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This page was generated on 2025-09-27 12:04 -0400 (Sat, 27 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4832
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4620
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4565
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: 2025-09-26 13:45 -0400 (Fri, 26 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 nebbiolo2

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: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings OmnipathR_3.17.6.tar.gz
StartedAt: 2025-09-27 02:24:49 -0400 (Sat, 27 Sep 2025)
EndedAt: 2025-09-27 03:01:00 -0400 (Sat, 27 Sep 2025)
EllapsedTime: 2170.5 seconds
RetCode: 1
Status:   ERROR  
CheckDir: OmnipathR.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings OmnipathR_3.17.6.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/OmnipathR.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘OmnipathR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OmnipathR’ version ‘3.17.6’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 35 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘OmnipathR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... NOTE
[2025-09-27 02:25:19] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-09-27 02:25:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-27 02:25:19] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-09-27 02:25:19] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-09-27 02:25:19] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-09-26
[2025-09-27 02:25:19] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-09-26 19:07:35 UTC; unix
[2025-09-27 02:25:19] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.17.6
[2025-09-27 02:25:19] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-09-27 02:25:19] [INFO]    [OmnipathR] Session info: [version=R version 4.5.1 Patched (2025-08-23 r88802); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-09-27; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2025-09-27 02:25:19] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.22-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-09-27 02:25:19] [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(2025-09-26); 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)
[2025-09-27 02:25:19] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: GnuTLS/3.8.3; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-09-27 02:25:19] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-09-27 02:25:19] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-09-27 02:25:19] [TRACE]   [OmnipathR] Contains 1 files.
[2025-09-27 02:25:19] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-09-27 02:25:19] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-09-27 02:25:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-27 02:25:19] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-09-27 02:25:19] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-09-27 02:25:19] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-09-27 02:25:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-27 02:25:19] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-09-27 02:25:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-27 02:25:19] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-09-27 02:25:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-27 02:25:19] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-09-27 02:25:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-27 02:25:19] [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
[2025-09-27 02:25:36] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-09-27 02:25:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-27 02:25:36] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-09-27 02:25:36] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-09-27 02:25:36] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-09-26
[2025-09-27 02:25:36] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-09-26 19:07:35 UTC; unix
[2025-09-27 02:25:36] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.17.6
[2025-09-27 02:25:36] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-09-27 02:25:36] [INFO]    [OmnipathR] Session info: [version=R version 4.5.1 Patched (2025-08-23 r88802); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-09-27; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2025-09-27 02:25:37] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.22-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-09-27 02:25:37] [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(2025-09-26); 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)
[2025-09-27 02:25:37] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: GnuTLS/3.8.3; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-09-27 02:25:37] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-09-27 02:25:37] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-09-27 02:25:37] [TRACE]   [OmnipathR] Contains 1 files.
[2025-09-27 02:25:37] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-09-27 02:25:37] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-09-27 02:25:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-27 02:25:37] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-09-27 02:25:37] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-09-27 02:25:37] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-09-27 02:25:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-27 02:25:37] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-09-27 02:25:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-27 02:25:37] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-09-27 02:25:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-27 02:25:37] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-09-27 02:25:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-27 02:25:37] [TRACE]   [OmnipathR] Cache locked: FALSE
.cosmos_pkn: no visible global function definition for
  ‘metabolite_idsc’
cosmos_ksn: no visible binding for global variable
  ‘substrate_genesymbol’
cosmos_ksn: no visible binding for global variable ‘residue_type’
cosmos_ksn: no visible binding for global variable ‘residue_offset’
cosmos_ksn: no visible binding for global variable ‘enzyme_genesymbol’
cosmos_ksn: no visible binding for global variable ‘mor’
recon3d_genes: no visible binding for global variable ‘notes’
recon3d_genes: no visible binding for global variable ‘annotation’
recon3d_genes: no visible binding for global variable
  ‘original_bigg_ids’
recon3d_metabolites: no visible binding for global variable ‘notes’
recon3d_metabolites: no visible binding for global variable
  ‘original_bigg_ids’
recon3d_metabolites: no visible binding for global variable
  ‘annotation’
recon3d_metabolites: no visible global function definition for
  ‘chalmers_gem_matlab_tibble’
recon3d_metabolites: no visible binding for global variable ‘hmdb’
recon3d_metabolites: no visible binding for global variable ‘metHMDBID’
recon3d_reactions: no visible binding for global variable ‘notes’
recon3d_reactions: no visible binding for global variable ‘metabolites’
recon3d_reactions: no visible binding for global variable
  ‘original_bigg_ids’
taxon_names_table: no visible binding for global variable
  ‘latin_name_uniprot’
taxon_names_table: no visible binding for global variable
  ‘latin_name_ensembl’
taxon_names_table: no visible binding for global variable
  ‘latin_name_oma’
taxon_names_table: no visible binding for global variable
  ‘common_name_ensembl’
taxon_names_table: no visible binding for global variable
  ‘common_name_uniprot’
Undefined global functions or variables:
  annotation chalmers_gem_matlab_tibble common_name_ensembl
  common_name_uniprot enzyme_genesymbol hmdb latin_name_ensembl
  latin_name_oma latin_name_uniprot metHMDBID metabolite_idsc
  metabolites mor notes original_bigg_ids residue_offset residue_type
  substrate_genesymbol
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘recon3d_raw’ ‘recon3d_raw_vmh’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in Rd file 'recon3d.Rd'
  ‘extra_hmdb’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: recon3d_metabolites
> ### Title: Metabolites from Recon-3D
> ### Aliases: recon3d_metabolites recon3d_reactions recon3d_genes
> ###   recon3d_compartments
> 
> ### ** Examples
> 
> recon3d_metabolites()
Warning in readLines(con = path, encoding = encoding) :
  incomplete final line found on '/home/biocbuild/.cache/OmnipathR/be81cd1c9a119b749e4206f26272806591e8fb4c-1.gz'
Error in chalmers_gem_matlab_tibble(., "mets", "metHMDBID") : 
  could not find function "chalmers_gem_matlab_tibble"
Calls: recon3d_metabolites ... same_src.data.frame -> is.data.frame -> %>% -> unnest -> unnest
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                                       user system elapsed
annotation_categories                82.508  0.053  83.838
curated_ligrec_stats                 44.365  3.721 122.678
omnipath-interactions                43.469  4.545 121.588
nichenet_gr_network_omnipath         31.790  2.596  54.899
filter_extra_attrs                   28.812  5.093  38.240
nichenet_signaling_network_omnipath  23.447  1.764  42.340
all_uniprots                         23.314  1.420  41.306
giant_component                      20.166  0.750  27.730
has_extra_attrs                      15.079  1.562  22.607
go_annot_download                    15.407  0.910  17.480
extra_attrs_to_cols                  14.541  1.287  15.841
extra_attr_values                    12.846  1.487  17.155
pivot_annotations                    12.833  1.072  24.898
filter_intercell                     10.988  0.710  17.078
omnipath_for_cosmos                   9.718  0.668  30.190
extra_attrs                           7.797  1.111   8.949
find_all_paths                        8.733  0.157   9.138
curated_ligand_receptor_interactions  7.348  0.911  18.265
filter_by_resource                    7.921  0.268  10.328
print_interactions                    7.379  0.299  12.185
pubmed_open                           5.751  0.200   6.130
hpo_download                          4.992  0.195   7.294
print_path_vs                         3.084  0.155   6.678
kegg_picture                          3.118  0.047   8.368
ensembl_id_mapping_table              2.581  0.249  22.384
metalinksdb_sqlite                    2.134  0.190  13.258
kegg_conv                             1.963  0.102  16.472
kinasephos                            1.714  0.094  19.377
kegg_link                             1.672  0.076   7.746
annotated_network                     1.591  0.103   5.077
biomart_query                         1.357  0.082   5.732
kegg_rm_prefix                        1.233  0.065   6.722
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

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


Installation output

OmnipathR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL OmnipathR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘OmnipathR’ ...
** this is package ‘OmnipathR’ version ‘3.17.6’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
[2025-09-26 15:07:49] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-09-26 15:07:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-26 15:07:49] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-09-26 15:07:49] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-09-26 15:07:49] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-09-26
[2025-09-26 15:07:49] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-09-26 19:07:35 UTC; unix
[2025-09-26 15:07:49] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.17.6
[2025-09-26 15:07:49] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-09-26 15:07:49] [INFO]    [OmnipathR] Session info: [version=R version 4.5.1 Patched (2025-08-23 r88802); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-09-26; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2025-09-26 15:07:49] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.22-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-09-26 15:07:50] [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(2025-09-26); 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)
[2025-09-26 15:07:50] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: GnuTLS/3.8.3; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-09-26 15:07:50] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-09-26 15:07:50] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-09-26 15:07:50] [TRACE]   [OmnipathR] Contains 9 files.
[2025-09-26 15:07:50] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-09-26 15:07:50] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-09-26 15:07:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-26 15:07:50] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-09-26 15:07:50] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-09-26 15:07:50] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-09-26 15:07:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-26 15:07:50] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-09-26 15:07:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-26 15:07:50] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-09-26 15:07:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-26 15:07:50] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-09-26 15:07:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-26 15:07:50] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2025-09-26 15:07:52] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-09-26 15:07:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-26 15:07:52] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-09-26 15:07:52] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-09-26 15:07:52] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-09-26
[2025-09-26 15:07:52] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-09-26 19:07:35 UTC; unix
[2025-09-26 15:07:52] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.17.6
[2025-09-26 15:07:52] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-09-26 15:07:52] [INFO]    [OmnipathR] Session info: [version=R version 4.5.1 Patched (2025-08-23 r88802); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-09-26; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2025-09-26 15:07:52] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.22-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-09-26 15:07:52] [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); 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(2025-09-26); 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)
[2025-09-26 15:07:52] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: GnuTLS/3.8.3; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-09-26 15:07:52] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-09-26 15:07:52] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-09-26 15:07:52] [TRACE]   [OmnipathR] Contains 1 files.
[2025-09-26 15:07:52] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-09-26 15:07:52] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-09-26 15:07:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-26 15:07:53] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-09-26 15:07:53] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-09-26 15:07:53] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-09-26 15:07:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-26 15:07:53] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-09-26 15:07:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-26 15:07:53] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-09-26 15:07:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-26 15:07:53] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-09-26 15:07:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-26 15:07:53] [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 (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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

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

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

> #!/usr/bin/env Rscript
> 
> #
> #  This file is part of the `OmnipathR` R package
> #
> #  Copyright
> #  2018-2024
> #  Saez Lab, Uniklinik RWTH Aachen, Heidelberg University
> #
> #  File author(s): Alberto Valdeolivas
> #                  Dénes Türei (turei.denes@gmail.com)
> #                  Attila Gábor
> #
> #  Distributed under the MIT (Expat) License.
> #  See accompanying file `LICENSE` or find a copy at
> #      https://directory.fsf.org/wiki/License:Expat
> #
> #  Website: https://r.omnipathdb.org/
> #  Git repo: https://github.com/saezlab/OmnipathR
> #
> 
> 
> library(testthat)
> library(OmnipathR)
[2025-09-27 02:42:42] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-09-27 02:42:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-27 02:42:42] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-09-27 02:42:42] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-09-27 02:42:42] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-09-26
[2025-09-27 02:42:42] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-09-26 19:07:35 UTC; unix
[2025-09-27 02:42:42] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.17.6
[2025-09-27 02:42:42] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-09-27 02:42:43] [INFO]    [OmnipathR] Session info: [version=R version 4.5.1 Patched (2025-08-23 r88802); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=C; collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-09-27; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2025-09-27 02:42:43] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.22-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-09-27 02:42:43] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); brio 1.1.5(2024-04-24); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.1.4(2025-01-23); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.17.6(2025-09-26); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.29(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); 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)
[2025-09-27 02:42:43] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: GnuTLS/3.8.3; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-09-27 02:42:43] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-09-27 02:42:43] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-09-27 02:42:43] [TRACE]   [OmnipathR] Contains 12 files.
[2025-09-27 02:42:43] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-09-27 02:42:43] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-09-27 02:42:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-27 02:42:43] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-09-27 02:42:43] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-09-27 02:42:43] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-09-27 02:42:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-27 02:42:43] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-09-27 02:42:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-27 02:42:43] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-09-27 02:42:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-27 02:42:43] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-09-27 02:42:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-27 02:42:43] [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 
 44.610   2.733  79.294 

Example timings

OmnipathR.Rcheck/OmnipathR-Ex.timings

nameusersystemelapsed
OmnipathR000
all_uniprot_acs0.0150.0020.017
all_uniprots23.314 1.42041.306
ancestors0.0090.0000.009
annotated_network1.5910.1035.077
annotation_categories82.508 0.05383.838
annotation_resources0.1780.0250.914
annotations0.8300.0741.856
biomart_query1.3570.0825.732
bioplex10.0090.0010.011
bioplex20.0080.0010.010
bioplex30.0090.0010.010
bioplex_all0.0080.0020.009
bioplex_hct116_10.0090.0010.009
bma_motif_es0.8560.0671.884
bma_motif_vs0.3380.0121.061
chalmers_gem0.0110.0000.011
chalmers_gem_id_mapping_table0.010.000.01
chalmers_gem_id_type0.0020.0000.002
chalmers_gem_metabolites0.010.000.01
chalmers_gem_network0.0080.0010.010
chalmers_gem_raw0.0090.0000.010
chalmers_gem_reactions0.0090.0010.009
common_name0.1690.0010.170
complex_genes0.9470.0402.812
complex_resources0.1310.0070.893
complexes0.2130.0100.957
consensuspathdb_download000
consensuspathdb_raw_table0.030.000.03
cosmos_pkn000
curated_ligand_receptor_interactions 7.348 0.91118.265
curated_ligrec_stats 44.365 3.721122.678
database_summary1.6910.0903.051
descendants0.0090.0010.010
ensembl_dataset0.0510.0000.051
ensembl_id_mapping_table 2.581 0.24922.384
ensembl_id_type0.0020.0000.002
ensembl_name0.3100.0010.311
ensembl_organisms0.1050.0130.118
ensembl_organisms_raw0.1050.0050.110
ensembl_orthology000
enzsub_graph2.4070.0874.613
enzsub_resources0.1560.0100.880
enzyme_substrate1.0790.0291.754
evex_download0.0040.0040.009
evidences000
extra_attr_values12.846 1.48717.155
extra_attrs7.7971.1118.949
extra_attrs_to_cols14.541 1.28715.841
filter_by_resource 7.921 0.26810.328
filter_extra_attrs28.812 5.09338.240
filter_intercell10.988 0.71017.078
filter_intercell_network0.0280.0030.031
find_all_paths8.7330.1579.138
from_evidences0.0010.0000.000
get_db0.0010.0000.000
get_ontology_db0.0150.0000.015
giant_component20.166 0.75027.730
go_annot_download15.407 0.91017.480
go_annot_slim0.0010.0000.000
go_ontology_download0.0150.0010.017
guide2pharma_download0.0170.0000.016
harmonizome_download0.0140.0010.015
has_extra_attrs15.079 1.56222.607
hmdb_id_mapping_table0.0180.0000.020
hmdb_id_type0.0050.0000.004
hmdb_metabolite_fields0.0020.0000.001
hmdb_protein_fields0.0000.0000.001
hmdb_table0.0190.0020.020
homologene_download0.0190.0040.046
homologene_raw0.1360.0000.263
homologene_uniprot_orthology0.0200.0010.025
hpo_download4.9920.1957.294
htridb_download0.0180.0000.018
id_translation_resources000
id_types0.0830.0070.090
inbiomap_download0.0000.0010.001
inbiomap_raw000
interaction_datasets1.0720.0611.364
interaction_graph0.6930.0251.455
interaction_resources0.1720.0110.919
interaction_types0.1200.0010.121
intercell0.9540.0701.858
intercell_categories0.7720.0351.020
intercell_consensus_filter1.9700.1163.628
intercell_generic_categories0.1270.0040.132
intercell_network0.0160.0000.015
intercell_resources0.1320.0080.888
intercell_summary0.0950.0050.100
is_ontology_id0.0010.0000.000
is_swissprot0.0620.0020.063
is_trembl0.0600.0030.063
is_uniprot0.0090.0000.010
kegg_api_templates0.0010.0000.001
kegg_conv 1.963 0.10216.472
kegg_databases0.0020.0000.005
kegg_ddi1.1250.0523.217
kegg_find1.3460.0484.123
kegg_info0.0220.0060.053
kegg_link1.6720.0767.746
kegg_list1.5370.0623.901
kegg_open0.0230.0010.024
kegg_operations0.0010.0000.001
kegg_organism_codes0.0180.0140.032
kegg_organisms0.0530.0020.055
kegg_pathway_annotations0.0010.0000.001
kegg_pathway_download0.0230.0000.022
kegg_pathway_list0.020.000.02
kegg_pathways_download000
kegg_picture3.1180.0478.368
kegg_process0.0450.0010.047
kegg_query0.0180.0000.018
kegg_request0.1590.0030.164
kegg_rm_prefix1.2330.0656.722
kinasephos 1.714 0.09419.377
latin_name0.4890.0071.061
load_db0.1760.0190.456
metalinksdb_sqlite 2.134 0.19013.258
metalinksdb_table0.4200.0380.462
metalinksdb_tables0.0360.0020.038
ncbi_taxid0.4790.0050.676
nichenet_build_model000
nichenet_expression_data0.0220.0010.046
nichenet_gr_network0.0490.0010.053
nichenet_gr_network_evex0.0160.0000.016
nichenet_gr_network_harmonizome0.0140.0020.016
nichenet_gr_network_htridb0.0160.0000.023
nichenet_gr_network_omnipath31.790 2.59654.899
nichenet_gr_network_pathwaycommons0.0270.0020.042
nichenet_gr_network_regnetwork0.0220.0040.025
nichenet_gr_network_remap0.0250.0040.033
nichenet_gr_network_trrust0.0240.0040.031
nichenet_ligand_activities000
nichenet_ligand_target_links0.0010.0000.000
nichenet_ligand_target_matrix000
nichenet_lr_network0.0610.0080.120
nichenet_lr_network_guide2pharma0.0210.0030.046
nichenet_lr_network_omnipath0.0630.0100.139
nichenet_lr_network_ramilowski0.0230.0010.045
nichenet_main000
nichenet_networks0.1020.0140.231
nichenet_optimization000
nichenet_remove_orphan_ligands0.0650.0040.140
nichenet_results_dir000
nichenet_signaling_network0.0670.0050.162
nichenet_signaling_network_cpdb0.0220.0010.047
nichenet_signaling_network_evex0.0260.0010.075
nichenet_signaling_network_harmonizome0.0230.0030.071
nichenet_signaling_network_inbiomap0.0000.0000.001
nichenet_signaling_network_omnipath23.447 1.76442.340
nichenet_signaling_network_pathwaycommons0.0240.0010.047
nichenet_signaling_network_vinayagam0.0240.0010.048
nichenet_test0.0010.0000.000
nichenet_workarounds000
obo_parser0.3240.0510.688
oma_code0.2670.0100.411
oma_organisms0.1410.0140.236
oma_pairwise0.0240.0020.041
oma_pairwise_genesymbols0.0230.0010.042
oma_pairwise_translated0.0230.0010.024
omnipath-interactions 43.469 4.545121.588
omnipath_cache_autoclean000
omnipath_cache_clean0.0080.0000.009
omnipath_cache_clean_db0.0870.0100.098
omnipath_cache_download_ready0.4790.0650.579
omnipath_cache_filter_versions0.0800.0090.095
omnipath_cache_get0.0680.0110.079
omnipath_cache_key0.0020.0000.002
omnipath_cache_latest_or_new0.0500.0050.055
omnipath_cache_load0.7580.0473.642
omnipath_cache_move_in0.1310.0280.164
omnipath_cache_remove0.0800.0180.104
omnipath_cache_save0.2040.0440.395
omnipath_cache_search0.0010.0000.001
omnipath_cache_set_ext0.0720.0110.088
omnipath_cache_update_status0.1050.0300.135
omnipath_cache_wipe000
omnipath_config_path0.0010.0000.002
omnipath_for_cosmos 9.718 0.66830.190
omnipath_load_config000
omnipath_log0.0010.0000.000
omnipath_logfile0.0010.0000.001
omnipath_msg0.0050.0000.005
omnipath_query3.2240.1683.391
omnipath_reset_config000
omnipath_save_config000
omnipath_set_cachedir0.0220.0000.022
omnipath_set_console_loglevel0.0030.0010.003
omnipath_set_logfile_loglevel0.0030.0000.003
omnipath_set_loglevel0.0020.0000.002
omnipath_show_db0.0540.0080.063
omnipath_unlock_cache_db000
only_from000
ontology_ensure_id0.0000.0000.001
ontology_ensure_name000
ontology_name_id0.0010.0000.001
organism_for0.1770.0090.186
pathwaycommons_download000
pivot_annotations12.833 1.07224.898
preppi_download0.0010.0000.000
preppi_filter0.0010.0000.001
print_bma_motif_es1.8780.2233.265
print_bma_motif_vs0.5520.0281.270
print_interactions 7.379 0.29912.185
print_path_es1.6990.1884.491
print_path_vs3.0840.1556.678
pubmed_open5.7510.2006.130
query_info0.3870.0200.633
ramilowski_download0.0010.0000.001
ramp_id_mapping_table0.0000.0000.001
ramp_id_type0.0020.0000.002
ramp_sqlite0.0010.0000.001
ramp_table0.0000.0000.001
ramp_tables000