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This page was generated on 2025-10-21 12:05 -0400 (Tue, 21 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4887
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4677
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4622
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4642
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1497/2353HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OmnipathR 3.17.6  (landing page)
Denes Turei
Snapshot Date: 2025-10-20 13:45 -0400 (Mon, 20 Oct 2025)
git_url: https://git.bioconductor.org/packages/OmnipathR
git_branch: devel
git_last_commit: 69ba6ef
git_last_commit_date: 2025-09-24 06:19:47 -0400 (Wed, 24 Sep 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    ERROR  
lconwaymacOS 12.7.6 Monterey / x86_64  OK    OK    ERROR    OK  
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    ERROR    OK  
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    ERROR  


CHECK results for OmnipathR on lconway

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

raw results


Summary

Package: OmnipathR
Version: 3.17.6
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings OmnipathR_3.17.6.tar.gz
StartedAt: 2025-10-21 00:26:08 -0400 (Tue, 21 Oct 2025)
EndedAt: 2025-10-21 00:42:10 -0400 (Tue, 21 Oct 2025)
EllapsedTime: 962.1 seconds
RetCode: 1
Status:   ERROR  
CheckDir: OmnipathR.Rcheck
Warnings: NA

Command output

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


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/OmnipathR.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OmnipathR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OmnipathR’ version ‘3.17.6’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 35 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘OmnipathR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking whether startup messages can be suppressed ... NOTE
[2025-10-21 00:26:48] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-21 00:26:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-21 00:26:48] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-10-21 00:26:48] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-10-21 00:26:48] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-10-20
[2025-10-21 00:26:48] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-10-20 19:10:38 UTC; unix
[2025-10-21 00:26:48] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.17.6
[2025-10-21 00:26:48] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-10-21 00:26:49] [INFO]    [OmnipathR] Session info: [version=R version 4.5.1 Patched (2025-09-10 r88807); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-10-21; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto]
[2025-10-21 00:26:49] [INFO]    [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.44 2024-06-07; ICU=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-10-21 00:26:49] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.4(2025-10-17); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.2.0(2025-10-13); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.17.6(2025-10-20); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.3.3(2025-05-29); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.3(2025-08-20); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.2(2025-09-08); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.53(2025-08-19); XML 3.99-0.19(2025-08-22); xml2 1.4.0(2025-08-20); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-10-21 00:26:49] [INFO]    [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: x86_64-apple-darwin22.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2025-10-21 00:26:49] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-10-21 00:26:49] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-10-21 00:26:49] [TRACE]   [OmnipathR] Contains 1 files.
[2025-10-21 00:26:49] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-10-21 00:26:49] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-21 00:26:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-21 00:26:50] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-10-21 00:26:50] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-10-21 00:26:50] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-10-21 00:26:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-21 00:26:50] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-10-21 00:26:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-21 00:26:50] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-10-21 00:26:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-21 00:26:50] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-10-21 00:26:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-21 00:26:50] [TRACE]   [OmnipathR] Cache locked: FALSE

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
[2025-10-21 00:27:16] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-21 00:27:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-21 00:27:16] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-10-21 00:27:16] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-10-21 00:27:16] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-10-20
[2025-10-21 00:27:16] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-10-20 19:10:38 UTC; unix
[2025-10-21 00:27:16] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.17.6
[2025-10-21 00:27:16] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-10-21 00:27:17] [INFO]    [OmnipathR] Session info: [version=R version 4.5.1 Patched (2025-09-10 r88807); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-10-21; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto]
[2025-10-21 00:27:17] [INFO]    [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.44 2024-06-07; ICU=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-10-21 00:27:17] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.4(2025-10-17); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.2.0(2025-10-13); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.17.6(2025-10-20); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.3.3(2025-05-29); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.3(2025-08-20); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.2(2025-09-08); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.53(2025-08-19); XML 3.99-0.19(2025-08-22); xml2 1.4.0(2025-08-20); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-10-21 00:27:17] [INFO]    [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: x86_64-apple-darwin22.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2025-10-21 00:27:17] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-10-21 00:27:17] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-10-21 00:27:17] [TRACE]   [OmnipathR] Contains 1 files.
[2025-10-21 00:27:17] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-10-21 00:27:17] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-21 00:27:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-21 00:27:17] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-10-21 00:27:17] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-10-21 00:27:17] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-10-21 00:27:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-21 00:27:17] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-10-21 00:27:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-21 00:27:17] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-10-21 00:27:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-21 00:27:17] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-10-21 00:27:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-21 00:27:17] [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: kinasephos
> ### Title: Kinase-PTM relationships from KinasePhos 3.0
> ### Aliases: kinasephos
> 
> ### ** Examples
> 
> kinasephos()
[2025-10-21 00:39:59] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-10-21 00:39:59] [TRACE]   [OmnipathR] Looking up in cache: `https://awi.cuhk.edu.cn/KinasePhos/dataset.csv`.
[2025-10-21 00:39:59] [INFO]    [OmnipathR] Cache record does not exist: `https://awi.cuhk.edu.cn/KinasePhos/dataset.csv`
[2025-10-21 00:39:59] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://awi.cuhk.edu.cn/KinasePhos/dataset.csv`.
[2025-10-21 00:39:59] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-21 00:39:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-21 00:39:59] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-21 00:39:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-21 00:39:59] [INFO]    [OmnipathR] Cache item `332c57703a2a947f42ea25504bcc6401dc01fb00` version 1: status changed from `unknown` to `started`.
[2025-10-21 00:39:59] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/332c57703a2a947f42ea25504bcc6401dc01fb00-1.rds`.
[2025-10-21 00:39:59] [INFO]    [OmnipathR] Retrieving URL: `https://awi.cuhk.edu.cn/KinasePhos/dataset.csv`
[2025-10-21 00:39:59] [TRACE]   [OmnipathR] Attempt 1/3: `https://awi.cuhk.edu.cn/KinasePhos/dataset.csv`
[2025-10-21 00:39:59] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-10-21 00:39:59] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-10-21 00:40:09] [TRACE]   [OmnipathR] HTTP vNA GET: status 0.
[2025-10-21 00:40:09] [TRACE]   [OmnipathR] Downloaded 0 bytes in 10.001867s from awi.cuhk.edu.cn (0 bytes/s); Redirect: 0s, DNS look up: 0.951957s, Connection: 0s, Pretransfer: 0s, First byte at: 0s
[2025-10-21 00:40:09] [TRACE]   [OmnipathR] HTTP headers: 
[2025-10-21 00:40:09] [WARN]    [OmnipathR] HTTP request failed with error: Failed to open 'https://awi.cuhk.edu.cn/KinasePhos/dataset.csv': Connection timed out after 10001 milliseconds
[2025-10-21 00:40:09] [WARN]    [OmnipathR] Failed to download `https://awi.cuhk.edu.cn/KinasePhos/dataset.csv` (attempt 1/3); error: Failed to open 'https://awi.cuhk.edu.cn/KinasePhos/dataset.csv': Connection timed out after 10001 milliseconds
[2025-10-21 00:40:14] [TRACE]   [OmnipathR] Attempt 2/3: `https://awi.cuhk.edu.cn/KinasePhos/dataset.csv`
[2025-10-21 00:40:14] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-10-21 00:40:14] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-10-21 00:40:17] [TRACE]   [OmnipathR] HTTP vNA GET: status 0.
[2025-10-21 00:40:17] [TRACE]   [OmnipathR] Downloaded 0 bytes in 2.172643s from awi.cuhk.edu.cn (0 bytes/s); Redirect: 0s, DNS look up: 0.001469s, Connection: 0.002451s, Pretransfer: 1.931778s, First byte at: 0s
[2025-10-21 00:40:17] [TRACE]   [OmnipathR] HTTP headers: 
[2025-10-21 00:40:17] [WARN]    [OmnipathR] HTTP request failed with error: Failed to open 'https://awi.cuhk.edu.cn/KinasePhos/dataset.csv': Empty reply from server
[2025-10-21 00:40:17] [WARN]    [OmnipathR] Failed to download `https://awi.cuhk.edu.cn/KinasePhos/dataset.csv` (attempt 2/3); error: Failed to open 'https://awi.cuhk.edu.cn/KinasePhos/dataset.csv': Empty reply from server
[2025-10-21 00:40:22] [TRACE]   [OmnipathR] Attempt 3/3: `https://awi.cuhk.edu.cn/KinasePhos/dataset.csv`
[2025-10-21 00:40:22] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-10-21 00:40:22] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-10-21 00:40:23] [TRACE]   [OmnipathR] HTTP vNA GET: status 0.
[2025-10-21 00:40:23] [TRACE]   [OmnipathR] Downloaded 0 bytes in 1.233509s from awi.cuhk.edu.cn (0 bytes/s); Redirect: 0s, DNS look up: 0.001113s, Connection: 0.002201s, Pretransfer: 0.982215s, First byte at: 0s
[2025-10-21 00:40:23] [TRACE]   [OmnipathR] HTTP headers: 
[2025-10-21 00:40:23] [WARN]    [OmnipathR] HTTP request failed with error: Failed to open 'https://awi.cuhk.edu.cn/KinasePhos/dataset.csv': Empty reply from server
[2025-10-21 00:40:23] [ERROR]   [OmnipathR] Failed to download `https://awi.cuhk.edu.cn/KinasePhos/dataset.csv` (attempt 3/3); error: Failed to open 'https://awi.cuhk.edu.cn/KinasePhos/dataset.csv': Empty reply from server
[2025-10-21 00:40:23] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-10-21 00:40:23] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-10-20
[2025-10-21 00:40:23] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-10-20 19:10:38 UTC; unix
[2025-10-21 00:40:23] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.17.6
[2025-10-21 00:40:23] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-10-21 00:40:24] [INFO]    [OmnipathR] Session info: [version=R version 4.5.1 Patched (2025-09-10 r88807); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=en; collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-10-21; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto]
[2025-10-21 00:40:24] [INFO]    [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.44 2024-06-07; ICU=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-10-21 00:40:24] [INFO]    [OmnipathR] Loaded packages: archive 1.1.12(2025-03-20); backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.4(2025-10-17); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.2.0(2025-10-13); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.17.6(2025-10-20); 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); selectr 0.4-2(2019-11-20); 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); utf8 1.2.6(2025-06-08); vctrs 0.6.5(2023-12-01); vroom 1.6.6(2025-09-19); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.53(2025-08-19); XML 3.99-0.19(2025-08-22); xml2 1.4.0(2025-08-20); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-10-21 00:40:24] [INFO]    [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: x86_64-apple-darwin22.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
Error in (function (url, curlopt = list(), callback = NULL, compr = NULL,  : 
  Failed to open 'https://awi.cuhk.edu.cn/KinasePhos/dataset.csv': Empty reply from server
Calls: kinasephos ... omnipath_cache_save -> saveRDS -> exec -> <Anonymous>
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                                       user system elapsed
annotation_categories                60.532  0.557  62.782
curated_ligrec_stats                 41.363 15.282 138.178
filter_extra_attrs                   40.353 12.581  61.866
all_uniprots                         27.945  3.169  49.370
extra_attrs_to_cols                  19.371  4.054  24.235
extra_attr_values                    18.367  3.382  33.666
curated_ligand_receptor_interactions  7.984 12.358  34.040
go_annot_download                    13.679  2.063  22.600
giant_component                      13.067  1.515  25.113
has_extra_attrs                      11.142  3.322  14.596
extra_attrs                           9.007  3.142  15.611
filter_by_resource                   10.427  0.886  13.915
find_all_paths                        8.704  0.651  14.342
filter_intercell                      7.452  1.207  18.767
ensembl_id_mapping_table              2.447  1.397  71.048
enzsub_graph                          2.805  0.566   7.211
biomart_query                         1.356  1.579   7.933
kegg_conv                             1.501  0.231  12.541
kegg_picture                          1.147  0.057   7.662
kegg_rm_prefix                        0.858  0.124   5.820
kegg_link                             0.752  0.106   6.608
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

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


Installation output

OmnipathR.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘OmnipathR’ ...
** this is package ‘OmnipathR’ version ‘3.17.6’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
[2025-10-20 15:10:51] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-20 15:10:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-20 15:10:52] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-10-20 15:10:52] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-10-20 15:10:52] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-10-20
[2025-10-20 15:10:52] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-10-20 19:10:38 UTC; unix
[2025-10-20 15:10:52] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.17.6
[2025-10-20 15:10:52] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-10-20 15:10:53] [INFO]    [OmnipathR] Session info: [version=R version 4.5.1 Patched (2025-09-10 r88807); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-10-20; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto]
[2025-10-20 15:10:53] [INFO]    [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.44 2024-06-07; ICU=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-10-20 15:10:53] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.4(2025-10-17); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.2.0(2025-10-13); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.17.6(2025-10-20); 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)
[2025-10-20 15:10:53] [INFO]    [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: x86_64-apple-darwin22.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2025-10-20 15:10:53] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-10-20 15:10:53] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-10-20 15:10:53] [TRACE]   [OmnipathR] Contains 1 files.
[2025-10-20 15:10:53] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-10-20 15:10:53] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-20 15:10:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-20 15:10:53] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-10-20 15:10:53] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-10-20 15:10:53] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-10-20 15:10:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-20 15:10:53] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-10-20 15:10:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-20 15:10:53] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-10-20 15:10:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-20 15:10:53] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-10-20 15:10:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-20 15:10:53] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2025-10-20 15:10:55] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-20 15:10:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-20 15:10:55] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-10-20 15:10:55] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-10-20 15:10:55] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-10-20
[2025-10-20 15:10:55] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-10-20 19:10:38 UTC; unix
[2025-10-20 15:10:55] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.17.6
[2025-10-20 15:10:55] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-10-20 15:10:56] [INFO]    [OmnipathR] Session info: [version=R version 4.5.1 Patched (2025-09-10 r88807); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-10-20; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto]
[2025-10-20 15:10:56] [INFO]    [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.44 2024-06-07; ICU=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-10-20 15:10:56] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.4(2025-10-17); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.2.0(2025-10-13); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.17.6(2025-10-20); 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)
[2025-10-20 15:10:56] [INFO]    [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: x86_64-apple-darwin22.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2025-10-20 15:10:56] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-10-20 15:10:56] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-10-20 15:10:56] [TRACE]   [OmnipathR] Contains 1 files.
[2025-10-20 15:10:56] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-10-20 15:10:56] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-20 15:10:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-20 15:10:56] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-10-20 15:10:56] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-10-20 15:10:56] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-10-20 15:10:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-20 15:10:56] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-10-20 15:10:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-20 15:10:56] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-10-20 15:10:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-20 15:10:56] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-10-20 15:10:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-20 15:10:56] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package keeps a record of temporary installation path
* DONE (OmnipathR)

Tests output

OmnipathR.Rcheck/tests/testthat.Rout


R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
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Platform: x86_64-apple-darwin20

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> #!/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)
[2025-10-21 00:40:29] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-21 00:40:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-21 00:40:29] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-10-21 00:40:29] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-10-21 00:40:29] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-10-20
[2025-10-21 00:40:29] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-10-20 19:10:38 UTC; unix
[2025-10-21 00:40:29] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.17.6
[2025-10-21 00:40:29] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-10-21 00:40:30] [INFO]    [OmnipathR] Session info: [version=R version 4.5.1 Patched (2025-09-10 r88807); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=C; collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-10-21; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto]
[2025-10-21 00:40:30] [INFO]    [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.44 2024-06-07; ICU=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-10-21 00:40:30] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); brio 1.1.5(2024-04-24); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.4(2025-10-17); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.2.0(2025-10-13); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.17.6(2025-10-20); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.3.3(2025-05-29); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.3(2025-08-20); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.2(2025-09-08); testthat 3.2.3(2025-01-13); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.53(2025-08-19); XML 3.99-0.19(2025-08-22); xml2 1.4.0(2025-08-20); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-10-21 00:40:30] [INFO]    [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: x86_64-apple-darwin22.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2025-10-21 00:40:30] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-10-21 00:40:30] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-10-21 00:40:30] [TRACE]   [OmnipathR] Contains 57 files.
[2025-10-21 00:40:30] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-10-21 00:40:30] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-21 00:40:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-21 00:40:30] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-10-21 00:40:30] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-10-21 00:40:30] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-10-21 00:40:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-21 00:40:30] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-10-21 00:40:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-21 00:40:30] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-10-21 00:40:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-21 00:40:30] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-10-21 00:40:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-21 00:40:30] [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 
 50.000   6.082  84.309 

Example timings

OmnipathR.Rcheck/OmnipathR-Ex.timings

nameusersystemelapsed
OmnipathR0.0000.0000.001
all_uniprot_acs0.0240.0030.027
all_uniprots27.945 3.16949.370
ancestors0.0120.0020.013
annotated_network1.5000.1474.459
annotation_categories60.532 0.55762.782
annotation_resources0.0680.0700.789
annotations0.5980.4572.524
biomart_query1.3561.5797.933
bioplex10.0110.0070.017
bioplex20.0110.0080.017
bioplex30.0100.0060.016
bioplex_all0.0110.0080.018
bioplex_hct116_10.0110.0090.035
bma_motif_es0.6640.6762.193
bma_motif_vs0.2260.1861.032
chalmers_gem0.0110.0070.016
chalmers_gem_id_mapping_table0.0110.0070.019
chalmers_gem_id_type0.0020.0020.003
chalmers_gem_metabolites0.0110.0070.015
chalmers_gem_network0.0110.0090.019
chalmers_gem_raw0.0110.0070.016
chalmers_gem_reactions0.0110.0090.036
common_name0.1180.0410.152
complex_genes0.7530.6593.892
complex_resources0.0690.0580.650
complexes0.1920.1380.994
consensuspathdb_download0.0000.0000.001
consensuspathdb_raw_table0.0100.0070.017
cosmos_pkn0.0000.0010.000
curated_ligand_receptor_interactions 7.98412.35834.040
curated_ligrec_stats 41.363 15.282138.178
database_summary1.3590.2254.912
descendants0.0090.0020.034
ensembl_dataset0.0370.0030.136
ensembl_id_mapping_table 2.447 1.39771.048
ensembl_id_type0.0020.0000.013
ensembl_name0.2510.0561.350
ensembl_organisms0.1360.0510.384
ensembl_organisms_raw0.1400.0390.346
ensembl_orthology0.0010.0010.000
enzsub_graph2.8050.5667.211
enzsub_resources0.0720.0170.605
enzyme_substrate1.5990.1872.685
evex_download0.0120.0020.017
evidences000
extra_attr_values18.367 3.38233.666
extra_attrs 9.007 3.14215.611
extra_attrs_to_cols19.371 4.05424.235
filter_by_resource10.427 0.88613.915
filter_extra_attrs40.35312.58161.866
filter_intercell 7.452 1.20718.767
filter_intercell_network0.0240.0040.028
find_all_paths 8.704 0.65114.342
from_evidences0.0000.0010.000
get_db000
get_ontology_db0.0080.0030.011
giant_component13.067 1.51525.113
go_annot_download13.679 2.06322.600
go_annot_slim000
go_ontology_download0.0130.0020.015
guide2pharma_download0.0130.0020.016
harmonizome_download0.0110.0030.013
has_extra_attrs11.142 3.32214.596
hmdb_id_mapping_table0.0110.0020.013
hmdb_id_type0.0030.0010.003
hmdb_metabolite_fields0.0010.0010.001
hmdb_protein_fields000
hmdb_table0.0110.0020.013
homologene_download0.0110.0020.012
homologene_raw0.0610.0040.065
homologene_uniprot_orthology0.0120.0020.014
hpo_download3.2190.5563.735
htridb_download0.0100.0020.012
id_translation_resources0.0000.0000.001
id_types0.0620.0130.076
inbiomap_download000
inbiomap_raw0.0000.0010.000
interaction_datasets0.8090.0921.112
interaction_graph0.5170.0401.293
interaction_resources0.0680.0120.590
interaction_types0.0900.0090.099
intercell0.9210.1291.934
intercell_categories0.7510.1041.069
intercell_consensus_filter1.6300.1853.359
intercell_generic_categories0.0870.0080.095
intercell_network0.0130.0030.016
intercell_resources0.0660.0110.666
intercell_summary0.0870.0220.111
is_ontology_id0.0000.0010.000
is_swissprot0.0610.0070.071
is_trembl0.0610.0050.067
is_uniprot0.0130.0030.016
kegg_api_templates0.0020.0030.005
kegg_conv 1.501 0.23112.541
kegg_databases0.0010.0000.001
kegg_ddi0.6720.0812.117
kegg_find0.6930.0852.293
kegg_info0.0110.0020.014
kegg_link0.7520.1066.608
kegg_list0.6870.0761.698
kegg_open0.0100.0020.012
kegg_operations0.0000.0010.001
kegg_organism_codes0.0270.0940.121
kegg_organisms0.0280.0070.033
kegg_pathway_annotations0.0000.0010.000
kegg_pathway_download0.0100.0020.014
kegg_pathway_list0.0110.0020.014
kegg_pathways_download0.0000.0000.001
kegg_picture1.1470.0577.662
kegg_process0.0220.0030.026
kegg_query0.0110.0010.011
kegg_request0.0800.0090.091
kegg_rm_prefix0.8580.1245.820