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This page was generated on 2025-10-04 12:04 -0400 (Sat, 04 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4853
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4640
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4585
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4576
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1490/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OmnipathR 3.17.6  (landing page)
Denes Turei
Snapshot Date: 2025-10-03 13:45 -0400 (Fri, 03 Oct 2025)
git_url: https://git.bioconductor.org/packages/OmnipathR
git_branch: devel
git_last_commit: 69ba6ef
git_last_commit_date: 2025-09-24 06:19:47 -0400 (Wed, 24 Sep 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    ERROR  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    ERROR    OK  
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    ERROR    OK  
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    ERROR  


CHECK results for OmnipathR on 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: 2025-10-04 02:27:06 -0400 (Sat, 04 Oct 2025)
EndedAt: 2025-10-04 03:02:03 -0400 (Sat, 04 Oct 2025)
EllapsedTime: 2096.5 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
[2025-10-04 02:27:36] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-04 02:27:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-04 02:27:36] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-10-04 02:27:36] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-10-04 02:27:36] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-10-03
[2025-10-04 02:27:36] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-10-03 19:08:01 UTC; unix
[2025-10-04 02:27:36] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.17.6
[2025-10-04 02:27:36] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-10-04 02:27:36] [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=2025-10-04; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2025-10-04 02:27:37] [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]
[2025-10-04 02:27:37] [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(2025-10-03); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.3.3(2025-05-29); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.3(2025-08-20); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.2(2025-09-08); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.53(2025-08-19); XML 3.99-0.19(2025-08-22); xml2 1.4.0(2025-08-20); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-10-04 02:27:37] [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
[2025-10-04 02:27:37] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-10-04 02:27:37] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-10-04 02:27:37] [TRACE]   [OmnipathR] Contains 1 files.
[2025-10-04 02:27:37] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-10-04 02:27:37] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-04 02:27:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-04 02:27:37] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-10-04 02:27:37] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-10-04 02:27:37] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-10-04 02:27:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-04 02:27:37] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-10-04 02:27:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-04 02:27:37] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-10-04 02:27:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-04 02:27:37] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-10-04 02:27:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-04 02:27:37] [TRACE]   [OmnipathR] Cache locked: FALSE

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
[2025-10-04 02:27:53] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-04 02:27:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-04 02:27:53] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-10-04 02:27:53] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-10-04 02:27:53] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-10-03
[2025-10-04 02:27:53] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-10-03 19:08:01 UTC; unix
[2025-10-04 02:27:53] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.17.6
[2025-10-04 02:27:53] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-10-04 02:27:54] [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=2025-10-04; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2025-10-04 02:27:54] [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]
[2025-10-04 02:27:54] [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(2025-10-03); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.3.3(2025-05-29); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.3(2025-08-20); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.2(2025-09-08); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.53(2025-08-19); XML 3.99-0.19(2025-08-22); xml2 1.4.0(2025-08-20); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-10-04 02:27:54] [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
[2025-10-04 02:27:54] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-10-04 02:27:54] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-10-04 02:27:54] [TRACE]   [OmnipathR] Contains 1 files.
[2025-10-04 02:27:54] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-10-04 02:27:54] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-04 02:27:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-04 02:27:54] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-10-04 02:27:54] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-10-04 02:27:54] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-10-04 02:27:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-04 02:27:54] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-10-04 02:27:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-04 02:27:54] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-10-04 02:27:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-04 02:27:54] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-10-04 02:27:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-04 02:27:54] [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                82.641  0.059  84.089
curated_ligrec_stats                 43.680  3.122 120.030
omnipath-interactions                42.985  2.978  73.497
filter_extra_attrs                   37.018  5.912  47.488
nichenet_gr_network_omnipath         28.772  1.341  42.129
all_uniprots                         22.547  1.533  38.165
go_annot_download                    21.292  1.206  30.691
nichenet_signaling_network_omnipath  20.904  0.772  30.600
extra_attrs_to_cols                  14.498  1.207  15.754
omnipath_for_cosmos                  13.216  0.526  45.756
extra_attr_values                    12.277  1.437  16.246
filter_intercell                     11.674  0.812  20.960
giant_component                      11.198  0.636  14.823
find_all_paths                       11.188  0.410  13.913
pivot_annotations                    10.434  0.590  20.202
has_extra_attrs                       8.645  1.117   9.792
extra_attrs                           7.789  1.118   8.926
filter_by_resource                    7.699  0.304  10.447
curated_ligand_receptor_interactions  6.659  0.793  17.616
print_interactions                    6.262  0.260  11.075
ensembl_id_mapping_table              2.628  0.195  22.217
print_path_vs                         2.613  0.122   5.412
kegg_conv                             2.532  0.118  16.253
kinasephos                            2.285  0.105  21.238
metalinksdb_sqlite                    1.852  0.331  12.438
kegg_link                             1.719  0.060   7.064
kegg_picture                          1.115  0.028   5.965
kegg_rm_prefix                        0.850  0.042   5.640
* 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
[2025-10-03 15:08:14] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-03 15:08:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-03 15:08:14] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-10-03 15:08:14] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-10-03 15:08:14] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-10-03
[2025-10-03 15:08:14] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-10-03 19:08:01 UTC; unix
[2025-10-03 15:08:14] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.17.6
[2025-10-03 15:08:14] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-10-03 15:08:15] [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=2025-10-03; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2025-10-03 15:08:15] [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]
[2025-10-03 15:08:15] [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(2025-10-03); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.3.3(2025-05-29); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.3(2025-08-20); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.2(2025-09-08); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.53(2025-08-19); XML 3.99-0.19(2025-08-22); xml2 1.4.0(2025-08-20); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-10-03 15:08:15] [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
[2025-10-03 15:08:15] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-10-03 15:08:15] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-10-03 15:08:15] [TRACE]   [OmnipathR] Contains 9 files.
[2025-10-03 15:08:15] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-10-03 15:08:15] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-03 15:08:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-03 15:08:15] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-10-03 15:08:15] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-10-03 15:08:15] [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).
[2025-10-03 15:08:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-03 15:08:15] [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).
[2025-10-03 15:08:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-03 15:08:15] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-10-03 15:08:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-03 15:08:15] [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).
[2025-10-03 15:08:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-03 15:08:15] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2025-10-03 15:08:17] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-03 15:08:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-03 15:08:17] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-10-03 15:08:17] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-10-03 15:08:17] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-10-03
[2025-10-03 15:08:17] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-10-03 19:08:01 UTC; unix
[2025-10-03 15:08:17] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.17.6
[2025-10-03 15:08:17] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-10-03 15:08:17] [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=2025-10-03; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2025-10-03 15:08:18] [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]
[2025-10-03 15:08:18] [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(2025-10-03); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.3.3(2025-05-29); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.3(2025-08-20); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.2(2025-09-08); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.53(2025-08-19); XML 3.99-0.19(2025-08-22); xml2 1.4.0(2025-08-20); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-10-03 15:08:18] [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
[2025-10-03 15:08:18] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-10-03 15:08:18] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-10-03 15:08:18] [TRACE]   [OmnipathR] Contains 1 files.
[2025-10-03 15:08:18] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-10-03 15:08:18] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-03 15:08:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-03 15:08:18] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-10-03 15:08:18] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-10-03 15:08:18] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-10-03 15:08:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-03 15:08:18] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-10-03 15:08:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-03 15:08:18] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-10-03 15:08:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-03 15:08:18] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-10-03 15:08:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-03 15:08:18] [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)
[2025-10-04 02:43:28] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-04 02:43:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-04 02:43:28] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-10-04 02:43:28] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-10-04 02:43:28] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-10-03
[2025-10-04 02:43:28] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-10-03 19:08:01 UTC; unix
[2025-10-04 02:43:28] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.17.6
[2025-10-04 02:43:28] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-10-04 02:43:28] [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=2025-10-04; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2025-10-04 02:43:28] [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]
[2025-10-04 02:43:28] [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(2025-10-03); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.3(2025-08-20); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.2(2025-09-08); testthat 3.2.3(2025-01-13); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); withr 3.0.2(2024-10-28); xfun 0.53(2025-08-19); XML 3.99-0.19(2025-08-22); xml2 1.4.0(2025-08-20); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-10-04 02:43:28] [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
[2025-10-04 02:43:28] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-10-04 02:43:28] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-10-04 02:43:28] [TRACE]   [OmnipathR] Contains 12 files.
[2025-10-04 02:43:28] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-10-04 02:43:28] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-04 02:43:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-04 02:43:28] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-10-04 02:43:28] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-10-04 02:43:28] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-10-04 02:43:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-04 02:43:28] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-10-04 02:43:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-04 02:43:28] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-10-04 02:43:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-04 02:43:28] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-10-04 02:43:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-04 02:43:28] [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 
 61.257   4.136 104.913 

Example timings

OmnipathR.Rcheck/OmnipathR-Ex.timings

nameusersystemelapsed
OmnipathR000
all_uniprot_acs0.0180.0010.019
all_uniprots22.547 1.53338.165
ancestors0.0090.0000.008
annotated_network1.450.094.78
annotation_categories82.641 0.05984.089
annotation_resources0.1780.0180.909
annotations0.6600.0621.601
biomart_query1.2920.0974.012
bioplex10.0090.0000.009
bioplex20.0080.0000.008
bioplex30.0070.0010.008
bioplex_all0.0080.0000.008
bioplex_hct116_10.0080.0000.008
bma_motif_es0.7040.0641.663
bma_motif_vs0.2290.0130.981
chalmers_gem0.0090.0000.009
chalmers_gem_id_mapping_table0.0080.0000.008
chalmers_gem_id_type0.0020.0000.002
chalmers_gem_metabolites0.0080.0000.007
chalmers_gem_network0.0080.0000.008
chalmers_gem_raw0.0080.0000.008
chalmers_gem_reactions0.0080.0000.008
common_name0.1490.0010.169
complex_genes0.7560.0312.417
complex_resources0.0950.0050.846
complexes0.3110.0161.063
consensuspathdb_download000
consensuspathdb_raw_table0.0290.0000.029
cosmos_pkn000
curated_ligand_receptor_interactions 6.659 0.79317.616
curated_ligrec_stats 43.680 3.122120.030
database_summary1.7010.0843.186
descendants0.0080.0010.009
ensembl_dataset0.0500.0000.049
ensembl_id_mapping_table 2.628 0.19522.217
ensembl_id_type0.0020.0000.002
ensembl_name0.2910.0020.294
ensembl_organisms0.1010.0110.112
ensembl_organisms_raw0.1000.0030.103
ensembl_orthology0.0010.0000.000
enzsub_graph2.2030.0864.619
enzsub_resources0.1290.0100.804
enzyme_substrate1.1620.0281.924
evex_download0.0090.0000.009
evidences000
extra_attr_values12.277 1.43716.246
extra_attrs7.7891.1188.926
extra_attrs_to_cols14.498 1.20715.754
filter_by_resource 7.699 0.30410.447
filter_extra_attrs37.018 5.91247.488
filter_intercell11.674 0.81220.960
filter_intercell_network0.0370.0060.042
find_all_paths11.188 0.41013.913
from_evidences000
get_db0.0000.0000.001
get_ontology_db0.0150.0000.015
giant_component11.198 0.63614.823
go_annot_download21.292 1.20630.691
go_annot_slim0.0000.0000.001
go_ontology_download0.0160.0000.016
guide2pharma_download0.0160.0000.015
harmonizome_download0.0140.0010.015
has_extra_attrs8.6451.1179.792
hmdb_id_mapping_table0.0110.0010.013
hmdb_id_type0.0030.0000.003
hmdb_metabolite_fields0.0010.0000.001
hmdb_protein_fields000
hmdb_table0.0120.0010.012
homologene_download0.0120.0000.012
homologene_raw0.0800.0010.081
homologene_uniprot_orthology0.0110.0020.014
hpo_download2.8290.2933.939
htridb_download0.0070.0020.010
id_translation_resources0.0000.0000.001
id_types0.0430.0040.047
inbiomap_download0.0000.0000.001
inbiomap_raw000
interaction_datasets0.8110.0401.224
interaction_graph0.5410.0201.499
interaction_resources0.1690.0080.819
interaction_types0.0790.0030.081
intercell0.8940.0681.847
intercell_categories0.7200.0350.984
intercell_consensus_filter1.4360.1092.948
intercell_generic_categories0.0860.0040.091
intercell_network0.0100.0010.011
intercell_resources0.1780.0140.902
intercell_summary0.0850.0060.091
is_ontology_id000
is_swissprot0.0600.0030.062
is_trembl0.0590.0050.063
is_uniprot0.010.000.01
kegg_api_templates0.0010.0010.002
kegg_conv 2.532 0.11816.253
kegg_databases0.0000.0000.001
kegg_ddi1.6000.0494.583
kegg_find1.5750.0584.351
kegg_info0.0230.0000.023
kegg_link1.7190.0607.064
kegg_list1.5160.0422.663
kegg_open0.0130.0010.013
kegg_operations000
kegg_organism_codes0.0140.0080.021
kegg_organisms0.0270.0020.029
kegg_pathway_annotations000
kegg_pathway_download0.0130.0000.013
kegg_pathway_list0.0110.0000.011
kegg_pathways_download000
kegg_picture1.1150.0285.965
kegg_process0.0150.0020.017
kegg_query0.0080.0000.008
kegg_request0.0590.0050.064
kegg_rm_prefix0.8500.0425.640
kinasephos 2.285 0.10521.238
latin_name0.5990.0061.095
load_db0.1910.0130.302
metalinksdb_sqlite 1.852 0.33112.438
metalinksdb_table0.2450.0200.265
metalinksdb_tables0.0210.0010.022
ncbi_taxid0.2980.0090.325
nichenet_build_model0.0010.0000.000
nichenet_expression_data0.0110.0000.011
nichenet_gr_network0.0240.0020.025
nichenet_gr_network_evex0.0090.0000.009
nichenet_gr_network_harmonizome0.0090.0000.009
nichenet_gr_network_htridb0.0080.0000.008
nichenet_gr_network_omnipath28.772 1.34142.129
nichenet_gr_network_pathwaycommons0.0100.0010.011
nichenet_gr_network_regnetwork0.010.000.01
nichenet_gr_network_remap0.0090.0010.010
nichenet_gr_network_trrust0.0080.0010.010
nichenet_ligand_activities000
nichenet_ligand_target_links000
nichenet_ligand_target_matrix000
nichenet_lr_network0.0210.0040.025
nichenet_lr_network_guide2pharma0.0060.0020.008
nichenet_lr_network_omnipath0.0230.0020.025
nichenet_lr_network_ramilowski0.0090.0000.008
nichenet_main000
nichenet_networks0.0430.0010.044
nichenet_optimization000
nichenet_remove_orphan_ligands0.0250.0010.026
nichenet_results_dir0.0010.0000.000
nichenet_signaling_network0.0240.0030.027
nichenet_signaling_network_cpdb0.0080.0010.008
nichenet_signaling_network_evex0.0090.0000.008
nichenet_signaling_network_harmonizome0.0080.0010.008
nichenet_signaling_network_inbiomap000
nichenet_signaling_network_omnipath20.904 0.77230.600
nichenet_signaling_network_pathwaycommons0.0280.0020.044
nichenet_signaling_network_vinayagam0.0300.0030.053
nichenet_test000
nichenet_workarounds000
obo_parser0.4510.0100.948
oma_code0.2820.0070.576
oma_organisms0.1800.0060.324
oma_pairwise0.0260.0000.026
oma_pairwise_genesymbols0.0290.0010.055
oma_pairwise_translated0.0390.0000.083
omnipath-interactions42.985 2.97873.497
omnipath_cache_autoclean0.0000.0000.001
omnipath_cache_clean0.0160.0000.016
omnipath_cache_clean_db0.1690.0150.183
omnipath_cache_download_ready0.9170.1231.070
omnipath_cache_filter_versions0.1460.0180.170
omnipath_cache_get0.1320.0110.142
omnipath_cache_key0.0020.0000.002
omnipath_cache_latest_or_new0.1000.0080.108
omnipath_cache_load0.9920.0423.423
omnipath_cache_move_in0.2020.0100.218
omnipath_cache_remove0.0780.0070.089
omnipath_cache_save0.1800.0100.308
omnipath_cache_search0.0010.0000.001
omnipath_cache_set_ext0.1570.0080.172
omnipath_cache_update_status0.1420.0100.153
omnipath_cache_wipe000
omnipath_config_path0.0020.0000.001
omnipath_for_cosmos13.216 0.52645.756
omnipath_load_config000
omnipath_log000
omnipath_logfile0.0010.0000.001
omnipath_msg0.0040.0010.005
omnipath_query3.4070.0793.483
omnipath_reset_config000
omnipath_save_config000
omnipath_set_cachedir0.0250.0000.025
omnipath_set_console_loglevel0.0040.0000.003
omnipath_set_logfile_loglevel0.0030.0000.003
omnipath_set_loglevel0.0020.0010.002
omnipath_show_db0.0570.0060.064
omnipath_unlock_cache_db000
only_from0.0010.0000.000
ontology_ensure_id0.0000.0000.001
ontology_ensure_name0.0000.0000.001
ontology_name_id0.0010.0000.001
organism_for0.1910.0030.194
pathwaycommons_download0.0000.0000.001
pivot_annotations10.434 0.59020.202
preppi_download000
preppi_filter0.0010.0000.001
print_bma_motif_es0.9270.0742.107
print_bma_motif_vs0.2340.0121.112
print_interactions 6.262 0.26011.075
print_path_es0.9440.0782.969
print_path_vs2.6130.1225.412
pubmed_open3.8900.0643.957
query_info0.4830.0090.704
ramilowski_download0.0010.0000.000
ramp_id_mapping_table000
ramp_id_type0.0010.0010.002
ramp_sqlite0.0010.0000.001
ramp_table000
ramp_tables000