_ligand_target_links0.0000.0010.000
nichenet_ligand_target_matrix000
nichenet_lr_network0.0060.0010.006
nichenet_lr_network_guide2pharma0.0020.0000.002
nichenet_lr_network_omnipath0.0060.0010.007
nichenet_lr_network_ramilowski0.0020.0000.002
nichenet_main000
nichenet_networks0.0110.0010.013
nichenet_optimization0.0000.0010.000
nichenet_remove_orphan_ligands0.0270.0010.028
nichenet_results_dir000
nichenet_signaling_network0.0070.0010.007
nichenet_signaling_network_cpdb0.0020.0000.002
nichenet_signaling_network_evex0.0020.0010.003
nichenet_signaling_network_harmonizome0.0020.0000.002
nichenet_signaling_network_inbiomap000
nichenet_signaling_network_omnipath4.1320.4488.625
nichenet_signaling_network_pathwaycommons0.0020.0000.003
nichenet_signaling_network_vinayagam0.0020.0010.003
nichenet_test000
nichenet_workarounds000
obo_parser0.0460.0070.092
oma_code0.0460.0020.049
oma_organisms0.0200.0060.028
oma_pairwise0.0020.0010.003
oma_pairwise_genesymbols0.0020.0000.002
oma_pairwise_translated0.0020.0010.003
omnipath-interactions11.344 1.08945.677
omnipath_cache_autoclean000
omnipath_cache_clean0.0020.0020.004
omnipath_cache_clean_db0.0320.0090.040
omnipath_cache_download_ready0.1610.0530.242
omnipath_cache_filter_versions0.0250.0090.040
omnipath_cache_get0.0210.0070.027
omnipath_cache_key0.0010.0000.001
omnipath_cache_latest_or_new0.0150.0050.020
omnipath_cache_load0.2150.0212.679
omnipath_cache_move_in0.0420.0150.062
omnipath_cache_remove0.0250.0090.039
omnipath_cache_save0.0410.0110.070
omnipath_cache_search0.0000.0000.001
omnipath_cache_set_ext0.0360.0080.050
omnipath_cache_update_status0.0240.0080.032
omnipath_cache_wipe000
omnipath_config_path000
omnipath_for_cosmos 3.922 0.27823.500
omnipath_load_config000
omnipath_log000
omnipath_logfile0.0010.0000.001
omnipath_msg0.0010.0010.002
omnipath_query1.2670.0721.340
omnipath_reset_config000
omnipath_save_config000
omnipath_set_cachedir0.0070.0010.008
omnipath_set_console_loglevel0.0010.0000.001
omnipath_set_logfile_loglevel0.0010.0000.001
omnipath_set_loglevel0.0010.0000.000
omnipath_show_db0.0160.0050.021
omnipath_unlock_cache_db000
only_from000
ontology_ensure_id000
ontology_ensure_name000
ontology_name_id000
organism_for0.0830.0030.095
pathwaycommons_download0.0010.0000.000
pivot_annotations 4.243 0.29119.536
preppi_download0.0000.0010.000
preppi_filter0.0000.0000.001
print_bma_motif_es0.2240.0251.028
print_bma_motif_vs0.0490.0090.614
print_interactions2.6810.1838.048
print_path_es0.3700.0431.795
print_path_vs0.9190.1013.800
pubmed_open1.9320.1142.105
query_info0.1930.0130.474
ramilowski_download000
ramp_id_mapping_table000
ramp_id_type0.0000.0000.001
ramp_sqlite000
ramp_table0.0000.0000.001
ramp_tables000