| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-03-13 11:34 -0400 (Fri, 13 Mar 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2026-03-05 r89546) -- "Unsuffered Consequences" | 4819 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2026-03-01 r89506) -- "Unsuffered Consequences" | 4049 |
| 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 1508/2360 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| OmnipathR 3.19.7 (landing page) Denes Turei
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
| See other builds for OmnipathR in R Universe. | ||||||||||||||
|
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: 3.19.7 |
| 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_3.19.7.tar.gz |
| StartedAt: 2026-03-12 19:34:47 -0400 (Thu, 12 Mar 2026) |
| EndedAt: 2026-03-12 19:42:37 -0400 (Thu, 12 Mar 2026) |
| EllapsedTime: 470.7 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: OmnipathR.Rcheck |
| Warnings: NA |
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings OmnipathR_3.19.7.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/OmnipathR.Rcheck’
* using R Under development (unstable) (2026-03-01 r89506)
* using platform: aarch64-apple-darwin23
* R was compiled by
Apple clang version 17.0.0 (clang-1700.3.19.1)
GNU Fortran (GCC) 14.2.0
* running under: macOS Sonoma 14.8.3
* using session charset: UTF-8
* current time: 2026-03-12 23:34:47 UTC
* using option ‘--no-vignettes’
* checking for file ‘OmnipathR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OmnipathR’ version ‘3.19.7’
* 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
[2026-03-12 19:35:02] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-12 19:35:02] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-03-12 19:35:02] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2026-03-12 19:35:02] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2026-03-12 19:35:02] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-03-12
[2026-03-12 19:35:02] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-03-12 19:04:23 UTC; unix
[2026-03-12 19:35:02] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.7
[2026-03-12 19:35:02] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23
[2026-03-12 19:35:02] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2026-03-01 r89506); os=macOS Sonoma 14.8.3; system=aarch64, darwin23; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2026-03-12; pandoc=3.1.12.3 @ /opt/homebrew/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2026-03-12 19:35:02] [INFO] [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=2.13.2/2.14.2; pango=; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.7.0; tcl=8.6; curl=8.7.1; zlib=1.2.12; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; zstd=1.5.5; PCRE=10.44 2024-06-07; ICU=74.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libR.dylib; readline=5.2; BLAS=/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2026-03-12 19:35:03] [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 1.3.0(2026-01-14); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); 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 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.0(2026-02-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.7(2026-03-06); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.2.2(2026-02-12); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.8(2026-03-05); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.19.7(2026-03-12); 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 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.1(2026-01-09); 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 0.3.4(2026-01-17); Rcpp 1.1.1(2026-01-10); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); rlang 1.1.7(2026-01-09); rmarkdown 2.30(2025-09-28); RSQLite 2.4.6(2026-02-06); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.1(2026-01-23); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.56(2026-01-18); XML 3.99-0.22(2026-02-10); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-03-12 19:35:03] [INFO] [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.12; libssh_version: NA; libidn_version: NA; host: aarch64-apple-darwin23.6.0; 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
[2026-03-12 19:35:03] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2026-03-12 19:35:03] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2026-03-12 19:35:03] [TRACE] [OmnipathR] Contains 1 files.
[2026-03-12 19:35:03] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2026-03-12 19:35:03] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-12 19:35:03] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-03-12 19:35:03] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2026-03-12 19:35:03] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`.
[2026-03-12 19:35:03] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-03-12 19:35:03] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-03-12 19:35:03] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-03-12 19:35:03] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-03-12 19:35:03] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-03-12 19:35:03] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-03-12 19:35:03] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-03-12 19:35:03] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-03-12 19:35:03] [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 ... WARNING
'::' or ':::' import not declared from: ‘SBMLR’
'loadNamespace' or 'requireNamespace' call not declared from: ‘SBMLR’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
[2026-03-12 19:35:14] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-12 19:35:14] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-03-12 19:35:14] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2026-03-12 19:35:14] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2026-03-12 19:35:14] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-03-12
[2026-03-12 19:35:14] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-03-12 19:04:23 UTC; unix
[2026-03-12 19:35:14] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.7
[2026-03-12 19:35:14] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23
[2026-03-12 19:35:14] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2026-03-01 r89506); os=macOS Sonoma 14.8.3; system=aarch64, darwin23; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2026-03-12; pandoc=3.1.12.3 @ /opt/homebrew/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2026-03-12 19:35:14] [INFO] [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=2.13.2/2.14.2; pango=; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.7.0; tcl=8.6; curl=8.7.1; zlib=1.2.12; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; zstd=1.5.5; PCRE=10.44 2024-06-07; ICU=74.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libR.dylib; readline=5.2; BLAS=/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2026-03-12 19:35:14] [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 1.3.0(2026-01-14); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); 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 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.0(2026-02-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.7(2026-03-06); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.2.2(2026-02-12); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.8(2026-03-05); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.19.7(2026-03-12); 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 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.1(2026-01-09); 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 0.3.4(2026-01-17); Rcpp 1.1.1(2026-01-10); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); rlang 1.1.7(2026-01-09); rmarkdown 2.30(2025-09-28); RSQLite 2.4.6(2026-02-06); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.1(2026-01-23); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.56(2026-01-18); XML 3.99-0.22(2026-02-10); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-03-12 19:35:14] [INFO] [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.12; libssh_version: NA; libidn_version: NA; host: aarch64-apple-darwin23.6.0; 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
[2026-03-12 19:35:14] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2026-03-12 19:35:14] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2026-03-12 19:35:14] [TRACE] [OmnipathR] Contains 1 files.
[2026-03-12 19:35:14] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2026-03-12 19:35:14] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-12 19:35:14] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-03-12 19:35:14] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2026-03-12 19:35:14] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`.
[2026-03-12 19:35:14] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-03-12 19:35:14] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-03-12 19:35:14] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-03-12 19:35:14] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-03-12 19:35:14] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-03-12 19:35:14] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-03-12 19:35:14] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-03-12 19:35:14] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-03-12 19:35:14] [TRACE] [OmnipathR] Cache locked: FALSE
cosmos_ksn: no visible binding for global variable ‘enzyme_genesymbol’
get_pathway_participants: no visible binding for global variable
‘pathway_id’
get_pathway_participants: no visible binding for global variable
‘chebi_id’
get_pathway_participants: no visible binding for global variable
‘pathway_name’
get_pathway_participants: no visible binding for global variable
‘pathway_url’
get_reactome_pathway_relations: no visible binding for global variable
‘Parent’
get_reactome_pathway_relations: no visible binding for global variable
‘Child’
get_reactome_pathways: no visible binding for global variable
‘pathway_id’
get_reactome_pathways: no visible binding for global variable
‘pathway_name’
get_wikipathways: no visible binding for global variable ‘metabolites’
get_wikipathways_metabolites_sparql: no visible binding for global
variable ‘met_xref_raw’
get_wikipathways_metabolites_sparql: no visible binding for global
variable ‘pathway_url’
get_wikipathways_pathways: no visible binding for global variable
‘organism_species’
get_wikipathways_pathways: no visible binding for global variable
‘pathway_id’
get_wikipathways_pathways: no visible binding for global variable
‘pathway_name’
get_wikipathways_pathways: no visible binding for global variable
‘pathway_url’
metabolic_atlas_list_gems: no visible binding for global variable
‘git_repo’
metabolic_atlas_list_gems: no visible binding for global variable
‘git_host’
metabolic_atlas_list_gems: no visible binding for global variable
‘gem_info’
metabolic_atlas_list_gems: no visible binding for global variable
‘latest_version’
metabolic_atlas_model: no visible binding for global variable ‘path’
metabolic_atlas_model : silent_sbml: no visible binding for global
variable ‘result’
metabolic_atlas_models: no visible binding for global variable ‘id’
patch_httr2_keep_handle: no visible binding for global variable
‘handle’
patch_httr2_keep_handle: no visible global function definition for
‘ORIGINAL’
Undefined global functions or variables:
Child ORIGINAL Parent chebi_id enzyme_genesymbol gem_info git_host
git_repo handle id latest_version met_xref_raw metabolites
organism_species path pathway_id pathway_name pathway_url result
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* 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: get_pathway_participants
> ### Title: Reactome pathway participants (ChEBI mapping)
> ### Aliases: get_pathway_participants
>
> ### ** Examples
>
> .slow_doctest()
Error in .slow_doctest() : could not find function ".slow_doctest"
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
annotation_categories 39.794 0.148 42.364
curated_ligrec_stats 18.431 3.536 103.484
filter_extra_attrs 9.964 6.875 29.390
all_uniprots 9.173 2.041 29.085
extra_attrs_to_cols 6.710 2.628 10.545
extra_attr_values 4.709 1.936 14.351
extra_attrs 2.867 1.518 7.476
curated_ligand_receptor_interactions 2.746 0.847 15.387
filter_by_resource 3.126 0.401 6.953
filter_intercell 3.187 0.258 8.119
ensembl_id_mapping_table 1.671 0.300 40.373
enzsub_graph 1.173 0.187 5.216
biomart_query 0.559 0.086 8.201
* 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, 1 WARNING, 2 NOTEs
See
‘/Users/biocbuild/bbs-3.23-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/4.6/Resources/library’ * installing *source* package ‘OmnipathR’ ... ** this is package ‘OmnipathR’ version ‘3.19.7’ ** 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 [2026-03-12 15:04:41] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-12 15:04:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-12 15:04:41] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2026-03-12 15:04:41] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2026-03-12 15:04:41] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-03-12 [2026-03-12 15:04:41] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-03-12 19:04:23 UTC; unix [2026-03-12 15:04:41] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.7 [2026-03-12 15:04:41] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23 [2026-03-12 15:04:41] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2026-03-01 r89506); os=macOS Sonoma 14.8.3; system=aarch64, darwin23; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2026-03-12; pandoc=3.1.12.3 @ /opt/homebrew/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto] [2026-03-12 15:04:42] [INFO] [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=2.13.2/2.14.2; pango=; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.7.0; tcl=8.6; curl=8.7.1; zlib=1.2.12; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; zstd=1.5.5; PCRE=10.44 2024-06-07; ICU=74.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libR.dylib; readline=5.2; BLAS=/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libRlapack.dylib; lapack_version=3.12.1] [2026-03-12 15:04:42] [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 1.3.0(2026-01-14); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); 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 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.0(2026-02-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.7(2026-03-06); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.2.2(2026-02-12); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.8(2026-03-05); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.19.7(2026-03-12); 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 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.1(2026-01-09); 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 0.3.4(2026-01-17); Rcpp 1.1.1(2026-01-10); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); rlang 1.1.7(2026-01-09); rmarkdown 2.30(2025-09-28); RSQLite 2.4.6(2026-02-06); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.1(2026-01-23); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.56(2026-01-18); XML 3.99-0.22(2026-02-10); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13) [2026-03-12 15:04:42] [INFO] [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.12; libssh_version: NA; libidn_version: NA; host: aarch64-apple-darwin23.6.0; 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 [2026-03-12 15:04:42] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-03-12 15:04:42] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2026-03-12 15:04:42] [TRACE] [OmnipathR] Contains 1 files. [2026-03-12 15:04:42] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-03-12 15:04:42] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-12 15:04:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-12 15:04:42] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2026-03-12 15:04:42] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`. [2026-03-12 15:04:42] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-03-12 15:04:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-12 15:04:42] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-03-12 15:04:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-12 15:04:42] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-03-12 15:04:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-12 15:04:42] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-03-12 15:04:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-12 15:04:42] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2026-03-12 15:04:43] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-12 15:04:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-12 15:04:43] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2026-03-12 15:04:43] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2026-03-12 15:04:43] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-03-12 [2026-03-12 15:04:43] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-03-12 19:04:23 UTC; unix [2026-03-12 15:04:43] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.7 [2026-03-12 15:04:43] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23 [2026-03-12 15:04:43] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2026-03-01 r89506); os=macOS Sonoma 14.8.3; system=aarch64, darwin23; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2026-03-12; pandoc=3.1.12.3 @ /opt/homebrew/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto] [2026-03-12 15:04:43] [INFO] [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=2.13.2/2.14.2; pango=; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.7.0; tcl=8.6; curl=8.7.1; zlib=1.2.12; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; zstd=1.5.5; PCRE=10.44 2024-06-07; ICU=74.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libR.dylib; readline=5.2; BLAS=/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libRlapack.dylib; lapack_version=3.12.1] [2026-03-12 15:04:43] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.3.0(2026-01-14); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); 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 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.0(2026-02-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.7(2026-03-06); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.2.2(2026-02-12); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.8(2026-03-05); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.19.7(2026-03-12); 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 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.1(2026-01-09); 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 0.3.4(2026-01-17); Rcpp 1.1.1(2026-01-10); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); rlang 1.1.7(2026-01-09); rmarkdown 2.30(2025-09-28); RSQLite 2.4.6(2026-02-06); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.1(2026-01-23); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.56(2026-01-18); XML 3.99-0.22(2026-02-10); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13) [2026-03-12 15:04:43] [INFO] [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.12; libssh_version: NA; libidn_version: NA; host: aarch64-apple-darwin23.6.0; 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 [2026-03-12 15:04:43] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-03-12 15:04:43] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2026-03-12 15:04:43] [TRACE] [OmnipathR] Contains 1 files. [2026-03-12 15:04:43] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-03-12 15:04:43] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-12 15:04:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-12 15:04:43] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2026-03-12 15:04:43] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`. [2026-03-12 15:04:43] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-03-12 15:04:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-12 15:04:43] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-03-12 15:04:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-12 15:04:43] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-03-12 15:04:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-12 15:04:43] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-03-12 15:04:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-12 15:04:43] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package keeps a record of temporary installation path * DONE (OmnipathR)
OmnipathR.Rcheck/tests/testthat.Rout
R Under development (unstable) (2026-03-01 r89506) -- "Unsuffered Consequences"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin23
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
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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)
[2026-03-12 19:41:30] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-12 19:41:30] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-03-12 19:41:30] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2026-03-12 19:41:30] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2026-03-12 19:41:30] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-03-12
[2026-03-12 19:41:30] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-03-12 19:04:23 UTC; unix
[2026-03-12 19:41:30] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.7
[2026-03-12 19:41:30] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23
[2026-03-12 19:41:30] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2026-03-01 r89506); os=macOS Sonoma 14.8.3; system=aarch64, darwin23; ui=X11; language=C; collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2026-03-12; pandoc=3.1.12.3 @ /opt/homebrew/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2026-03-12 19:41:30] [INFO] [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=2.13.2/2.14.2; pango=; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.7.0; tcl=8.6; curl=8.7.1; zlib=1.2.12; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; zstd=1.5.5; PCRE=10.44 2024-06-07; ICU=74.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libR.dylib; readline=5.2; BLAS=/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2026-03-12 19:41:30] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.3.0(2026-01-14); brio 1.1.5(2024-04-24); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); 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 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.0(2026-02-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.7(2026-03-06); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.2.2(2026-02-12); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.8(2026-03-05); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.19.7(2026-03-12); 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 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.1(2026-01-09); 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 0.3.4(2026-01-17); Rcpp 1.1.1(2026-01-10); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); rlang 1.1.7(2026-01-09); rmarkdown 2.30(2025-09-28); RSQLite 2.4.6(2026-02-06); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); testthat 3.3.2(2026-01-11); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.1(2026-01-23); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.56(2026-01-18); XML 3.99-0.22(2026-02-10); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-03-12 19:41:30] [INFO] [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.12; libssh_version: NA; libidn_version: NA; host: aarch64-apple-darwin23.6.0; 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
[2026-03-12 19:41:30] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2026-03-12 19:41:30] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2026-03-12 19:41:30] [TRACE] [OmnipathR] Contains 44 files.
[2026-03-12 19:41:30] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2026-03-12 19:41:30] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-12 19:41:30] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-03-12 19:41:30] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2026-03-12 19:41:30] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`.
[2026-03-12 19:41:30] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-03-12 19:41:30] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-03-12 19:41:30] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-03-12 19:41:30] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-03-12 19:41:30] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-03-12 19:41:30] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-03-12 19:41:30] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-03-12 19:41:30] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-03-12 19:41:30] [TRACE] [OmnipathR] Cache locked: FALSE
>
> test_check('OmnipathR')
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 38 ]
>
> proc.time()
user system elapsed
17.395 3.072 61.041
OmnipathR.Rcheck/OmnipathR-Ex.timings
| name | user | system | elapsed | |
| OmnipathR | 0 | 0 | 0 | |
| all_uniprot_acs | 0.006 | 0.002 | 0.009 | |
| all_uniprots | 9.173 | 2.041 | 29.085 | |
| ancestors | 0.003 | 0.001 | 0.006 | |
| annotated_network | 0.568 | 0.104 | 4.049 | |
| annotation_categories | 39.794 | 0.148 | 42.364 | |
| annotation_resources | 0.024 | 0.010 | 0.760 | |
| annotations | 0.241 | 0.027 | 1.124 | |
| biomart_query | 0.559 | 0.086 | 8.201 | |
| bioplex1 | 0.002 | 0.001 | 0.003 | |
| bioplex2 | 0.002 | 0.001 | 0.004 | |
| bioplex3 | 0.003 | 0.001 | 0.004 | |
| bioplex_all | 0.002 | 0.001 | 0.004 | |
| bioplex_hct116_1 | 0.003 | 0.000 | 0.003 | |
| bma_motif_es | 0.276 | 0.054 | 1.271 | |
| bma_motif_vs | 0.084 | 0.018 | 0.756 | |
| chalmers_gem | 0.004 | 0.001 | 0.007 | |
| chalmers_gem_id_mapping_table | 0.004 | 0.001 | 0.007 | |
| chalmers_gem_id_type | 0.001 | 0.001 | 0.000 | |
| chalmers_gem_metabolites | 0.003 | 0.001 | 0.006 | |
| chalmers_gem_network | 0.003 | 0.001 | 0.005 | |
| chalmers_gem_raw | 0.004 | 0.001 | 0.008 | |
| chalmers_gem_reactions | 0.004 | 0.001 | 0.014 | |
| common_name | 0.045 | 0.004 | 0.064 | |
| complex_genes | 0.327 | 0.046 | 2.067 | |
| complex_resources | 0.023 | 0.005 | 0.737 | |
| complexes | 0.079 | 0.013 | 0.783 | |
| consensuspathdb_download | 0 | 0 | 0 | |
| consensuspathdb_raw_table | 0.003 | 0.001 | 0.004 | |
| cosmos_pkn | 0 | 0 | 0 | |
| curated_ligand_receptor_interactions | 2.746 | 0.847 | 15.387 | |
| curated_ligrec_stats | 18.431 | 3.536 | 103.484 | |
| database_summary | 0.660 | 0.144 | 3.043 | |
| descendants | 0.004 | 0.001 | 0.037 | |
| ensembl_dataset | 0.019 | 0.002 | 0.027 | |
| ensembl_id_mapping_table | 1.671 | 0.300 | 40.373 | |
| ensembl_id_type | 0.001 | 0.001 | 0.002 | |
| ensembl_name | 0.293 | 0.015 | 0.573 | |
| ensembl_organisms | 0.089 | 0.030 | 0.372 | |
| ensembl_organisms_raw | 0.046 | 0.023 | 0.315 | |
| ensembl_orthology | 0.000 | 0.001 | 0.000 | |
| enzsub_graph | 1.173 | 0.187 | 5.216 | |
| enzsub_resources | 0.023 | 0.006 | 0.684 | |
| enzyme_substrate | 0.516 | 0.070 | 1.342 | |
| evex_download | 0.004 | 0.002 | 0.006 | |
| evidences | 0 | 0 | 0 | |
| extra_attr_values | 4.709 | 1.936 | 14.351 | |
| extra_attrs | 2.867 | 1.518 | 7.476 | |
| extra_attrs_to_cols | 6.710 | 2.628 | 10.545 | |
| filter_by_resource | 3.126 | 0.401 | 6.953 | |
| filter_extra_attrs | 9.964 | 6.875 | 29.390 | |
| filter_intercell | 3.187 | 0.258 | 8.119 | |
| filter_intercell_network | 0.006 | 0.002 | 0.011 | |
| find_all_paths | 2.938 | 0.345 | 3.692 | |
| from_evidences | 0 | 0 | 0 | |
| get_db | 0 | 0 | 0 | |
| get_ontology_db | 0.004 | 0.001 | 0.005 | |