| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-25 12:05 -0400 (Sat, 25 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4901 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4691 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4637 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4658 |
| 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 1505/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| OmnipathR 3.17.7 (landing page) Denes Turei
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | NA | NA | ||||||||||
|
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. |
| Package: OmnipathR |
| Version: 3.17.7 |
| 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_3.17.7.tar.gz |
| StartedAt: 2025-10-24 23:03:01 -0400 (Fri, 24 Oct 2025) |
| EndedAt: 2025-10-24 23:21:25 -0400 (Fri, 24 Oct 2025) |
| EllapsedTime: 1103.5 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: OmnipathR.Rcheck |
| Warnings: NA |
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### Running command:
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### /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_3.17.7.tar.gz
###
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* 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 ‘3.17.7’
* 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
[2025-10-24 23:03:40] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-24 23:03:40] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-24 23:03:40] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-10-24 23:03:40] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-10-24 23:03:40] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-10-24
[2025-10-24 23:03:40] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-10-24 19:18:43 UTC; unix
[2025-10-24 23:03:40] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.7
[2025-10-24 23:03:40] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-10-24 23:03:41] [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=2025-10-24; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto]
[2025-10-24 23:03:41] [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]
[2025-10-24 23:03:41] [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 3.17.7(2025-10-24); otel 0.2.0(2025-08-29); 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 1.4.0(2025-10-22); 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)
[2025-10-24 23:03:41] [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
[2025-10-24 23:03:41] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-10-24 23:03:41] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-10-24 23:03:41] [TRACE] [OmnipathR] Contains 1 files.
[2025-10-24 23:03:41] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-10-24 23:03:41] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-24 23:03:41] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-24 23:03:41] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-10-24 23:03:41] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-10-24 23:03:41] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-10-24 23:03:41] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-24 23:03:41] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-10-24 23:03:41] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-24 23:03:41] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-10-24 23:03:41] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-24 23:03:41] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-10-24 23:03:41] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-24 23:03:41] [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
[2025-10-24 23:04:07] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-24 23:04:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-24 23:04:07] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-10-24 23:04:07] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-10-24 23:04:07] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-10-24
[2025-10-24 23:04:07] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-10-24 19:18:43 UTC; unix
[2025-10-24 23:04:07] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.7
[2025-10-24 23:04:07] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-10-24 23:04:07] [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=2025-10-24; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto]
[2025-10-24 23:04:08] [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]
[2025-10-24 23:04:08] [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 3.17.7(2025-10-24); otel 0.2.0(2025-08-29); 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 1.4.0(2025-10-22); 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)
[2025-10-24 23:04:08] [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
[2025-10-24 23:04:08] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-10-24 23:04:08] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-10-24 23:04:08] [TRACE] [OmnipathR] Contains 1 files.
[2025-10-24 23:04:08] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-10-24 23:04:08] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-24 23:04:08] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-24 23:04:08] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-10-24 23:04:08] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-10-24 23:04:08] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-10-24 23:04:08] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-24 23:04:08] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-10-24 23:04:08] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-24 23:04:08] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-10-24 23:04:08] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-24 23:04:08] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-10-24 23:04:08] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-24 23:04:08] [TRACE] [OmnipathR] Cache locked: FALSE
.cosmos_pkn: no visible global function definition for
‘metabolite_idsc’
cosmos_ksn: no visible binding for global variable
‘substrate_genesymbol’
cosmos_ksn: no visible binding for global variable ‘residue_type’
cosmos_ksn: no visible binding for global variable ‘residue_offset’
cosmos_ksn: no visible binding for global variable ‘enzyme_genesymbol’
cosmos_ksn: no visible binding for global variable ‘mor’
recon3d_genes: no visible binding for global variable ‘notes’
recon3d_genes: no visible binding for global variable ‘annotation’
recon3d_genes: no visible binding for global variable
‘original_bigg_ids’
recon3d_metabolites: no visible binding for global variable ‘notes’
recon3d_metabolites: no visible binding for global variable
‘original_bigg_ids’
recon3d_metabolites: no visible binding for global variable
‘annotation’
recon3d_metabolites: no visible global function definition for
‘chalmers_gem_matlab_tibble’
recon3d_metabolites: no visible binding for global variable ‘hmdb’
recon3d_metabolites: no visible binding for global variable ‘metHMDBID’
recon3d_reactions: no visible binding for global variable ‘notes’
recon3d_reactions: no visible binding for global variable ‘metabolites’
recon3d_reactions: no visible binding for global variable
‘original_bigg_ids’
taxon_names_table: no visible binding for global variable
‘latin_name_uniprot’
taxon_names_table: no visible binding for global variable
‘latin_name_ensembl’
taxon_names_table: no visible binding for global variable
‘latin_name_oma’
taxon_names_table: no visible binding for global variable
‘common_name_ensembl’
taxon_names_table: no visible binding for global variable
‘common_name_uniprot’
Undefined global functions or variables:
annotation chalmers_gem_matlab_tibble common_name_ensembl
common_name_uniprot enzyme_genesymbol hmdb latin_name_ensembl
latin_name_oma latin_name_uniprot metHMDBID metabolite_idsc
metabolites mor notes original_bigg_ids residue_offset residue_type
substrate_genesymbol
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
‘recon3d_raw’ ‘recon3d_raw_vmh’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in Rd file 'recon3d.Rd'
‘extra_hmdb’
Undocumented arguments in Rd file 'translate_ids_multi.Rd'
‘ramp’ ‘expand’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘OmnipathR-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: recon3d_metabolites
> ### Title: Metabolites from Recon-3D
> ### Aliases: recon3d_metabolites recon3d_reactions recon3d_genes
> ### recon3d_compartments
>
> ### ** Examples
>
> recon3d_metabolites()
Warning in readLines(con = path, encoding = encoding) :
incomplete final line found on '/Users/biocbuild/Library/Caches/OmnipathR/be81cd1c9a119b749e4206f26272806591e8fb4c-1.gz'
Error in chalmers_gem_matlab_tibble(., "mets", "metHMDBID") :
could not find function "chalmers_gem_matlab_tibble"
Calls: recon3d_metabolites ... same_src.data.frame -> is.data.frame -> %>% -> unnest -> unnest
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
curated_ligrec_stats 43.952 21.341 137.901
annotation_categories 57.856 0.336 59.888
filter_extra_attrs 42.837 12.882 68.148
omnipath-interactions 33.539 3.376 60.956
all_uniprots 26.622 3.107 50.809
extra_attrs_to_cols 20.799 3.110 31.370
extra_attr_values 19.649 3.799 35.776
nichenet_gr_network_omnipath 16.910 1.706 20.965
extra_attrs 12.437 3.105 19.207
go_annot_download 13.695 1.832 14.790
curated_ligand_receptor_interactions 7.908 6.690 24.432
nichenet_signaling_network_omnipath 12.559 1.222 16.300
giant_component 12.542 1.188 16.512
has_extra_attrs 9.990 2.914 12.945
omnipath_for_cosmos 10.659 0.867 31.705
pivot_annotations 10.345 0.991 19.537
filter_by_resource 9.795 0.753 12.687
filter_intercell 8.577 0.690 17.145
find_all_paths 7.528 0.523 8.215
print_interactions 7.023 0.537 11.739
pubmed_open 4.816 0.245 5.091
ensembl_id_mapping_table 3.205 0.408 22.991
enzsub_graph 3.249 0.270 6.323
print_path_vs 2.764 0.273 5.692
kegg_conv 1.585 0.223 11.098
metalinksdb_sqlite 1.037 0.357 10.703
kinasephos 1.132 0.204 30.298
kegg_picture 0.998 0.069 5.329
kegg_rm_prefix 0.823 0.103 5.991
kegg_link 0.768 0.109 5.982
* 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.
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 ‘3.17.7’ ** 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 [2025-10-24 15:18:56] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-24 15:18:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-24 15:18:56] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-10-24 15:18:56] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-10-24 15:18:56] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-10-24 [2025-10-24 15:18:56] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-10-24 19:18:43 UTC; unix [2025-10-24 15:18:56] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.7 [2025-10-24 15:18:56] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22 [2025-10-24 15:18:57] [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=2025-10-24; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto] [2025-10-24 15:18:58] [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] [2025-10-24 15:18:58] [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 3.17.7(2025-10-24); otel 0.2.0(2025-08-29); 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 1.4.0(2025-10-22); 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) [2025-10-24 15:18:58] [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 [2025-10-24 15:18:58] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-10-24 15:18:58] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-10-24 15:18:58] [TRACE] [OmnipathR] Contains 1 files. [2025-10-24 15:18:58] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-10-24 15:18:58] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-24 15:18:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-24 15:18:58] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-10-24 15:18:58] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-10-24 15:18:58] [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). [2025-10-24 15:18:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-24 15:18:58] [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). [2025-10-24 15:18:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-24 15:18:58] [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). [2025-10-24 15:18:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-24 15:18:58] [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). [2025-10-24 15:18:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-24 15:18:58] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2025-10-24 15:19:00] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-24 15:19:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-24 15:19:00] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-10-24 15:19:00] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-10-24 15:19:00] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-10-24 [2025-10-24 15:19:00] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-10-24 19:18:43 UTC; unix [2025-10-24 15:19:00] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.7 [2025-10-24 15:19:00] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22 [2025-10-24 15:19:01] [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=2025-10-24; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto] [2025-10-24 15:19:01] [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] [2025-10-24 15:19:01] [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 3.17.7(2025-10-24); otel 0.2.0(2025-08-29); 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 1.4.0(2025-10-22); 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) [2025-10-24 15:19:01] [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 [2025-10-24 15:19:01] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-10-24 15:19:01] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-10-24 15:19:01] [TRACE] [OmnipathR] Contains 1 files. [2025-10-24 15:19:01] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-10-24 15:19:01] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-24 15:19:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-24 15:19:01] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-10-24 15:19:01] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-10-24 15:19:01] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-10-24 15:19:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-24 15:19:01] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-10-24 15:19:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-24 15:19:01] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-10-24 15:19:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-24 15:19:01] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-10-24 15:19:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-24 15:19:01] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package keeps a record of temporary installation path * DONE (OmnipathR)
OmnipathR.Rcheck/tests/testthat.Rout
R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> #!/usr/bin/env Rscript
>
> #
> # This file is part of the `OmnipathR` R package
> #
> # Copyright
> # 2018-2024
> # Saez Lab, Uniklinik RWTH Aachen, Heidelberg University
> #
> # File author(s): Alberto Valdeolivas
> # Dénes Türei (turei.denes@gmail.com)
> # Attila Gábor
> #
> # Distributed under the MIT (Expat) License.
> # See accompanying file `LICENSE` or find a copy at
> # https://directory.fsf.org/wiki/License:Expat
> #
> # Website: https://r.omnipathdb.org/
> # Git repo: https://github.com/saezlab/OmnipathR
> #
>
>
> library(testthat)
> library(OmnipathR)
[2025-10-24 23:19:46] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-24 23:19:46] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-24 23:19:46] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-10-24 23:19:46] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-10-24 23:19:46] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-10-24
[2025-10-24 23:19:46] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-10-24 19:18:43 UTC; unix
[2025-10-24 23:19:46] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.7
[2025-10-24 23:19:46] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-10-24 23:19:47] [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=2025-10-24; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto]
[2025-10-24 23:19:47] [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]
[2025-10-24 23:19:48] [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 3.17.7(2025-10-24); otel 0.2.0(2025-08-29); 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 1.4.0(2025-10-22); 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)
[2025-10-24 23:19:48] [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
[2025-10-24 23:19:48] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-10-24 23:19:48] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-10-24 23:19:48] [TRACE] [OmnipathR] Contains 12 files.
[2025-10-24 23:19:48] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-10-24 23:19:48] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-24 23:19:48] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-24 23:19:48] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-10-24 23:19:48] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-10-24 23:19:48] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-10-24 23:19:48] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-24 23:19:48] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-10-24 23:19:48] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-24 23:19:48] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-10-24 23:19:48] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-24 23:19:48] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-10-24 23:19:48] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-24 23:19:48] [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
47.760 5.951 82.141
OmnipathR.Rcheck/OmnipathR-Ex.timings
| name | user | system | elapsed | |
| OmnipathR | 0.001 | 0.001 | 0.001 | |
| all_uniprot_acs | 0.022 | 0.003 | 0.025 | |
| all_uniprots | 26.622 | 3.107 | 50.809 | |
| ancestors | 0.012 | 0.002 | 0.014 | |
| annotated_network | 1.433 | 0.134 | 4.673 | |
| annotation_categories | 57.856 | 0.336 | 59.888 | |
| annotation_resources | 0.060 | 0.009 | 0.746 | |
| annotations | 0.631 | 0.052 | 1.421 | |
| biomart_query | 1.416 | 0.194 | 4.528 | |
| bioplex1 | 0.011 | 0.002 | 0.013 | |
| bioplex2 | 0.012 | 0.002 | 0.013 | |
| bioplex3 | 0.011 | 0.002 | 0.011 | |
| bioplex_all | 0.011 | 0.002 | 0.013 | |
| bioplex_hct116_1 | 0.011 | 0.002 | 0.013 | |
| bma_motif_es | 0.684 | 0.088 | 1.488 | |
| bma_motif_vs | 0.216 | 0.025 | 0.753 | |
| chalmers_gem | 0.011 | 0.001 | 0.011 | |
| chalmers_gem_id_mapping_table | 0.010 | 0.001 | 0.012 | |
| chalmers_gem_id_type | 0.002 | 0.000 | 0.003 | |
| chalmers_gem_metabolites | 0.010 | 0.002 | 0.011 | |
| chalmers_gem_network | 0.009 | 0.002 | 0.011 | |
| chalmers_gem_raw | 0.010 | 0.002 | 0.012 | |
| chalmers_gem_reactions | 0.011 | 0.002 | 0.012 | |
| common_name | 0.118 | 0.007 | 0.126 | |
| complex_genes | 0.761 | 0.066 | 2.437 | |
| complex_resources | 0.065 | 0.008 | 0.659 | |
| complexes | 0.182 | 0.020 | 0.714 | |
| consensuspathdb_download | 0.000 | 0.001 | 0.000 | |
| consensuspathdb_raw_table | 0.012 | 0.003 | 0.014 | |
| cosmos_pkn | 0 | 0 | 0 | |
| curated_ligand_receptor_interactions | 7.908 | 6.690 | 24.432 | |
| curated_ligrec_stats | 43.952 | 21.341 | 137.901 | |
| database_summary | 1.931 | 0.234 | 3.546 | |
| descendants | 0.012 | 0.002 | 0.015 | |
| ensembl_dataset | 0.058 | 0.003 | 0.060 | |
| ensembl_id_mapping_table | 3.205 | 0.408 | 22.991 | |
| ensembl_id_type | 0.003 | 0.000 | 0.004 | |
| ensembl_name | 0.382 | 0.020 | 0.715 | |
| ensembl_organisms | 0.202 | 0.031 | 0.360 | |
| ensembl_organisms_raw | 0.197 | 0.032 | 0.364 | |
| ensembl_orthology | 0.000 | 0.001 | 0.001 | |
| enzsub_graph | 3.249 | 0.270 | 6.323 | |
| enzsub_resources | 0.057 | 0.011 | 0.757 | |
| enzyme_substrate | 1.048 | 0.056 | 2.325 | |
| evex_download | 0.027 | 0.001 | 0.039 | |
| evidences | 0 | 0 | 0 | |
| extra_attr_values | 19.649 | 3.799 | 35.776 | |
| extra_attrs | 12.437 | 3.105 | 19.207 | |
| extra_attrs_to_cols | 20.799 | 3.110 | 31.370 | |
| filter_by_resource | 9.795 | 0.753 | 12.687 | |
| filter_extra_attrs | 42.837 | 12.882 | 68.148 | |
| filter_intercell | 8.577 | 0.690 | 17.145 | |
| filter_intercell_network | 0.023 | 0.003 | 0.027 | |
| find_all_paths | 7.528 | 0.523 | 8.215 | |
| from_evidences | 0.000 | 0.000 | 0.001 | |
| get_db | 0 | 0 | 0 | |
| get_ontology_db | 0.011 | 0.001 | 0.013 | |
| giant_component | 12.542 | 1.188 | 16.512 | |
| go_annot_download | 13.695 | 1.832 | 14.790 | |
| go_annot_slim | 0.000 | 0.001 | 0.000 | |
| go_ontology_download | 0.011 | 0.002 | 0.013 | |
| guide2pharma_download | 0.010 | 0.002 | 0.012 | |
| harmonizome_download | 0.010 | 0.002 | 0.012 | |
| has_extra_attrs | 9.990 | 2.914 | 12.945 | |
| hmdb_id_mapping_table | 0.011 | 0.001 | 0.012 | |
| hmdb_id_type | 0.002 | 0.000 | 0.003 | |
| hmdb_metabolite_fields | 0.001 | 0.000 | 0.002 | |
| hmdb_protein_fields | 0.001 | 0.000 | 0.000 | |
| hmdb_table | 0.012 | 0.006 | 0.022 | |
| homologene_download | 0.012 | 0.012 | 0.036 | |
| homologene_raw | 0.058 | 0.031 | 0.097 | |
| homologene_uniprot_orthology | 0.010 | 0.002 | 0.012 | |
| hpo_download | 2.801 | 0.476 | 3.389 | |
| htridb_download | 0.011 | 0.002 | 0.013 | |
| id_translation_resources | 0 | 0 | 0 | |
| id_types | 0.065 | 0.088 | 0.219 | |
| inbiomap_download | 0 | 0 | 0 | |
| inbiomap_raw | 0.000 | 0.000 | 0.001 | |
| interaction_datasets | 0.711 | 0.115 | 1.287 | |
| interaction_graph | 0.489 | 0.036 | 1.044 | |
| interaction_resources | 0.063 | 0.011 | 0.554 | |
| interaction_types | 0.078 | 0.014 | 0.100 | |
| intercell | 0.901 | 0.138 | 1.906 | |
| intercell_categories | 0.708 | 0.089 | 1.022 | |
| intercell_consensus_filter | 1.490 | 0.162 | 3.252 | |
| intercell_generic_categories | 0.084 | 0.010 | 0.094 | |
| intercell_network | 0.011 | 0.002 | 0.013 | |
| intercell_resources | 0.065 | 0.009 | 0.628 | |
| intercell_summary | 0.086 | 0.027 | 0.114 | |
| is_ontology_id | 0 | 0 | 0 | |
| is_swissprot | 0.064 | 0.006 | 0.071 | |
| is_trembl | 0.061 | 0.005 | 0.066 | |
| is_uniprot | 0.015 | 0.003 | 0.025 | |
| kegg_api_templates | 0.002 | 0.003 | 0.004 | |
| kegg_conv | 1.585 | 0.223 | 11.098 | |
| kegg_databases | 0.000 | 0.001 | 0.001 | |
| kegg_ddi | 0.706 | 0.088 | 2.900 | |
| kegg_find | 0.731 | 0.090 | 3.323 | |
| kegg_info | 0.011 | 0.002 | 0.014 | |
| kegg_link | 0.768 | 0.109 | 5.982 | |
| kegg_list | 0.700 | 0.083 | 1.763 | |
| kegg_open | 0.011 | 0.002 | 0.013 | |
| kegg_operations | 0 | 0 | 0 | |
| kegg_organism_codes | 0.023 | 0.065 | 0.090 | |
| kegg_organisms | 0.028 | 0.007 | 0.035 | |
| kegg_pathway_annotations | 0.001 | 0.000 | 0.001 | |
| kegg_pathway_download | 0.011 | 0.002 | 0.013 | |
| kegg_pathway_list | 0.011 | 0.002 | 0.013 | |
| kegg_pathways_download | 0.000 | 0.001 | 0.000 | |
| kegg_picture | 0.998 | 0.069 | 5.329 | |
| kegg_process | 0.021 | 0.003 | 0.025 | |
| kegg_query | 0.009 | 0.000 | 0.010 | |
| kegg_request | 0.074 | 0.009 | 0.083 | |
| kegg_rm_prefix | 0.823 | 0.103 | 5.991 | |
| kinasephos | 1.132 | 0.204 | 30.298 | |
| latin_name | 0.233 | 0.009 | 0.242 | |
| load_db | 0.099 | 0.022 | 0.122 | |
| metalinksdb_sqlite | 1.037 | 0.357 | 10.703 | |
| metalinksdb_table | 0.272 | 0.050 | 0.328 | |
| metalinksdb_tables | 0.021 | 0.005 | 0.026 | |
| ncbi_taxid | 0.244 | 0.010 | 0.256 | |
| nichenet_build_model | 0.001 | 0.000 | 0.000 | |
| nichenet_expression_data | 0.011 | 0.002 | 0.013 | |
| nichenet_gr_network | 0.029 | 0.006 | 0.036 | |
| nichenet_gr_network_evex | 0.010 | 0.002 | 0.011 | |
| nichenet_gr_network_harmonizome | 0.011 | 0.001 | 0.013 | |
| nichenet_gr_network_htridb | 0.010 | 0.002 | 0.012 | |
| nichenet_gr_network_omnipath | 16.910 | 1.706 | 20.965 | |
| nichenet_gr_network_pathwaycommons | 0.012 | 0.002 | 0.014 | |
| nichenet_gr_network_regnetwork | 0.013 | 0.002 | 0.015 | |
| nichenet_gr_network_remap | 0.013 | 0.002 | 0.015 | |
| nichenet_gr_network_trrust | 0.011 | 0.001 | 0.012 | |
| nichenet_ligand_activities | 0.000 | 0.000 | 0.001 | |
| nichenet_ligand_target_links | 0.000 | 0.001 | 0.001 | |
| nichenet_ligand_target_matrix | 0 | 0 | 0 | |
| nichenet_lr_network | 0.034 | 0.005 | 0.039 | |
| nichenet_lr_network_guide2pharma | 0.011 | 0.002 | 0.012 | |
| nichenet_lr_network_omnipath | 0.029 | 0.004 | 0.034 | |
| nichenet_lr_network_ramilowski | 0.011 | 0.002 | 0.013 | |
| nichenet_main | 0 | 0 | 0 | |
| nichenet_networks | 0.054 | 0.009 | 0.065 | |
| nichenet_optimization | 0.000 | 0.001 | 0.000 | |
| nichenet_remove_orphan_ligands | 0.029 | 0.005 | 0.035 | |
| nichenet_results_dir | 0.000 | 0.000 | 0.001 | |
| nichenet_signaling_network | 0.037 | 0.006 | 0.042 | |
| nichenet_signaling_network_cpdb | 0.012 | 0.002 | 0.014 | |
| nichenet_signaling_network_evex | 0.012 | 0.002 | 0.014 | |
| nichenet_signaling_network_harmonizome | 0.012 | 0.001 | 0.013 | |
| nichenet_signaling_network_inbiomap | 0.000 | 0.000 | 0.001 | |
| nichenet_signaling_network_omnipath | 12.559 | 1.222 | 16.300 | |
| nichenet_signaling_network_pathwaycommons | 0.010 | 0.002 | 0.011 | |
| nichenet_signaling_network_vinayagam | 0.011 | 0.002 | 0.013 | |
| nichenet_test | 0 | 0 | 0 | |
| nichenet_workarounds | 0.000 | 0.000 | 0.001 | |
| obo_parser | 0.152 | 0.019 | 0.201 | |
| oma_code | 0.126 | 0.005 | 0.130 | |
| oma_organisms | 0.073 | 0.015 | 0.089 | |
| oma_pairwise | 0.010 | 0.002 | 0.012 | |
| oma_pairwise_genesymbols | 0.011 | 0.001 | 0.013 | |
| oma_pairwise_translated | 0.011 | 0.001 | 0.013 | |
| omnipath-interactions | 33.539 | 3.376 | 60.956 | |
| omnipath_cache_autoclean | 0 | 0 | 0 | |
| omnipath_cache_clean | 0.009 | 0.003 | 0.012 | |
| omnipath_cache_clean_db | 0.102 | 0.022 | 0.123 | |
| omnipath_cache_download_ready | 0.557 | 0.126 | 0.753 | |
| omnipath_cache_filter_versions | 0.096 | 0.026 | 0.129 | |
| omnipath_cache_get | 0.082 | 0.020 | 0.104 | |
| omnipath_cache_key | 0.001 | 0.001 | 0.001 | |
| omnipath_cache_latest_or_new | 0.059 | 0.014 | 0.073 | |
| omnipath_cache_load | 0.564 | 0.048 | 2.908 | |
| omnipath_cache_move_in | 0.190 | 0.047 | 0.249 | |
| omnipath_cache_remove | 0.116 | 0.030 | 0.156 | |
| omnipath_cache_save | 0.155 | 0.031 | 0.344 | |
| omnipath_cache_search | 0.001 | 0.000 | 0.000 | |
| omnipath_cache_set_ext | 0.136 | 0.024 | 0.167 | |
| omnipath_cache_update_status | 0.127 | 0.028 | 0.188 | |
| omnipath_cache_wipe | 0.001 | 0.000 | 0.001 | |
| omnipath_config_path | 0.001 | 0.000 | 0.001 | |
| omnipath_for_cosmos | 10.659 | 0.867 | 31.705 | |
| omnipath_load_config | 0.001 | 0.000 | 0.001 | |
| omnipath_log | 0.000 | 0.001 | 0.000 | |
| omnipath_logfile | 0.001 | 0.000 | 0.002 | |
| omnipath_msg | 0.007 | 0.001 | 0.008 | |
| omnipath_query | 4.239 | 0.249 | 4.515 | |
| omnipath_reset_config | 0.000 | 0.001 | 0.000 | |
| omnipath_save_config | 0 | 0 | 0 | |
| omnipath_set_cachedir | 0.030 | 0.006 | 0.037 | |
| omnipath_set_console_loglevel | 0.004 | 0.001 | 0.005 | |
| omnipath_set_logfile_loglevel | 0.004 | 0.001 | 0.005 | |
| omnipath_set_loglevel | 0.002 | 0.001 | 0.002 | |
| omnipath_show_db | 0.076 | 0.018 | 0.094 | |
| omnipath_unlock_cache_db | 0.000 | 0.000 | 0.001 | |
| only_from | 0 | 0 | 0 | |
| ontology_ensure_id | 0.000 | 0.000 | 0.001 | |
| ontology_ensure_name | 0 | 0 | 0 | |
| ontology_name_id | 0.001 | 0.001 | 0.001 | |
| organism_for | 0.171 | 0.007 | 0.178 | |
| pathwaycommons_download | 0.001 | 0.001 | 0.001 | |
| pivot_annotations | 10.345 | 0.991 | 19.537 | |
| preppi_download | 0.000 | 0.000 | 0.001 | |
| preppi_filter | 0.001 | 0.001 | 0.001 | |
| print_bma_motif_es | 0.581 | 0.085 | 1.732 | |
| print_bma_motif_vs | 0.161 | 0.016 | 0.661 | |
| print_interactions | 7.023 | 0.537 | 11.739 | |
| print_path_es | 0.953 | 0.078 | 2.399 | |
| print_path_vs | 2.764 | 0.273 | 5.692 | |
| pubmed_open | 4.816 | 0.245 | 5.091 | |
| query_info | 0.442 | 0.031 | 0.682 | |
| ramilowski_download | 0.001 | 0.000 | 0.002 | |
| ramp_id_mapping_table | 0.001 | 0.000 | 0.001 | |
| ramp_id_type | 0.003 | 0.000 | 0.003 | |
| ramp_sqlite | 0.001 | 0.000 | 0.001 | |
| ramp_table | 0.000 | 0.000 | 0.001 | |
| ramp_tables | 0.001 | 0.001 | 0.000 | |