| Back to Build/check report for BioC 3.23: simplified long |
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This page was generated on 2025-11-13 11:32 -0500 (Thu, 13 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4013 |
| 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 1485/2325 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| OmnipathR 3.19.0 (landing page) Denes Turei
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | ERROR | OK | ||||||||
|
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: 3.19.0 |
| 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_3.19.0.tar.gz |
| StartedAt: 2025-11-12 19:43:50 -0500 (Wed, 12 Nov 2025) |
| EndedAt: 2025-11-12 20:03:12 -0500 (Wed, 12 Nov 2025) |
| EllapsedTime: 1162.1 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_3.19.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/OmnipathR.Rcheck’
* using R Under development (unstable) (2025-11-04 r88984)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 16.0.0 (clang-1600.0.26.6)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OmnipathR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OmnipathR’ version ‘3.19.0’
* 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
[2025-11-12 19:44:06] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-12 19:44:06] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-12 19:44:06] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-11-12 19:44:06] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-11-12 19:44:06] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-11-12
[2025-11-12 19:44:06] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2025-11-12 20:19:41 UTC; unix
[2025-11-12 19:44:06] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.0
[2025-11-12 19:44:06] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23
[2025-11-12 19:44:06] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-11-04 r88984); os=macOS Ventura 13.7.8; system=aarch64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-11-12; pandoc=3.1.12.3 @ /opt/homebrew/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2025-11-12 19:44:06] [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; curl=8.7.1; zlib=1.2.11; 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=70.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.6-arm64/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-arm64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-11-12 19:44:06] [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 0.6.38(2025-11-12); dplyr 1.1.4(2023-11-17); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.4(2025-10-17); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.2.1(2025-10-27); 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 3.19.0(2025-11-12); 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 1.2.0(2025-11-04); 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 2.4.4(2025-11-10); 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 3.3.0(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 0.54(2025-10-30); XML 3.99-0.20(2025-11-08); xml2 1.4.1(2025-10-27); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-11-12 19:44:06] [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: 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
[2025-11-12 19:44:06] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-11-12 19:44:06] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-11-12 19:44:06] [TRACE] [OmnipathR] Contains 1 files.
[2025-11-12 19:44:06] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-11-12 19:44:06] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-12 19:44:06] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-12 19:44:06] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-11-12 19:44:06] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`.
[2025-11-12 19:44:06] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-11-12 19:44:06] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-12 19:44:06] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-11-12 19:44:06] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-12 19:44:06] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-11-12 19:44:06] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-12 19:44:06] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-11-12 19:44:06] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-12 19:44:06] [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
[2025-11-12 19:44:19] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-12 19:44:19] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-12 19:44:19] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-11-12 19:44:19] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-11-12 19:44:19] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-11-12
[2025-11-12 19:44:19] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2025-11-12 20:19:41 UTC; unix
[2025-11-12 19:44:19] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.0
[2025-11-12 19:44:19] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23
[2025-11-12 19:44:19] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-11-04 r88984); os=macOS Ventura 13.7.8; system=aarch64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-11-12; pandoc=3.1.12.3 @ /opt/homebrew/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2025-11-12 19:44:19] [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; curl=8.7.1; zlib=1.2.11; 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=70.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.6-arm64/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-arm64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-11-12 19:44:19] [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 0.6.38(2025-11-12); dplyr 1.1.4(2023-11-17); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.4(2025-10-17); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.2.1(2025-10-27); 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 3.19.0(2025-11-12); 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 1.2.0(2025-11-04); 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 2.4.4(2025-11-10); 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 3.3.0(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 0.54(2025-10-30); XML 3.99-0.20(2025-11-08); xml2 1.4.1(2025-10-27); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-11-12 19:44:19] [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: 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
[2025-11-12 19:44:19] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-11-12 19:44:19] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-11-12 19:44:19] [TRACE] [OmnipathR] Contains 1 files.
[2025-11-12 19:44:19] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-11-12 19:44:19] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-12 19:44:19] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-12 19:44:19] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-11-12 19:44:19] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`.
[2025-11-12 19:44:19] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-11-12 19:44:19] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-12 19:44:19] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-11-12 19:44:19] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-12 19:44:19] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-11-12 19:44:19] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-12 19:44:19] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-11-12 19:44:19] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-12 19:44:19] [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_compartments: no visible global function definition for
‘.slow_dowtest’
recon3d_genes: no visible global function definition for
‘.slow_dowtest’
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 global function definition for
‘.slow_dowtest’
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 binding for global variable ‘hmdb’
recon3d_metabolites: no visible binding for global variable ‘metHMDBID’
recon3d_raw: no visible global function definition for ‘.slow_dowtest’
recon3d_raw_vmh: no visible global function definition for
‘.slow_dowtest’
recon3d_reactions: no visible global function definition for
‘.slow_dowtest’
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’
recon3d_table: no visible global function definition for
‘.slow_dowtest’
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:
.slow_dowtest annotation 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 ... 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: recon3d_metabolites
> ### Title: Metabolites from Recon-3D
> ### Aliases: recon3d_metabolites recon3d_reactions recon3d_genes
> ### recon3d_compartments
>
> ### ** Examples
>
> recon3d_metabolites()
Error in .slow_dowtest() : could not find function ".slow_dowtest"
Calls: recon3d_metabolites
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
annotation_categories 40.176 0.078 43.024
curated_ligrec_stats 15.704 2.184 93.809
omnipath-interactions 13.873 1.345 51.098
filter_extra_attrs 10.479 4.555 36.462
all_uniprots 8.881 1.616 287.493
extra_attrs_to_cols 7.437 1.519 14.800
nichenet_gr_network_omnipath 6.677 0.797 12.373
go_annot_download 6.591 0.516 7.423
extra_attr_values 5.129 1.201 16.649
extra_attrs 4.625 1.525 7.735
filter_by_resource 5.358 0.349 8.528
pivot_annotations 5.289 0.375 20.747
giant_component 4.874 0.501 11.449
nichenet_signaling_network_omnipath 4.682 0.499 11.020
omnipath_for_cosmos 4.277 0.347 26.870
has_extra_attrs 2.812 1.016 8.024
filter_intercell 3.214 0.230 8.826
print_interactions 3.124 0.263 9.359
curated_ligand_receptor_interactions 2.746 0.537 14.836
ensembl_id_mapping_table 1.533 0.147 20.300
ensembl_organisms 0.779 0.334 12.757
ensembl_organisms_raw 0.755 0.351 72.084
kegg_conv 0.652 0.082 10.790
metalinksdb_sqlite 0.557 0.132 10.424
kinasephos 0.458 0.069 19.846
kegg_link 0.337 0.049 6.229
kegg_rm_prefix 0.339 0.040 5.657
* 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 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-arm64/Resources/library’ * installing *source* package ‘OmnipathR’ ... ** this is package ‘OmnipathR’ version ‘3.19.0’ ** 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 [2025-11-12 15:19:46] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-11-12 15:19:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-11-12 15:19:46] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-11-12 15:19:46] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-11-12 15:19:46] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-11-12 [2025-11-12 15:19:46] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2025-11-12 20:19:41 UTC; unix [2025-11-12 15:19:46] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.0 [2025-11-12 15:19:46] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23 [2025-11-12 15:19:46] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-11-04 r88984); os=macOS Ventura 13.7.8; system=aarch64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-11-12; pandoc=3.1.12.3 @ /opt/homebrew/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto] [2025-11-12 15:19:47] [INFO] [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6; curl=8.7.1; zlib=1.2.11; 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=70.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.6-arm64/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-arm64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1] [2025-11-12 15:19:47] [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 0.6.38(2025-11-12); dplyr 1.1.4(2023-11-17); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.4(2025-10-17); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.2.1(2025-10-27); 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 3.19.0(2025-11-12); 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 1.2.0(2025-11-04); 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 2.4.4(2025-11-10); 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 3.3.0(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 0.54(2025-10-30); XML 3.99-0.20(2025-11-08); xml2 1.4.1(2025-10-27); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13) [2025-11-12 15:19:47] [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: 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 [2025-11-12 15:19:47] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-11-12 15:19:47] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-11-12 15:19:47] [TRACE] [OmnipathR] Contains 1 files. [2025-11-12 15:19:47] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-11-12 15:19:47] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-11-12 15:19:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-11-12 15:19:47] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-11-12 15:19:47] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`. [2025-11-12 15:19:47] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-11-12 15:19:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-11-12 15:19:47] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-11-12 15:19:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-11-12 15:19:47] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-11-12 15:19:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-11-12 15:19:47] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-11-12 15:19:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-11-12 15:19:47] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2025-11-12 15:19:47] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-11-12 15:19:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-11-12 15:19:48] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-11-12 15:19:48] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-11-12 15:19:48] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-11-12 [2025-11-12 15:19:48] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2025-11-12 20:19:41 UTC; unix [2025-11-12 15:19:48] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.0 [2025-11-12 15:19:48] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23 [2025-11-12 15:19:48] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-11-04 r88984); os=macOS Ventura 13.7.8; system=aarch64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-11-12; pandoc=3.1.12.3 @ /opt/homebrew/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto] [2025-11-12 15:19:48] [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; curl=8.7.1; zlib=1.2.11; 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=70.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.6-arm64/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-arm64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1] [2025-11-12 15:19:48] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); 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 0.6.38(2025-11-12); dplyr 1.1.4(2023-11-17); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.4(2025-10-17); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.2.1(2025-10-27); 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 3.19.0(2025-11-12); 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 1.2.0(2025-11-04); 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 2.4.4(2025-11-10); 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 3.3.0(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 0.54(2025-10-30); XML 3.99-0.20(2025-11-08); xml2 1.4.1(2025-10-27); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13) [2025-11-12 15:19:48] [INFO] [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: 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 [2025-11-12 15:19:48] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-11-12 15:19:48] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-11-12 15:19:48] [TRACE] [OmnipathR] Contains 1 files. [2025-11-12 15:19:48] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-11-12 15:19:48] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-11-12 15:19:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-11-12 15:19:48] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-11-12 15:19:48] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`. [2025-11-12 15:19:48] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-11-12 15:19:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-11-12 15:19:48] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-11-12 15:19:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-11-12 15:19:48] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-11-12 15:19:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-11-12 15:19:48] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-11-12 15:19:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-11-12 15:19:48] [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) (2025-11-04 r88984) -- "Unsuffered Consequences"
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Platform: aarch64-apple-darwin20
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You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
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> #!/usr/bin/env Rscript
>
> #
> # This file is part of the `OmnipathR` R package
> #
> # Copyright
> # 2018-2024
> # Saez Lab, Uniklinik RWTH Aachen, Heidelberg University
> #
> # File author(s): Alberto Valdeolivas
> # Dénes Türei (turei.denes@gmail.com)
> # Attila Gábor
> #
> # Distributed under the MIT (Expat) License.
> # See accompanying file `LICENSE` or find a copy at
> # https://directory.fsf.org/wiki/License:Expat
> #
> # Website: https://r.omnipathdb.org/
> # Git repo: https://github.com/saezlab/OmnipathR
> #
>
>
> library(testthat)
> library(OmnipathR)
[2025-11-12 20:00:13] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-12 20:00:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-12 20:00:13] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-11-12 20:00:13] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-11-12 20:00:13] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-11-12
[2025-11-12 20:00:13] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2025-11-12 20:19:41 UTC; unix
[2025-11-12 20:00:13] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.0
[2025-11-12 20:00:13] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23
[2025-11-12 20:00:13] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-11-04 r88984); os=macOS Ventura 13.7.8; system=aarch64, darwin20; ui=X11; language=C; collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-11-12; pandoc=3.1.12.3 @ /opt/homebrew/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2025-11-12 20:00:13] [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; curl=8.7.1; zlib=1.2.11; 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=70.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.6-arm64/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-arm64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-11-12 20:00:13] [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 0.6.38(2025-11-12); dplyr 1.1.4(2023-11-17); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.4(2025-10-17); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.2.1(2025-10-27); 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 3.19.0(2025-11-12); 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 1.2.0(2025-11-04); 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 2.4.4(2025-11-10); 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 3.2.3(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 0.54(2025-10-30); XML 3.99-0.20(2025-11-08); xml2 1.4.1(2025-10-27); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-11-12 20:00:13] [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: 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
[2025-11-12 20:00:13] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-11-12 20:00:13] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-11-12 20:00:13] [TRACE] [OmnipathR] Contains 11 files.
[2025-11-12 20:00:13] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-11-12 20:00:13] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-12 20:00:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-12 20:00:13] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-11-12 20:00:13] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`.
[2025-11-12 20:00:13] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-11-12 20:00:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-12 20:00:13] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-11-12 20:00:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-12 20:00:13] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-11-12 20:00:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-12 20:00:13] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-11-12 20:00:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-12 20:00:13] [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
17.902 2.891 171.237
OmnipathR.Rcheck/OmnipathR-Ex.timings
| name | user | system | elapsed | |
| OmnipathR | 0 | 0 | 0 | |
| all_uniprot_acs | 0.006 | 0.001 | 0.008 | |
| all_uniprots | 8.881 | 1.616 | 287.493 | |
| ancestors | 0.004 | 0.001 | 0.005 | |
| annotated_network | 0.593 | 0.064 | 3.876 | |
| annotation_categories | 40.176 | 0.078 | 43.024 | |
| annotation_resources | 0.047 | 0.007 | 0.575 | |
| annotations | 0.273 | 0.027 | 1.374 | |
| biomart_query | 0.604 | 0.083 | 3.639 | |
| bioplex1 | 0.004 | 0.001 | 0.012 | |
| bioplex2 | 0.004 | 0.001 | 0.021 | |
| bioplex3 | 0.008 | 0.002 | 0.026 | |
| bioplex_all | 0.004 | 0.001 | 0.023 | |
| bioplex_hct116_1 | 0.004 | 0.001 | 0.005 | |
| bma_motif_es | 0.282 | 0.040 | 1.370 | |
| bma_motif_vs | 0.078 | 0.013 | 0.764 | |
| chalmers_gem | 0.003 | 0.001 | 0.003 | |
| chalmers_gem_id_mapping_table | 0.004 | 0.001 | 0.017 | |
| chalmers_gem_id_type | 0.001 | 0.000 | 0.002 | |
| chalmers_gem_metabolites | 0.003 | 0.001 | 0.007 | |
| chalmers_gem_network | 0.004 | 0.001 | 0.026 | |
| chalmers_gem_raw | 0.004 | 0.001 | 0.028 | |
| chalmers_gem_reactions | 0.003 | 0.001 | 0.005 | |
| common_name | 0.050 | 0.004 | 0.126 | |
| complex_genes | 0.326 | 0.035 | 2.385 | |
| complex_resources | 0.023 | 0.005 | 0.647 | |
| complexes | 0.077 | 0.010 | 0.742 | |
| consensuspathdb_download | 0.000 | 0.000 | 0.001 | |
| consensuspathdb_raw_table | 0.006 | 0.001 | 0.008 | |
| cosmos_pkn | 0 | 0 | 0 | |
| curated_ligand_receptor_interactions | 2.746 | 0.537 | 14.836 | |
| curated_ligrec_stats | 15.704 | 2.184 | 93.809 | |
| database_summary | 0.817 | 0.107 | 3.254 | |
| descendants | 0.004 | 0.001 | 0.005 | |
| ensembl_dataset | 0.024 | 0.002 | 0.038 | |
| ensembl_id_mapping_table | 1.533 | 0.147 | 20.300 | |
| ensembl_id_type | 0.000 | 0.000 | 0.001 | |
| ensembl_name | 0.118 | 0.006 | 0.176 | |
| ensembl_organisms | 0.779 | 0.334 | 12.757 | |
| ensembl_organisms_raw | 0.755 | 0.351 | 72.084 | |
| ensembl_orthology | 0 | 0 | 0 | |
| enzsub_graph | 0.911 | 0.091 | 4.365 | |
| enzsub_resources | 0.021 | 0.004 | 0.529 | |
| enzyme_substrate | 0.427 | 0.029 | 1.281 | |
| evex_download | 0.002 | 0.000 | 0.002 | |
| evidences | 0 | 0 | 0 | |
| extra_attr_values | 5.129 | 1.201 | 16.649 | |
| extra_attrs | 4.625 | 1.525 | 7.735 | |
| extra_attrs_to_cols | 7.437 | 1.519 | 14.800 | |
| filter_by_resource | 5.358 | 0.349 | 8.528 | |
| filter_extra_attrs | 10.479 | 4.555 | 36.462 | |
| filter_intercell | 3.214 | 0.230 | 8.826 | |
| filter_intercell_network | 0.008 | 0.002 | 0.041 | |
| find_all_paths | 2.437 | 0.193 | 3.632 | |
| from_evidences | 0 | 0 | 0 | |
| get_db | 0 | 0 | 0 | |
| get_ontology_db | 0.005 | 0.001 | 0.051 | |
| giant_component | 4.874 | 0.501 | 11.449 | |
| go_annot_download | 6.591 | 0.516 | 7.423 | |
| go_annot_slim | 0 | 0 | 0 | |
| go_ontology_download | 0.004 | 0.001 | 0.026 | |
| guide2pharma_download | 0.004 | 0.001 | 0.013 | |
| harmonizome_download | 0.003 | 0.001 | 0.011 | |
| has_extra_attrs | 2.812 | 1.016 | 8.024 | |
| hmdb_id_mapping_table | 0.004 | 0.001 | 0.015 | |
| hmdb_id_type | 0.001 | 0.000 | 0.003 | |
| hmdb_metabolite_fields | 0.000 | 0.000 | 0.001 | |
| hmdb_protein_fields | 0 | 0 | 0 | |
| hmdb_table | 0.003 | 0.001 | 0.006 | |
| homologene_download | 0.003 | 0.001 | 0.003 | |
| homologene_raw | 0.023 | 0.001 | 0.036 | |
| homologene_uniprot_orthology | 0.003 | 0.001 | 0.029 | |
| hpo_download | 1.462 | 0.145 | 2.296 | |
| htridb_download | 0.006 | 0.001 | 0.009 | |
| id_translation_resources | 0 | 0 | 0 | |
| id_types | 0.030 | 0.004 | 0.034 | |
| inbiomap_download | 0 | 0 | 0 | |
| inbiomap_raw | 0 | 0 | 0 | |
| interaction_datasets | 0.357 | 0.034 | 0.820 | |
| interaction_graph | 0.173 | 0.021 | 0.960 | |
| interaction_resources | 0.023 | 0.005 | 0.507 | |
| interaction_types | 0.026 | 0.004 | 0.044 | |
| intercell | 0.383 | 0.056 | 1.882 | |
| intercell_categories | 0.296 | 0.038 | 0.724 | |
| intercell_consensus_filter | 0.665 | 0.075 | 3.064 | |
| intercell_generic_categories | 0.033 | 0.003 | 0.076 | |
| intercell_network | 0.004 | 0.001 | 0.004 | |
| intercell_resources | 0.023 | 0.004 | 0.594 | |
| intercell_summary | 0.031 | 0.009 | 0.085 | |
| is_ontology_id | 0 | 0 | 0 | |
| is_swissprot | 0.020 | 0.002 | 0.037 | |
| is_trembl | 0.020 | 0.002 | 0.038 | |
| is_uniprot | 0.003 | 0.001 | 0.005 | |
| kegg_api_templates | 0.000 | 0.001 | 0.001 | |
| kegg_conv | 0.652 | 0.082 | 10.790 | |
| kegg_databases | 0 | 0 | 0 | |
| kegg_ddi | 0.264 | 0.035 | 1.805 | |
| kegg_find | 0.275 | 0.033 | 2.146 | |
| kegg_info | 0.003 | 0.001 | 0.010 | |
| kegg_link | 0.337 | 0.049 | 6.229 | |
| kegg_list | 0.288 | 0.037 | 2.033 | |
| kegg_open | 0.003 | 0.001 | 0.004 | |
| kegg_operations | 0 | 0 | 0 | |
| kegg_organism_codes | 0.008 | 0.029 | 0.075 | |
| kegg_organisms | 0.008 | 0.004 | 0.019 | |
| kegg_pathway_annotations | 0.000 | 0.001 | 0.000 | |
| kegg_pathway_download | 0.005 | 0.001 | 0.024 | |
| kegg_pathway_list | 0.003 | 0.001 | 0.004 | |
| kegg_pathways_download | 0 | 0 | 0 | |
| kegg_picture | 0.548 | 0.025 | 4.564 | |
| kegg_process | 0.007 | 0.002 | 0.013 | |
| kegg_query | 0.003 | 0.000 | 0.006 | |
| kegg_request | 0.028 | 0.005 | 0.096 | |
| kegg_rm_prefix | 0.339 | 0.040 | 5.657 | |
| kinasephos | 0.458 | 0.069 | 19.846 | |
| latin_name | 0.096 | 0.006 | 0.138 | |
| load_db | 0.025 | 0.009 | 0.051 | |
| metalinksdb_sqlite | 0.557 | 0.132 | 10.424 | |
| metalinksdb_table | 0.094 | 0.018 | 0.172 | |
| metalinksdb_tables | 0.008 | 0.001 | 0.030 | |
| ncbi_taxid | 0.100 | 0.008 | 0.114 | |
| nichenet_build_model | 0 | 0 | 0 | |
| nichenet_expression_data | 0.003 | 0.001 | 0.004 | |
| nichenet_gr_network | 0.010 | 0.003 | 0.017 | |
| nichenet_gr_network_evex | 0.003 | 0.001 | 0.003 | |
| nichenet_gr_network_harmonizome | 0.003 | 0.001 | 0.013 | |
| nichenet_gr_network_htridb | 0.006 | 0.001 | 0.038 | |
| nichenet_gr_network_omnipath | 6.677 | 0.797 | 12.373 | |
| nichenet_gr_network_pathwaycommons | 0.003 | 0.001 | 0.005 | |
| nichenet_gr_network_regnetwork | 0.003 | 0.000 | 0.003 | |
| nichenet_gr_network_remap | 0.003 | 0.001 | 0.010 | |
| nichenet_gr_network_trrust | 0.003 | 0.001 | 0.005 | |
| nichenet_ligand_activities | 0 | 0 | 0 | |
| nichenet_ligand_target_links | 0 | 0 | 0 | |
| nichenet_ligand_target_matrix | 0 | 0 | 0 | |
| nichenet_lr_network | 0.008 | 0.002 | 0.018 | |
| nichenet_lr_network_guide2pharma | 0.004 | 0.001 | 0.025 | |
| nichenet_lr_network_omnipath | 0.036 | 0.002 | 0.050 | |
| nichenet_lr_network_ramilowski | 0.003 | 0.001 | 0.003 | |
| nichenet_main | 0.000 | 0.000 | 0.001 | |
| nichenet_networks | 0.015 | 0.005 | 0.067 | |
| nichenet_optimization | 0 | 0 | 0 | |
| nichenet_remove_orphan_ligands | 0.009 | 0.002 | 0.021 | |
| nichenet_results_dir | 0 | 0 | 0 | |
| nichenet_signaling_network | 0.009 | 0.002 | 0.014 | |
| nichenet_signaling_network_cpdb | 0.003 | 0.001 | 0.005 | |
| nichenet_signaling_network_evex | 0.003 | 0.001 | 0.004 | |
| nichenet_signaling_network_harmonizome | 0.003 | 0.001 | 0.006 | |
| nichenet_signaling_network_inbiomap | 0 | 0 | 0 | |
| nichenet_signaling_network_omnipath | 4.682 | 0.499 | 11.020 | |
| nichenet_signaling_network_pathwaycommons | 0.004 | 0.001 | 0.008 | |
| nichenet_signaling_network_vinayagam | 0.002 | 0.000 | 0.003 | |
| nichenet_test | 0 | 0 | 0 | |
| nichenet_workarounds | 0 | 0 | 0 | |
| obo_parser | 0.033 | 0.007 | 0.160 | |
| oma_code | 0.054 | 0.003 | 0.060 | |
| oma_organisms | 0.052 | 0.008 | 0.075 | |
| oma_pairwise | 0.003 | 0.001 | 0.005 | |
| oma_pairwise_genesymbols | 0.003 | 0.001 | 0.004 | |
| oma_pairwise_translated | 0.003 | 0.001 | 0.004 | |
| omnipath-interactions | 13.873 | 1.345 | 51.098 | |
| omnipath_cache_autoclean | 0 | 0 | 0 | |
| omnipath_cache_clean | 0.022 | 0.003 | 0.026 | |
| omnipath_cache_clean_db | 0.048 | 0.013 | 0.065 | |
| omnipath_cache_download_ready | 0.217 | 0.071 | 0.335 | |
| omnipath_cache_filter_versions | 0.041 | 0.013 | 0.071 | |
| omnipath_cache_get | 0.029 | 0.010 | 0.041 | |
| omnipath_cache_key | 0.001 | 0.000 | 0.000 | |
| omnipath_cache_latest_or_new | 0.027 | 0.008 | 0.038 | |
| omnipath_cache_load | 0.209 | 0.023 | 2.643 | |
| omnipath_cache_move_in | 0.070 | 0.017 | 0.146 | |
| omnipath_cache_remove | 0.026 | 0.010 | 0.056 | |
| omnipath_cache_save | 0.044 | 0.011 | 0.099 | |
| omnipath_cache_search | 0.000 | 0.001 | 0.001 | |
| omnipath_cache_set_ext | 0.026 | 0.010 | 0.078 | |
| omnipath_cache_update_status | 0.028 | 0.008 | 0.071 | |
| omnipath_cache_wipe | 0 | 0 | 0 | |
| omnipath_config_path | 0.000 | 0.000 | 0.001 | |
| omnipath_for_cosmos | 4.277 | 0.347 | 26.870 | |
| omnipath_load_config | 0 | 0 | 0 | |
| omnipath_log | 0.000 | 0.000 | 0.001 | |
| omnipath_logfile | 0.001 | 0.000 | 0.000 | |
| omnipath_msg | 0.001 | 0.000 | 0.002 | |
| omnipath_query | 1.790 | 0.112 | 2.359 | |
| omnipath_reset_config | 0 | 0 | 0 | |
| omnipath_save_config | 0 | 0 | 0 | |
| omnipath_set_cachedir | 0.010 | 0.003 | 0.044 | |
| omnipath_set_console_loglevel | 0.001 | 0.000 | 0.002 | |
| omnipath_set_logfile_loglevel | 0.001 | 0.000 | 0.001 | |
| omnipath_set_loglevel | 0.000 | 0.000 | 0.001 | |
| omnipath_show_db | 0.020 | 0.005 | 0.077 | |
| omnipath_unlock_cache_db | 0 | 0 | 0 | |
| only_from | 0 | 0 | 0 | |
| ontology_ensure_id | 0 | 0 | 0 | |
| ontology_ensure_name | 0 | 0 | 0 | |
| ontology_name_id | 0.001 | 0.000 | 0.001 | |
| organism_for | 0.065 | 0.004 | 0.099 | |
| pathwaycommons_download | 0.001 | 0.000 | 0.000 | |
| pivot_annotations | 5.289 | 0.375 | 20.747 | |
| preppi_download | 0 | 0 | 0 | |
| preppi_filter | 0 | 0 | 0 | |
| print_bma_motif_es | 0.283 | 0.037 | 1.070 | |
| print_bma_motif_vs | 0.058 | 0.011 | 0.737 | |
| print_interactions | 3.124 | 0.263 | 9.359 | |
| print_path_es | 0.373 | 0.041 | 2.182 | |
| print_path_vs | 1.095 | 0.158 | 4.749 | |
| pubmed_open | 2.546 | 0.144 | 2.780 | |
| query_info | 0.220 | 0.018 | 0.556 | |
| ramilowski_download | 0 | 0 | 0 | |
| ramp_id_mapping_table | 0 | 0 | 0 | |
| ramp_id_type | 0.001 | 0.001 | 0.001 | |
| ramp_sqlite | 0 | 0 | 0 | |
| ramp_table | 0.001 | 0.000 | 0.001 | |
| ramp_tables | 0 | 0 | 0 | |