| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-21 12:05 -0400 (Tue, 21 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4887 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4677 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4622 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4642 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 1497/2353 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| OmnipathR 3.17.6 (landing page) Denes Turei
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | ERROR | ||||||||||
|
To the developers/maintainers of the OmnipathR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/OmnipathR.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: OmnipathR |
| Version: 3.17.6 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings OmnipathR_3.17.6.tar.gz |
| StartedAt: 2025-10-21 00:26:08 -0400 (Tue, 21 Oct 2025) |
| EndedAt: 2025-10-21 00:42:10 -0400 (Tue, 21 Oct 2025) |
| EllapsedTime: 962.1 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: OmnipathR.Rcheck |
| Warnings: NA |
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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings OmnipathR_3.17.6.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/OmnipathR.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OmnipathR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OmnipathR’ version ‘3.17.6’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 35 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable. Move as many as possible to Suggests and
use conditionally.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘OmnipathR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking whether startup messages can be suppressed ... NOTE
[2025-10-21 00:26:48] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-21 00:26:48] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-21 00:26:48] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-10-21 00:26:48] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-10-21 00:26:48] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-10-20
[2025-10-21 00:26:48] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-10-20 19:10:38 UTC; unix
[2025-10-21 00:26:48] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.6
[2025-10-21 00:26:48] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-10-21 00:26:49] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 Patched (2025-09-10 r88807); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-10-21; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto]
[2025-10-21 00:26:49] [INFO] [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.44 2024-06-07; ICU=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-10-21 00:26:49] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.4(2025-10-17); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.2.0(2025-10-13); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.17.6(2025-10-20); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.3.3(2025-05-29); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.3(2025-08-20); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.2(2025-09-08); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.53(2025-08-19); XML 3.99-0.19(2025-08-22); xml2 1.4.0(2025-08-20); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-10-21 00:26:49] [INFO] [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: x86_64-apple-darwin22.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2025-10-21 00:26:49] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-10-21 00:26:49] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-10-21 00:26:49] [TRACE] [OmnipathR] Contains 1 files.
[2025-10-21 00:26:49] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-10-21 00:26:49] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-21 00:26:50] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-21 00:26:50] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-10-21 00:26:50] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-10-21 00:26:50] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-10-21 00:26:50] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-21 00:26:50] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-10-21 00:26:50] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-21 00:26:50] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-10-21 00:26:50] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-21 00:26:50] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-10-21 00:26:50] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-21 00:26:50] [TRACE] [OmnipathR] Cache locked: FALSE
It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
[2025-10-21 00:27:16] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-21 00:27:16] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-21 00:27:16] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-10-21 00:27:16] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-10-21 00:27:16] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-10-20
[2025-10-21 00:27:16] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-10-20 19:10:38 UTC; unix
[2025-10-21 00:27:16] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.6
[2025-10-21 00:27:16] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-10-21 00:27:17] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 Patched (2025-09-10 r88807); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-10-21; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto]
[2025-10-21 00:27:17] [INFO] [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.44 2024-06-07; ICU=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-10-21 00:27:17] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.4(2025-10-17); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.2.0(2025-10-13); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.17.6(2025-10-20); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.3.3(2025-05-29); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.3(2025-08-20); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.2(2025-09-08); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.53(2025-08-19); XML 3.99-0.19(2025-08-22); xml2 1.4.0(2025-08-20); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-10-21 00:27:17] [INFO] [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: x86_64-apple-darwin22.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2025-10-21 00:27:17] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-10-21 00:27:17] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-10-21 00:27:17] [TRACE] [OmnipathR] Contains 1 files.
[2025-10-21 00:27:17] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-10-21 00:27:17] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-21 00:27:17] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-21 00:27:17] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-10-21 00:27:17] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-10-21 00:27:17] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-10-21 00:27:17] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-21 00:27:17] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-10-21 00:27:17] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-21 00:27:17] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-10-21 00:27:17] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-21 00:27:17] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-10-21 00:27:17] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-21 00:27:17] [TRACE] [OmnipathR] Cache locked: FALSE
.cosmos_pkn: no visible global function definition for
‘metabolite_idsc’
cosmos_ksn: no visible binding for global variable
‘substrate_genesymbol’
cosmos_ksn: no visible binding for global variable ‘residue_type’
cosmos_ksn: no visible binding for global variable ‘residue_offset’
cosmos_ksn: no visible binding for global variable ‘enzyme_genesymbol’
cosmos_ksn: no visible binding for global variable ‘mor’
recon3d_genes: no visible binding for global variable ‘notes’
recon3d_genes: no visible binding for global variable ‘annotation’
recon3d_genes: no visible binding for global variable
‘original_bigg_ids’
recon3d_metabolites: no visible binding for global variable ‘notes’
recon3d_metabolites: no visible binding for global variable
‘original_bigg_ids’
recon3d_metabolites: no visible binding for global variable
‘annotation’
recon3d_metabolites: no visible global function definition for
‘chalmers_gem_matlab_tibble’
recon3d_metabolites: no visible binding for global variable ‘hmdb’
recon3d_metabolites: no visible binding for global variable ‘metHMDBID’
recon3d_reactions: no visible binding for global variable ‘notes’
recon3d_reactions: no visible binding for global variable ‘metabolites’
recon3d_reactions: no visible binding for global variable
‘original_bigg_ids’
taxon_names_table: no visible binding for global variable
‘latin_name_uniprot’
taxon_names_table: no visible binding for global variable
‘latin_name_ensembl’
taxon_names_table: no visible binding for global variable
‘latin_name_oma’
taxon_names_table: no visible binding for global variable
‘common_name_ensembl’
taxon_names_table: no visible binding for global variable
‘common_name_uniprot’
Undefined global functions or variables:
annotation chalmers_gem_matlab_tibble common_name_ensembl
common_name_uniprot enzyme_genesymbol hmdb latin_name_ensembl
latin_name_oma latin_name_uniprot metHMDBID metabolite_idsc
metabolites mor notes original_bigg_ids residue_offset residue_type
substrate_genesymbol
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
‘recon3d_raw’ ‘recon3d_raw_vmh’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in Rd file 'recon3d.Rd'
‘extra_hmdb’
Undocumented arguments in Rd file 'translate_ids_multi.Rd'
‘ramp’ ‘expand’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘OmnipathR-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: kinasephos
> ### Title: Kinase-PTM relationships from KinasePhos 3.0
> ### Aliases: kinasephos
>
> ### ** Examples
>
> kinasephos()
[2025-10-21 00:39:59] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2025-10-21 00:39:59] [TRACE] [OmnipathR] Looking up in cache: `https://awi.cuhk.edu.cn/KinasePhos/dataset.csv`.
[2025-10-21 00:39:59] [INFO] [OmnipathR] Cache record does not exist: `https://awi.cuhk.edu.cn/KinasePhos/dataset.csv`
[2025-10-21 00:39:59] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://awi.cuhk.edu.cn/KinasePhos/dataset.csv`.
[2025-10-21 00:39:59] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-21 00:39:59] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-21 00:39:59] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-21 00:39:59] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-21 00:39:59] [INFO] [OmnipathR] Cache item `332c57703a2a947f42ea25504bcc6401dc01fb00` version 1: status changed from `unknown` to `started`.
[2025-10-21 00:39:59] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/332c57703a2a947f42ea25504bcc6401dc01fb00-1.rds`.
[2025-10-21 00:39:59] [INFO] [OmnipathR] Retrieving URL: `https://awi.cuhk.edu.cn/KinasePhos/dataset.csv`
[2025-10-21 00:39:59] [TRACE] [OmnipathR] Attempt 1/3: `https://awi.cuhk.edu.cn/KinasePhos/dataset.csv`
[2025-10-21 00:39:59] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-10-21 00:39:59] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-10-21 00:40:09] [TRACE] [OmnipathR] HTTP vNA GET: status 0.
[2025-10-21 00:40:09] [TRACE] [OmnipathR] Downloaded 0 bytes in 10.001867s from awi.cuhk.edu.cn (0 bytes/s); Redirect: 0s, DNS look up: 0.951957s, Connection: 0s, Pretransfer: 0s, First byte at: 0s
[2025-10-21 00:40:09] [TRACE] [OmnipathR] HTTP headers:
[2025-10-21 00:40:09] [WARN] [OmnipathR] HTTP request failed with error: Failed to open 'https://awi.cuhk.edu.cn/KinasePhos/dataset.csv': Connection timed out after 10001 milliseconds
[2025-10-21 00:40:09] [WARN] [OmnipathR] Failed to download `https://awi.cuhk.edu.cn/KinasePhos/dataset.csv` (attempt 1/3); error: Failed to open 'https://awi.cuhk.edu.cn/KinasePhos/dataset.csv': Connection timed out after 10001 milliseconds
[2025-10-21 00:40:14] [TRACE] [OmnipathR] Attempt 2/3: `https://awi.cuhk.edu.cn/KinasePhos/dataset.csv`
[2025-10-21 00:40:14] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-10-21 00:40:14] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-10-21 00:40:17] [TRACE] [OmnipathR] HTTP vNA GET: status 0.
[2025-10-21 00:40:17] [TRACE] [OmnipathR] Downloaded 0 bytes in 2.172643s from awi.cuhk.edu.cn (0 bytes/s); Redirect: 0s, DNS look up: 0.001469s, Connection: 0.002451s, Pretransfer: 1.931778s, First byte at: 0s
[2025-10-21 00:40:17] [TRACE] [OmnipathR] HTTP headers:
[2025-10-21 00:40:17] [WARN] [OmnipathR] HTTP request failed with error: Failed to open 'https://awi.cuhk.edu.cn/KinasePhos/dataset.csv': Empty reply from server
[2025-10-21 00:40:17] [WARN] [OmnipathR] Failed to download `https://awi.cuhk.edu.cn/KinasePhos/dataset.csv` (attempt 2/3); error: Failed to open 'https://awi.cuhk.edu.cn/KinasePhos/dataset.csv': Empty reply from server
[2025-10-21 00:40:22] [TRACE] [OmnipathR] Attempt 3/3: `https://awi.cuhk.edu.cn/KinasePhos/dataset.csv`
[2025-10-21 00:40:22] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-10-21 00:40:22] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-10-21 00:40:23] [TRACE] [OmnipathR] HTTP vNA GET: status 0.
[2025-10-21 00:40:23] [TRACE] [OmnipathR] Downloaded 0 bytes in 1.233509s from awi.cuhk.edu.cn (0 bytes/s); Redirect: 0s, DNS look up: 0.001113s, Connection: 0.002201s, Pretransfer: 0.982215s, First byte at: 0s
[2025-10-21 00:40:23] [TRACE] [OmnipathR] HTTP headers:
[2025-10-21 00:40:23] [WARN] [OmnipathR] HTTP request failed with error: Failed to open 'https://awi.cuhk.edu.cn/KinasePhos/dataset.csv': Empty reply from server
[2025-10-21 00:40:23] [ERROR] [OmnipathR] Failed to download `https://awi.cuhk.edu.cn/KinasePhos/dataset.csv` (attempt 3/3); error: Failed to open 'https://awi.cuhk.edu.cn/KinasePhos/dataset.csv': Empty reply from server
[2025-10-21 00:40:23] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-10-21 00:40:23] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-10-20
[2025-10-21 00:40:23] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-10-20 19:10:38 UTC; unix
[2025-10-21 00:40:23] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.6
[2025-10-21 00:40:23] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-10-21 00:40:24] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 Patched (2025-09-10 r88807); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=en; collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-10-21; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto]
[2025-10-21 00:40:24] [INFO] [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.44 2024-06-07; ICU=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-10-21 00:40:24] [INFO] [OmnipathR] Loaded packages: archive 1.1.12(2025-03-20); backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.4(2025-10-17); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.2.0(2025-10-13); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.17.6(2025-10-20); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.3.3(2025-05-29); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.3(2025-08-20); rvest 1.0.5(2025-08-29); selectr 0.4-2(2019-11-20); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.2(2025-09-08); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); utf8 1.2.6(2025-06-08); vctrs 0.6.5(2023-12-01); vroom 1.6.6(2025-09-19); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.53(2025-08-19); XML 3.99-0.19(2025-08-22); xml2 1.4.0(2025-08-20); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-10-21 00:40:24] [INFO] [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: x86_64-apple-darwin22.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
Error in (function (url, curlopt = list(), callback = NULL, compr = NULL, :
Failed to open 'https://awi.cuhk.edu.cn/KinasePhos/dataset.csv': Empty reply from server
Calls: kinasephos ... omnipath_cache_save -> saveRDS -> exec -> <Anonymous>
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
annotation_categories 60.532 0.557 62.782
curated_ligrec_stats 41.363 15.282 138.178
filter_extra_attrs 40.353 12.581 61.866
all_uniprots 27.945 3.169 49.370
extra_attrs_to_cols 19.371 4.054 24.235
extra_attr_values 18.367 3.382 33.666
curated_ligand_receptor_interactions 7.984 12.358 34.040
go_annot_download 13.679 2.063 22.600
giant_component 13.067 1.515 25.113
has_extra_attrs 11.142 3.322 14.596
extra_attrs 9.007 3.142 15.611
filter_by_resource 10.427 0.886 13.915
find_all_paths 8.704 0.651 14.342
filter_intercell 7.452 1.207 18.767
ensembl_id_mapping_table 2.447 1.397 71.048
enzsub_graph 2.805 0.566 7.211
biomart_query 1.356 1.579 7.933
kegg_conv 1.501 0.231 12.541
kegg_picture 1.147 0.057 7.662
kegg_rm_prefix 0.858 0.124 5.820
kegg_link 0.752 0.106 6.608
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 2 WARNINGs, 2 NOTEs
See
‘/Users/biocbuild/bbs-3.22-bioc/meat/OmnipathR.Rcheck/00check.log’
for details.
OmnipathR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL OmnipathR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’ * installing *source* package ‘OmnipathR’ ... ** this is package ‘OmnipathR’ version ‘3.17.6’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location [2025-10-20 15:10:51] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-20 15:10:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-20 15:10:52] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-10-20 15:10:52] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-10-20 15:10:52] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-10-20 [2025-10-20 15:10:52] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-10-20 19:10:38 UTC; unix [2025-10-20 15:10:52] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.6 [2025-10-20 15:10:52] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22 [2025-10-20 15:10:53] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 Patched (2025-09-10 r88807); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-10-20; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto] [2025-10-20 15:10:53] [INFO] [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.44 2024-06-07; ICU=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1] [2025-10-20 15:10:53] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.4(2025-10-17); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.2.0(2025-10-13); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.17.6(2025-10-20); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.3.3(2025-05-29); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.3(2025-08-20); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.2(2025-09-08); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.53(2025-08-19); XML 3.99-0.19(2025-08-22); xml2 1.4.0(2025-08-20); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13) [2025-10-20 15:10:53] [INFO] [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: x86_64-apple-darwin22.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE [2025-10-20 15:10:53] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-10-20 15:10:53] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-10-20 15:10:53] [TRACE] [OmnipathR] Contains 1 files. [2025-10-20 15:10:53] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-10-20 15:10:53] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-20 15:10:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-20 15:10:53] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-10-20 15:10:53] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-10-20 15:10:53] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-10-20 15:10:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-20 15:10:53] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-10-20 15:10:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-20 15:10:53] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-10-20 15:10:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-20 15:10:53] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-10-20 15:10:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-20 15:10:53] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2025-10-20 15:10:55] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-20 15:10:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-20 15:10:55] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-10-20 15:10:55] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-10-20 15:10:55] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-10-20 [2025-10-20 15:10:55] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-10-20 19:10:38 UTC; unix [2025-10-20 15:10:55] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.6 [2025-10-20 15:10:55] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22 [2025-10-20 15:10:56] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 Patched (2025-09-10 r88807); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-10-20; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto] [2025-10-20 15:10:56] [INFO] [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.44 2024-06-07; ICU=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1] [2025-10-20 15:10:56] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.4(2025-10-17); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.2.0(2025-10-13); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.17.6(2025-10-20); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.3.3(2025-05-29); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.3(2025-08-20); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.2(2025-09-08); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.53(2025-08-19); XML 3.99-0.19(2025-08-22); xml2 1.4.0(2025-08-20); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13) [2025-10-20 15:10:56] [INFO] [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: x86_64-apple-darwin22.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE [2025-10-20 15:10:56] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-10-20 15:10:56] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-10-20 15:10:56] [TRACE] [OmnipathR] Contains 1 files. [2025-10-20 15:10:56] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-10-20 15:10:56] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-20 15:10:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-20 15:10:56] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-10-20 15:10:56] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-10-20 15:10:56] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-10-20 15:10:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-20 15:10:56] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-10-20 15:10:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-20 15:10:56] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-10-20 15:10:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-20 15:10:56] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-10-20 15:10:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-20 15:10:56] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package keeps a record of temporary installation path * DONE (OmnipathR)
OmnipathR.Rcheck/tests/testthat.Rout
R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
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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)
[2025-10-21 00:40:29] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-21 00:40:29] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-21 00:40:29] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-10-21 00:40:29] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-10-21 00:40:29] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-10-20
[2025-10-21 00:40:29] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-10-20 19:10:38 UTC; unix
[2025-10-21 00:40:29] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.6
[2025-10-21 00:40:29] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-10-21 00:40:30] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 Patched (2025-09-10 r88807); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=C; collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-10-21; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto]
[2025-10-21 00:40:30] [INFO] [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.44 2024-06-07; ICU=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-10-21 00:40:30] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); brio 1.1.5(2024-04-24); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.4(2025-10-17); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.2.0(2025-10-13); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.17.6(2025-10-20); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.3.3(2025-05-29); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.3(2025-08-20); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.2(2025-09-08); testthat 3.2.3(2025-01-13); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.53(2025-08-19); XML 3.99-0.19(2025-08-22); xml2 1.4.0(2025-08-20); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-10-21 00:40:30] [INFO] [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: x86_64-apple-darwin22.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2025-10-21 00:40:30] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-10-21 00:40:30] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-10-21 00:40:30] [TRACE] [OmnipathR] Contains 57 files.
[2025-10-21 00:40:30] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-10-21 00:40:30] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-21 00:40:30] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-21 00:40:30] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-10-21 00:40:30] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-10-21 00:40:30] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-10-21 00:40:30] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-21 00:40:30] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-10-21 00:40:30] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-21 00:40:30] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-10-21 00:40:30] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-21 00:40:30] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-10-21 00:40:30] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-21 00:40:30] [TRACE] [OmnipathR] Cache locked: FALSE
>
> test_check('OmnipathR')
[ FAIL 0 | WARN 12 | SKIP 0 | PASS 38 ]
[ FAIL 0 | WARN 12 | SKIP 0 | PASS 38 ]
>
> proc.time()
user system elapsed
50.000 6.082 84.309
OmnipathR.Rcheck/OmnipathR-Ex.timings
| name | user | system | elapsed | |
| OmnipathR | 0.000 | 0.000 | 0.001 | |
| all_uniprot_acs | 0.024 | 0.003 | 0.027 | |
| all_uniprots | 27.945 | 3.169 | 49.370 | |
| ancestors | 0.012 | 0.002 | 0.013 | |
| annotated_network | 1.500 | 0.147 | 4.459 | |
| annotation_categories | 60.532 | 0.557 | 62.782 | |
| annotation_resources | 0.068 | 0.070 | 0.789 | |
| annotations | 0.598 | 0.457 | 2.524 | |
| biomart_query | 1.356 | 1.579 | 7.933 | |
| bioplex1 | 0.011 | 0.007 | 0.017 | |
| bioplex2 | 0.011 | 0.008 | 0.017 | |
| bioplex3 | 0.010 | 0.006 | 0.016 | |
| bioplex_all | 0.011 | 0.008 | 0.018 | |
| bioplex_hct116_1 | 0.011 | 0.009 | 0.035 | |
| bma_motif_es | 0.664 | 0.676 | 2.193 | |
| bma_motif_vs | 0.226 | 0.186 | 1.032 | |
| chalmers_gem | 0.011 | 0.007 | 0.016 | |
| chalmers_gem_id_mapping_table | 0.011 | 0.007 | 0.019 | |
| chalmers_gem_id_type | 0.002 | 0.002 | 0.003 | |
| chalmers_gem_metabolites | 0.011 | 0.007 | 0.015 | |
| chalmers_gem_network | 0.011 | 0.009 | 0.019 | |
| chalmers_gem_raw | 0.011 | 0.007 | 0.016 | |
| chalmers_gem_reactions | 0.011 | 0.009 | 0.036 | |
| common_name | 0.118 | 0.041 | 0.152 | |
| complex_genes | 0.753 | 0.659 | 3.892 | |
| complex_resources | 0.069 | 0.058 | 0.650 | |
| complexes | 0.192 | 0.138 | 0.994 | |
| consensuspathdb_download | 0.000 | 0.000 | 0.001 | |
| consensuspathdb_raw_table | 0.010 | 0.007 | 0.017 | |
| cosmos_pkn | 0.000 | 0.001 | 0.000 | |
| curated_ligand_receptor_interactions | 7.984 | 12.358 | 34.040 | |
| curated_ligrec_stats | 41.363 | 15.282 | 138.178 | |
| database_summary | 1.359 | 0.225 | 4.912 | |
| descendants | 0.009 | 0.002 | 0.034 | |
| ensembl_dataset | 0.037 | 0.003 | 0.136 | |
| ensembl_id_mapping_table | 2.447 | 1.397 | 71.048 | |
| ensembl_id_type | 0.002 | 0.000 | 0.013 | |
| ensembl_name | 0.251 | 0.056 | 1.350 | |
| ensembl_organisms | 0.136 | 0.051 | 0.384 | |
| ensembl_organisms_raw | 0.140 | 0.039 | 0.346 | |
| ensembl_orthology | 0.001 | 0.001 | 0.000 | |
| enzsub_graph | 2.805 | 0.566 | 7.211 | |
| enzsub_resources | 0.072 | 0.017 | 0.605 | |
| enzyme_substrate | 1.599 | 0.187 | 2.685 | |
| evex_download | 0.012 | 0.002 | 0.017 | |
| evidences | 0 | 0 | 0 | |
| extra_attr_values | 18.367 | 3.382 | 33.666 | |
| extra_attrs | 9.007 | 3.142 | 15.611 | |
| extra_attrs_to_cols | 19.371 | 4.054 | 24.235 | |
| filter_by_resource | 10.427 | 0.886 | 13.915 | |
| filter_extra_attrs | 40.353 | 12.581 | 61.866 | |
| filter_intercell | 7.452 | 1.207 | 18.767 | |
| filter_intercell_network | 0.024 | 0.004 | 0.028 | |
| find_all_paths | 8.704 | 0.651 | 14.342 | |
| from_evidences | 0.000 | 0.001 | 0.000 | |
| get_db | 0 | 0 | 0 | |
| get_ontology_db | 0.008 | 0.003 | 0.011 | |
| giant_component | 13.067 | 1.515 | 25.113 | |
| go_annot_download | 13.679 | 2.063 | 22.600 | |
| go_annot_slim | 0 | 0 | 0 | |
| go_ontology_download | 0.013 | 0.002 | 0.015 | |
| guide2pharma_download | 0.013 | 0.002 | 0.016 | |
| harmonizome_download | 0.011 | 0.003 | 0.013 | |
| has_extra_attrs | 11.142 | 3.322 | 14.596 | |
| hmdb_id_mapping_table | 0.011 | 0.002 | 0.013 | |
| hmdb_id_type | 0.003 | 0.001 | 0.003 | |
| hmdb_metabolite_fields | 0.001 | 0.001 | 0.001 | |
| hmdb_protein_fields | 0 | 0 | 0 | |
| hmdb_table | 0.011 | 0.002 | 0.013 | |
| homologene_download | 0.011 | 0.002 | 0.012 | |
| homologene_raw | 0.061 | 0.004 | 0.065 | |
| homologene_uniprot_orthology | 0.012 | 0.002 | 0.014 | |
| hpo_download | 3.219 | 0.556 | 3.735 | |
| htridb_download | 0.010 | 0.002 | 0.012 | |
| id_translation_resources | 0.000 | 0.000 | 0.001 | |
| id_types | 0.062 | 0.013 | 0.076 | |
| inbiomap_download | 0 | 0 | 0 | |
| inbiomap_raw | 0.000 | 0.001 | 0.000 | |
| interaction_datasets | 0.809 | 0.092 | 1.112 | |
| interaction_graph | 0.517 | 0.040 | 1.293 | |
| interaction_resources | 0.068 | 0.012 | 0.590 | |
| interaction_types | 0.090 | 0.009 | 0.099 | |
| intercell | 0.921 | 0.129 | 1.934 | |
| intercell_categories | 0.751 | 0.104 | 1.069 | |
| intercell_consensus_filter | 1.630 | 0.185 | 3.359 | |
| intercell_generic_categories | 0.087 | 0.008 | 0.095 | |
| intercell_network | 0.013 | 0.003 | 0.016 | |
| intercell_resources | 0.066 | 0.011 | 0.666 | |
| intercell_summary | 0.087 | 0.022 | 0.111 | |
| is_ontology_id | 0.000 | 0.001 | 0.000 | |
| is_swissprot | 0.061 | 0.007 | 0.071 | |
| is_trembl | 0.061 | 0.005 | 0.067 | |
| is_uniprot | 0.013 | 0.003 | 0.016 | |
| kegg_api_templates | 0.002 | 0.003 | 0.005 | |
| kegg_conv | 1.501 | 0.231 | 12.541 | |
| kegg_databases | 0.001 | 0.000 | 0.001 | |
| kegg_ddi | 0.672 | 0.081 | 2.117 | |
| kegg_find | 0.693 | 0.085 | 2.293 | |
| kegg_info | 0.011 | 0.002 | 0.014 | |
| kegg_link | 0.752 | 0.106 | 6.608 | |
| kegg_list | 0.687 | 0.076 | 1.698 | |
| kegg_open | 0.010 | 0.002 | 0.012 | |
| kegg_operations | 0.000 | 0.001 | 0.001 | |
| kegg_organism_codes | 0.027 | 0.094 | 0.121 | |
| kegg_organisms | 0.028 | 0.007 | 0.033 | |
| kegg_pathway_annotations | 0.000 | 0.001 | 0.000 | |
| kegg_pathway_download | 0.010 | 0.002 | 0.014 | |
| kegg_pathway_list | 0.011 | 0.002 | 0.014 | |
| kegg_pathways_download | 0.000 | 0.000 | 0.001 | |
| kegg_picture | 1.147 | 0.057 | 7.662 | |
| kegg_process | 0.022 | 0.003 | 0.026 | |
| kegg_query | 0.011 | 0.001 | 0.011 | |
| kegg_request | 0.080 | 0.009 | 0.091 | |
| kegg_rm_prefix | 0.858 | 0.124 | 5.820 | |