| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-04 12:05 -0400 (Sat, 04 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" | 4853 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4640 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4585 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4576 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 1490/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| OmnipathR 3.17.6 (landing page) Denes Turei
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| lconway | macOS 12.7.1 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 | OK | ERROR | ||||||||||
|
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: 3.17.6 |
| 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: 2025-10-03 23:25:07 -0400 (Fri, 03 Oct 2025) |
| EndedAt: 2025-10-03 23:45:23 -0400 (Fri, 03 Oct 2025) |
| EllapsedTime: 1216.4 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_3.17.6.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 ‘3.17.6’
* 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
[2025-10-03 23:25:47] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-03 23:25:47] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-03 23:25:47] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-10-03 23:25:47] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-10-03 23:25:47] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-10-03
[2025-10-03 23:25:47] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-10-03 19:10:23 UTC; unix
[2025-10-03 23:25:47] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.6
[2025-10-03 23:25:47] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-10-03 23:25:48] [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=2025-10-03; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto]
[2025-10-03 23:25:48] [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]
[2025-10-03 23:25:49] [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 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.1.4(2025-01-23); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.17.6(2025-10-03); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.3.3(2025-05-29); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.3(2025-08-20); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.2(2025-09-08); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.53(2025-08-19); XML 3.99-0.19(2025-08-22); xml2 1.4.0(2025-08-20); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-10-03 23:25:49] [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
[2025-10-03 23:25:49] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-10-03 23:25:49] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-10-03 23:25:49] [TRACE] [OmnipathR] Contains 1 files.
[2025-10-03 23:25:49] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-10-03 23:25:49] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-03 23:25:49] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-03 23:25:49] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-10-03 23:25:49] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-10-03 23:25:49] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-10-03 23:25:49] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-03 23:25:49] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-10-03 23:25:49] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-03 23:25:49] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-10-03 23:25:49] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-03 23:25:49] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-10-03 23:25:49] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-03 23:25:49] [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
[2025-10-03 23:26:15] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-03 23:26:15] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-03 23:26:15] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-10-03 23:26:15] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-10-03 23:26:15] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-10-03
[2025-10-03 23:26:15] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-10-03 19:10:23 UTC; unix
[2025-10-03 23:26:15] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.6
[2025-10-03 23:26:15] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-10-03 23:26:16] [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=2025-10-03; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto]
[2025-10-03 23:26:16] [INFO] [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.44 2024-06-07; ICU=70.1; 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]
[2025-10-03 23:26:16] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.1.4(2025-01-23); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.17.6(2025-10-03); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.3.3(2025-05-29); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.3(2025-08-20); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.2(2025-09-08); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.53(2025-08-19); XML 3.99-0.19(2025-08-22); xml2 1.4.0(2025-08-20); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-10-03 23:26:16] [INFO] [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: 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
[2025-10-03 23:26:16] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-10-03 23:26:16] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-10-03 23:26:16] [TRACE] [OmnipathR] Contains 1 files.
[2025-10-03 23:26:16] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-10-03 23:26:16] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-03 23:26:16] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-03 23:26:16] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-10-03 23:26:16] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-10-03 23:26:16] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-10-03 23:26:16] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-03 23:26:16] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-10-03 23:26:16] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-03 23:26:16] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-10-03 23:26:16] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-03 23:26:16] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-10-03 23:26:16] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-03 23:26:16] [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 43.560 22.767 143.983
annotation_categories 64.631 0.366 66.773
filter_extra_attrs 36.161 17.474 66.681
omnipath-interactions 34.891 3.261 61.548
all_uniprots 28.469 3.250 53.122
extra_attrs_to_cols 17.728 3.075 33.443
nichenet_gr_network_omnipath 18.540 2.117 22.847
go_annot_download 14.008 3.409 29.150
extra_attr_values 13.519 3.685 26.841
has_extra_attrs 12.008 4.049 16.460
giant_component 11.792 3.716 35.013
extra_attrs 12.305 3.053 27.020
nichenet_signaling_network_omnipath 13.355 1.291 16.859
pivot_annotations 10.576 1.330 20.484
omnipath_for_cosmos 10.772 0.982 36.271
filter_by_resource 8.446 0.951 16.981
curated_ligand_receptor_interactions 7.927 1.305 17.931
find_all_paths 6.534 2.622 22.349
filter_intercell 7.957 0.999 34.506
print_interactions 7.379 0.574 11.895
pubmed_open 4.740 0.276 5.079
ensembl_id_mapping_table 2.548 0.549 27.397
print_path_vs 2.791 0.300 5.701
enzsub_graph 2.334 0.247 8.190
kegg_conv 1.598 0.237 12.668
metalinksdb_sqlite 1.129 0.338 10.844
kinasephos 1.136 0.175 18.996
kegg_picture 1.129 0.058 5.060
kegg_rm_prefix 0.910 0.121 5.542
kegg_link 0.799 0.112 5.973
* 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 ‘3.17.6’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location [2025-10-03 15:10:36] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-03 15:10:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-03 15:10:36] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-10-03 15:10:36] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-10-03 15:10:36] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-10-03 [2025-10-03 15:10:36] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-10-03 19:10:23 UTC; unix [2025-10-03 15:10:36] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.6 [2025-10-03 15:10:36] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22 [2025-10-03 15:10:38] [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=2025-10-03; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto] [2025-10-03 15:10:38] [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] [2025-10-03 15:10:39] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.1.4(2025-01-23); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.17.6(2025-10-03); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.3.3(2025-05-29); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.3(2025-08-20); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.2(2025-09-08); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.53(2025-08-19); XML 3.99-0.19(2025-08-22); xml2 1.4.0(2025-08-20); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13) [2025-10-03 15:10:39] [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 [2025-10-03 15:10:39] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-10-03 15:10:39] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-10-03 15:10:39] [TRACE] [OmnipathR] Contains 1 files. [2025-10-03 15:10:39] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-10-03 15:10:39] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-03 15:10:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-03 15:10:39] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-10-03 15:10:39] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-10-03 15:10:39] [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). [2025-10-03 15:10:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-03 15:10:39] [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). [2025-10-03 15:10:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-03 15:10:39] [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). [2025-10-03 15:10:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-03 15:10:39] [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). [2025-10-03 15:10:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-03 15:10:39] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2025-10-03 15:10:41] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-03 15:10:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-03 15:10:41] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-10-03 15:10:41] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-10-03 15:10:41] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-10-03 [2025-10-03 15:10:41] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-10-03 19:10:23 UTC; unix [2025-10-03 15:10:41] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.6 [2025-10-03 15:10:41] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22 [2025-10-03 15:10:41] [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=2025-10-03; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto] [2025-10-03 15:10:42] [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] [2025-10-03 15:10:42] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.1.4(2025-01-23); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.17.6(2025-10-03); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.3.3(2025-05-29); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.3(2025-08-20); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.2(2025-09-08); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.53(2025-08-19); XML 3.99-0.19(2025-08-22); xml2 1.4.0(2025-08-20); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13) [2025-10-03 15:10:42] [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 [2025-10-03 15:10:42] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-10-03 15:10:42] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-10-03 15:10:42] [TRACE] [OmnipathR] Contains 1 files. [2025-10-03 15:10:42] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-10-03 15:10:42] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-03 15:10:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-03 15:10:42] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-10-03 15:10:42] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-10-03 15:10:42] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-10-03 15:10:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-03 15:10:42] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-10-03 15:10:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-03 15:10:42] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-10-03 15:10:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-03 15:10:42] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-10-03 15:10:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-03 15:10:42] [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)
[2025-10-03 23:43:32] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-03 23:43:32] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-03 23:43:32] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-10-03 23:43:32] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-10-03 23:43:32] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-10-03
[2025-10-03 23:43:32] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-10-03 19:10:23 UTC; unix
[2025-10-03 23:43:32] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.6
[2025-10-03 23:43:32] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-10-03 23:43:33] [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=2025-10-03; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto]
[2025-10-03 23:43:33] [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]
[2025-10-03 23:43:33] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); brio 1.1.5(2024-04-24); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.1.4(2025-01-23); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.17.6(2025-10-03); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.3.3(2025-05-29); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.3(2025-08-20); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.2(2025-09-08); 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)
[2025-10-03 23:43:33] [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
[2025-10-03 23:43:33] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-10-03 23:43:33] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-10-03 23:43:33] [TRACE] [OmnipathR] Contains 12 files.
[2025-10-03 23:43:33] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-10-03 23:43:33] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-03 23:43:33] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-03 23:43:33] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-10-03 23:43:33] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-10-03 23:43:33] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-10-03 23:43:33] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-03 23:43:33] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-10-03 23:43:33] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-03 23:43:34] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-10-03 23:43:34] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-03 23:43:34] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-10-03 23:43:34] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-03 23:43:34] [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
51.039 6.393 92.936
OmnipathR.Rcheck/OmnipathR-Ex.timings
| name | user | system | elapsed | |
| OmnipathR | 0.001 | 0.000 | 0.000 | |
| all_uniprot_acs | 0.022 | 0.003 | 0.026 | |
| all_uniprots | 28.469 | 3.250 | 53.122 | |
| ancestors | 0.011 | 0.002 | 0.016 | |
| annotated_network | 1.552 | 0.165 | 4.824 | |
| annotation_categories | 64.631 | 0.366 | 66.773 | |
| annotation_resources | 0.070 | 0.011 | 0.626 | |
| annotations | 0.693 | 0.060 | 1.525 | |
| biomart_query | 1.465 | 0.232 | 4.260 | |
| bioplex1 | 0.011 | 0.001 | 0.012 | |
| bioplex2 | 0.009 | 0.001 | 0.011 | |
| bioplex3 | 0.011 | 0.002 | 0.012 | |
| bioplex_all | 0.010 | 0.002 | 0.011 | |
| bioplex_hct116_1 | 0.010 | 0.002 | 0.012 | |
| bma_motif_es | 0.685 | 0.086 | 1.529 | |
| bma_motif_vs | 0.226 | 0.027 | 0.768 | |
| chalmers_gem | 0.011 | 0.002 | 0.013 | |
| chalmers_gem_id_mapping_table | 0.009 | 0.002 | 0.011 | |
| chalmers_gem_id_type | 0.002 | 0.000 | 0.003 | |
| chalmers_gem_metabolites | 0.010 | 0.001 | 0.012 | |
| chalmers_gem_network | 0.010 | 0.001 | 0.011 | |
| chalmers_gem_raw | 0.012 | 0.002 | 0.013 | |
| chalmers_gem_reactions | 0.011 | 0.002 | 0.014 | |
| common_name | 0.127 | 0.009 | 0.137 | |
| complex_genes | 0.801 | 0.073 | 2.410 | |
| complex_resources | 0.069 | 0.008 | 0.558 | |
| complexes | 0.186 | 0.019 | 0.719 | |
| consensuspathdb_download | 0.000 | 0.001 | 0.000 | |
| consensuspathdb_raw_table | 0.010 | 0.002 | 0.012 | |
| cosmos_pkn | 0.000 | 0.000 | 0.001 | |
| curated_ligand_receptor_interactions | 7.927 | 1.305 | 17.931 | |
| curated_ligrec_stats | 43.560 | 22.767 | 143.983 | |
| database_summary | 1.783 | 0.214 | 3.462 | |
| descendants | 0.011 | 0.002 | 0.012 | |
| ensembl_dataset | 0.051 | 0.003 | 0.055 | |
| ensembl_id_mapping_table | 2.548 | 0.549 | 27.397 | |
| ensembl_id_type | 0.003 | 0.001 | 0.004 | |
| ensembl_name | 0.450 | 0.027 | 0.869 | |
| ensembl_organisms | 0.215 | 0.034 | 0.392 | |
| ensembl_organisms_raw | 0.139 | 0.030 | 0.635 | |
| ensembl_orthology | 0.000 | 0.001 | 0.001 | |
| enzsub_graph | 2.334 | 0.247 | 8.190 | |
| enzsub_resources | 0.081 | 0.017 | 0.743 | |
| enzyme_substrate | 1.558 | 0.110 | 3.446 | |
| evex_download | 0.011 | 0.002 | 0.014 | |
| evidences | 0 | 0 | 0 | |
| extra_attr_values | 13.519 | 3.685 | 26.841 | |
| extra_attrs | 12.305 | 3.053 | 27.020 | |
| extra_attrs_to_cols | 17.728 | 3.075 | 33.443 | |
| filter_by_resource | 8.446 | 0.951 | 16.981 | |
| filter_extra_attrs | 36.161 | 17.474 | 66.681 | |
| filter_intercell | 7.957 | 0.999 | 34.506 | |
| filter_intercell_network | 0.016 | 0.004 | 0.038 | |
| find_all_paths | 6.534 | 2.622 | 22.349 | |
| from_evidences | 0 | 0 | 0 | |
| get_db | 0.001 | 0.000 | 0.000 | |
| get_ontology_db | 0.009 | 0.003 | 0.025 | |
| giant_component | 11.792 | 3.716 | 35.013 | |
| go_annot_download | 14.008 | 3.409 | 29.150 | |
| go_annot_slim | 0.000 | 0.000 | 0.001 | |
| go_ontology_download | 0.013 | 0.002 | 0.015 | |
| guide2pharma_download | 0.011 | 0.002 | 0.014 | |
| harmonizome_download | 0.012 | 0.002 | 0.015 | |
| has_extra_attrs | 12.008 | 4.049 | 16.460 | |
| hmdb_id_mapping_table | 0.012 | 0.002 | 0.015 | |
| hmdb_id_type | 0.003 | 0.001 | 0.003 | |
| hmdb_metabolite_fields | 0.001 | 0.002 | 0.002 | |
| hmdb_protein_fields | 0.000 | 0.001 | 0.001 | |
| hmdb_table | 0.014 | 0.002 | 0.028 | |
| homologene_download | 0.013 | 0.002 | 0.017 | |
| homologene_raw | 0.068 | 0.006 | 0.075 | |
| homologene_uniprot_orthology | 0.012 | 0.002 | 0.015 | |
| hpo_download | 3.273 | 0.682 | 4.018 | |
| htridb_download | 0.011 | 0.002 | 0.012 | |
| id_translation_resources | 0.000 | 0.000 | 0.001 | |
| id_types | 0.054 | 0.012 | 0.069 | |
| inbiomap_download | 0 | 0 | 0 | |
| inbiomap_raw | 0 | 0 | 0 | |
| interaction_datasets | 0.802 | 0.088 | 1.259 | |
| interaction_graph | 0.517 | 0.043 | 1.202 | |
| interaction_resources | 0.068 | 0.010 | 0.661 | |
| interaction_types | 0.095 | 0.009 | 0.104 | |
| intercell | 0.945 | 0.142 | 1.871 | |
| intercell_categories | 0.762 | 0.101 | 1.065 | |
| intercell_consensus_filter | 1.662 | 0.193 | 3.251 | |
| intercell_generic_categories | 0.094 | 0.009 | 0.103 | |
| intercell_network | 0.014 | 0.002 | 0.017 | |
| intercell_resources | 0.072 | 0.011 | 0.562 | |
| intercell_summary | 0.094 | 0.024 | 0.120 | |
| is_ontology_id | 0.000 | 0.000 | 0.001 | |
| is_swissprot | 0.065 | 0.005 | 0.071 | |
| is_trembl | 0.067 | 0.008 | 0.076 | |
| is_uniprot | 0.012 | 0.002 | 0.014 | |
| kegg_api_templates | 0.001 | 0.003 | 0.004 | |
| kegg_conv | 1.598 | 0.237 | 12.668 | |
| kegg_databases | 0.000 | 0.000 | 0.001 | |
| kegg_ddi | 0.722 | 0.087 | 2.232 | |
| kegg_find | 0.707 | 0.089 | 2.853 | |
| kegg_info | 0.013 | 0.002 | 0.014 | |
| kegg_link | 0.799 | 0.112 | 5.973 | |
| kegg_list | 0.690 | 0.085 | 1.716 | |
| kegg_open | 0.012 | 0.002 | 0.014 | |
| kegg_operations | 0.000 | 0.001 | 0.000 | |
| kegg_organism_codes | 0.027 | 0.070 | 0.097 | |
| kegg_organisms | 0.028 | 0.007 | 0.034 | |
| kegg_pathway_annotations | 0 | 0 | 0 | |
| kegg_pathway_download | 0.011 | 0.002 | 0.013 | |
| kegg_pathway_list | 0.011 | 0.002 | 0.012 | |
| kegg_pathways_download | 0.000 | 0.000 | 0.001 | |
| kegg_picture | 1.129 | 0.058 | 5.060 | |
| kegg_process | 0.023 | 0.003 | 0.027 | |
| kegg_query | 0.009 | 0.001 | 0.010 | |
| kegg_request | 0.079 | 0.011 | 0.089 | |
| kegg_rm_prefix | 0.910 | 0.121 | 5.542 | |
| kinasephos | 1.136 | 0.175 | 18.996 | |
| latin_name | 0.249 | 0.010 | 0.259 | |
| load_db | 0.106 | 0.023 | 0.128 | |
| metalinksdb_sqlite | 1.129 | 0.338 | 10.844 | |
| metalinksdb_table | 0.301 | 0.058 | 0.361 | |
| metalinksdb_tables | 0.023 | 0.004 | 0.028 | |
| ncbi_taxid | 0.262 | 0.010 | 0.273 | |
| nichenet_build_model | 0 | 0 | 0 | |
| nichenet_expression_data | 0.014 | 0.002 | 0.016 | |
| nichenet_gr_network | 0.032 | 0.005 | 0.037 | |
| nichenet_gr_network_evex | 0.009 | 0.001 | 0.011 | |
| nichenet_gr_network_harmonizome | 0.012 | 0.002 | 0.014 | |
| nichenet_gr_network_htridb | 0.014 | 0.006 | 0.039 | |
| nichenet_gr_network_omnipath | 18.540 | 2.117 | 22.847 | |
| nichenet_gr_network_pathwaycommons | 0.011 | 0.002 | 0.013 | |
| nichenet_gr_network_regnetwork | 0.010 | 0.002 | 0.012 | |
| nichenet_gr_network_remap | 0.012 | 0.001 | 0.013 | |
| nichenet_gr_network_trrust | 0.011 | 0.002 | 0.013 | |
| nichenet_ligand_activities | 0.000 | 0.001 | 0.000 | |
| nichenet_ligand_target_links | 0.000 | 0.001 | 0.001 | |
| nichenet_ligand_target_matrix | 0 | 0 | 0 | |
| nichenet_lr_network | 0.032 | 0.005 | 0.038 | |
| nichenet_lr_network_guide2pharma | 0.012 | 0.001 | 0.013 | |
| nichenet_lr_network_omnipath | 0.033 | 0.005 | 0.038 | |
| nichenet_lr_network_ramilowski | 0.011 | 0.002 | 0.013 | |
| nichenet_main | 0.000 | 0.000 | 0.001 | |
| nichenet_networks | 0.054 | 0.010 | 0.064 | |
| nichenet_optimization | 0.000 | 0.001 | 0.000 | |
| nichenet_remove_orphan_ligands | 0.033 | 0.006 | 0.039 | |
| nichenet_results_dir | 0 | 0 | 0 | |
| nichenet_signaling_network | 0.032 | 0.006 | 0.039 | |
| nichenet_signaling_network_cpdb | 0.012 | 0.002 | 0.014 | |
| nichenet_signaling_network_evex | 0.013 | 0.002 | 0.015 | |
| nichenet_signaling_network_harmonizome | 0.011 | 0.002 | 0.013 | |
| nichenet_signaling_network_inbiomap | 0.000 | 0.001 | 0.001 | |
| nichenet_signaling_network_omnipath | 13.355 | 1.291 | 16.859 | |
| nichenet_signaling_network_pathwaycommons | 0.015 | 0.002 | 0.018 | |
| nichenet_signaling_network_vinayagam | 0.011 | 0.002 | 0.013 | |
| nichenet_test | 0.000 | 0.000 | 0.001 | |
| nichenet_workarounds | 0 | 0 | 0 | |
| obo_parser | 0.109 | 0.023 | 0.265 | |
| oma_code | 0.132 | 0.005 | 0.137 | |
| oma_organisms | 0.083 | 0.016 | 0.103 | |
| oma_pairwise | 0.012 | 0.002 | 0.014 | |
| oma_pairwise_genesymbols | 0.012 | 0.002 | 0.014 | |
| oma_pairwise_translated | 0.012 | 0.001 | 0.013 | |
| omnipath-interactions | 34.891 | 3.261 | 61.548 | |
| omnipath_cache_autoclean | 0.000 | 0.000 | 0.001 | |
| omnipath_cache_clean | 0.012 | 0.004 | 0.016 | |
| omnipath_cache_clean_db | 0.118 | 0.023 | 0.143 | |
| omnipath_cache_download_ready | 0.596 | 0.133 | 0.808 | |
| omnipath_cache_filter_versions | 0.104 | 0.029 | 0.142 | |
| omnipath_cache_get | 0.099 | 0.023 | 0.125 | |
| omnipath_cache_key | 0.001 | 0.001 | 0.002 | |
| omnipath_cache_latest_or_new | 0.069 | 0.015 | 0.085 | |
| omnipath_cache_load | 0.575 | 0.051 | 2.825 | |
| omnipath_cache_move_in | 0.170 | 0.043 | 0.225 | |
| omnipath_cache_remove | 0.105 | 0.025 | 0.137 | |
| omnipath_cache_save | 0.157 | 0.032 | 0.200 | |
| omnipath_cache_search | 0.001 | 0.001 | 0.001 | |
| omnipath_cache_set_ext | 0.125 | 0.024 | 0.158 | |
| omnipath_cache_update_status | 0.099 | 0.020 | 0.121 | |
| omnipath_cache_wipe | 0 | 0 | 0 | |
| omnipath_config_path | 0.000 | 0.001 | 0.001 | |
| omnipath_for_cosmos | 10.772 | 0.982 | 36.271 | |
| omnipath_load_config | 0.001 | 0.000 | 0.000 | |
| omnipath_log | 0.000 | 0.000 | 0.001 | |
| omnipath_logfile | 0.001 | 0.001 | 0.002 | |
| omnipath_msg | 0.005 | 0.001 | 0.006 | |
| omnipath_query | 4.340 | 0.258 | 4.626 | |
| omnipath_reset_config | 0 | 0 | 0 | |
| omnipath_save_config | 0.001 | 0.001 | 0.000 | |
| omnipath_set_cachedir | 0.032 | 0.006 | 0.038 | |
| omnipath_set_console_loglevel | 0.005 | 0.001 | 0.005 | |
| omnipath_set_logfile_loglevel | 0.004 | 0.000 | 0.005 | |
| omnipath_set_loglevel | 0.002 | 0.001 | 0.003 | |
| omnipath_show_db | 0.089 | 0.020 | 0.108 | |
| 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 | 0.000 | 0.000 | 0.001 | |
| ontology_name_id | 0.001 | 0.001 | 0.001 | |
| organism_for | 0.180 | 0.008 | 0.188 | |
| pathwaycommons_download | 0.001 | 0.001 | 0.001 | |
| pivot_annotations | 10.576 | 1.330 | 20.484 | |
| preppi_download | 0 | 0 | 0 | |
| preppi_filter | 0.001 | 0.001 | 0.002 | |
| print_bma_motif_es | 0.549 | 0.103 | 1.595 | |
| print_bma_motif_vs | 0.174 | 0.019 | 0.706 | |
| print_interactions | 7.379 | 0.574 | 11.895 | |
| print_path_es | 0.990 | 0.087 | 2.524 | |
| print_path_vs | 2.791 | 0.300 | 5.701 | |
| pubmed_open | 4.740 | 0.276 | 5.079 | |
| query_info | 0.420 | 0.032 | 0.658 | |
| ramilowski_download | 0.001 | 0.001 | 0.001 | |
| ramp_id_mapping_table | 0.001 | 0.000 | 0.001 | |
| ramp_id_type | 0.003 | 0.000 | 0.003 | |
| ramp_sqlite | 0.000 | 0.000 | 0.001 | |
| ramp_table | 0.000 | 0.001 | 0.001 | |
| ramp_tables | 0.000 | 0.000 | 0.001 | |