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This page was generated on 2025-08-23 12:05 -0400 (Sat, 23 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4821
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4599
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4553
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4539
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 1475/2319HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OmnipathR 3.17.4  (landing page)
Denes Turei
Snapshot Date: 2025-08-22 13:45 -0400 (Fri, 22 Aug 2025)
git_url: https://git.bioconductor.org/packages/OmnipathR
git_branch: devel
git_last_commit: a7f3b9d
git_last_commit_date: 2025-07-16 10:03:35 -0400 (Wed, 16 Jul 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for OmnipathR on lconway

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.

raw results


Summary

Package: OmnipathR
Version: 3.17.4
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_3.17.4.tar.gz
StartedAt: 2025-08-22 22:28:17 -0400 (Fri, 22 Aug 2025)
EndedAt: 2025-08-22 22:47:58 -0400 (Fri, 22 Aug 2025)
EllapsedTime: 1181.3 seconds
RetCode: 0
Status:   OK  
CheckDir: OmnipathR.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings OmnipathR_3.17.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/OmnipathR.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 ‘3.17.4’
* 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
[2025-08-22 22:28:55] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-22 22:28:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-22 22:28:55] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-08-22 22:28:55] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-08-22 22:28:55] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-08-22
[2025-08-22 22:28:55] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-08-22 19:10:55 UTC; unix
[2025-08-22 22:28:55] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.17.4
[2025-08-22 22:28:55] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-08-22 22:28:56] [INFO]    [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); 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=2025-08-22; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto]
[2025-08-22 22:28:56] [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]
[2025-08-22 22:28:56] [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 1.0.4(2025-06-18); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.1.4(2025-01-23); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.3(2025-08-20); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); memoise 2.0.1(2021-11-26); OmnipathR 3.17.4(2025-08-22); pillar 1.11.0(2025-07-04); 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 2.29(2024-11-04); RSQLite 2.4.3(2025-08-20); rvest 1.0.4(2024-02-12); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); 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)
[2025-08-22 22:28:57] [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
[2025-08-22 22:28:57] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-08-22 22:28:57] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-08-22 22:28:57] [TRACE]   [OmnipathR] Contains 1 files.
[2025-08-22 22:28:57] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-08-22 22:28:57] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-22 22:28:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-22 22:28:57] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-08-22 22:28:57] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-08-22 22:28:57] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-08-22 22:28:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-22 22:28:57] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-08-22 22:28:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-22 22:28:57] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-08-22 22:28:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-22 22:28:57] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-08-22 22:28:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-22 22:28:57] [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
[2025-08-22 22:29:22] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-22 22:29:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-22 22:29:22] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-08-22 22:29:22] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-08-22 22:29:22] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-08-22
[2025-08-22 22:29:22] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-08-22 19:10:55 UTC; unix
[2025-08-22 22:29:22] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.17.4
[2025-08-22 22:29:22] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-08-22 22:29:22] [INFO]    [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); 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=2025-08-22; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto]
[2025-08-22 22:29:23] [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]
[2025-08-22 22:29:23] [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 1.0.4(2025-06-18); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.1.4(2025-01-23); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.3(2025-08-20); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); memoise 2.0.1(2021-11-26); OmnipathR 3.17.4(2025-08-22); pillar 1.11.0(2025-07-04); 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 2.29(2024-11-04); RSQLite 2.4.3(2025-08-20); rvest 1.0.4(2024-02-12); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); 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)
[2025-08-22 22:29:23] [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
[2025-08-22 22:29:23] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-08-22 22:29:23] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-08-22 22:29:23] [TRACE]   [OmnipathR] Contains 1 files.
[2025-08-22 22:29:23] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-08-22 22:29:23] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-22 22:29:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-22 22:29:23] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-08-22 22:29:23] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-08-22 22:29:23] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-08-22 22:29:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-22 22:29:23] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-08-22 22:29:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-22 22:29:23] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-08-22 22:29:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-22 22:29:23] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-08-22 22:29:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-22 22:29:23] [TRACE]   [OmnipathR] Cache locked: FALSE
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:
  common_name_ensembl common_name_uniprot latin_name_ensembl
  latin_name_oma latin_name_uniprot
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                       user system elapsed
curated_ligrec_stats                 43.198 19.693 136.605
annotation_categories                60.932  0.361  62.857
filter_extra_attrs                   42.793 12.368  68.249
omnipath-interactions                33.756  3.087  60.344
all_uniprots                         27.266  3.094  44.989
uniprot_organisms                    22.684  2.894  28.595
extra_attrs_to_cols                  21.457  3.516  33.357
extra_attr_values                    17.683  4.034  31.512
with_extra_attrs                     16.711  3.476  22.572
nichenet_gr_network_omnipath         17.598  1.784  21.716
go_annot_download                    13.870  1.805  14.763
nichenet_signaling_network_omnipath  13.286  1.235  16.837
giant_component                      12.278  1.264  16.320
has_extra_attrs                      10.331  3.141  13.524
extra_attrs                          10.591  2.237  17.596
pivot_annotations                    10.816  1.037  19.969
filter_by_resource                   10.746  0.862  16.464
omnipath_for_cosmos                  10.310  0.866  27.821
curated_ligand_receptor_interactions  7.805  1.278  18.222
translate_ids_multi                   8.440  0.609  16.472
filter_intercell                      8.135  0.717  15.911
print_interactions                    7.271  0.549  11.806
static_table                          7.169  0.589   8.319
find_all_paths                        6.945  0.513   7.578
signed_ptms                           5.796  0.296   6.755
pubmed_open                           4.788  0.274   5.115
print_path_vs                         2.824  0.299   5.688
enzsub_graph                          2.589  0.318   6.151
ensembl_id_mapping_table              2.305  0.316  12.662
kegg_conv                             1.610  0.215  11.531
translate_ids                         1.249  0.181  11.093
metalinksdb_sqlite                    1.075  0.327  10.185
uniprot_full_id_mapping_table         1.217  0.179  12.557
kegg_picture                          1.053  0.058  10.007
kegg_rm_prefix                        0.825  0.102   5.587
kegg_link                             0.744  0.102   5.884
obo_parser                            0.112  0.026   6.260
relations_list_to_table               0.100  0.026   6.260
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/OmnipathR.Rcheck/00check.log’
for details.


Installation output

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 ‘3.17.4’
** 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
[2025-08-22 15:11:09] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-22 15:11:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-22 15:11:09] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-08-22 15:11:09] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-08-22 15:11:09] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-08-22
[2025-08-22 15:11:09] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-08-22 19:10:55 UTC; unix
[2025-08-22 15:11:09] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.17.4
[2025-08-22 15:11:09] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-08-22 15:11:10] [INFO]    [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); 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=2025-08-22; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto]
[2025-08-22 15:11:11] [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]
[2025-08-22 15:11:11] [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 1.0.4(2025-06-18); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.1.4(2025-01-23); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.3(2025-08-20); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); memoise 2.0.1(2021-11-26); OmnipathR 3.17.4(2025-08-22); pillar 1.11.0(2025-07-04); 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 2.29(2024-11-04); RSQLite 2.4.3(2025-08-20); rvest 1.0.4(2024-02-12); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); 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)
[2025-08-22 15:11:11] [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
[2025-08-22 15:11:11] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-08-22 15:11:11] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-08-22 15:11:11] [TRACE]   [OmnipathR] Contains 1 files.
[2025-08-22 15:11:11] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-08-22 15:11:11] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-22 15:11:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-22 15:11:11] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-08-22 15:11:11] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-08-22 15:11:11] [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).
[2025-08-22 15:11:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-22 15:11:11] [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).
[2025-08-22 15:11:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-22 15:11:11] [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).
[2025-08-22 15:11:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-22 15:11:11] [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).
[2025-08-22 15:11:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-22 15:11:11] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2025-08-22 15:11:13] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-22 15:11:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-22 15:11:13] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-08-22 15:11:13] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-08-22 15:11:13] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-08-22
[2025-08-22 15:11:13] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-08-22 19:10:55 UTC; unix
[2025-08-22 15:11:13] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.17.4
[2025-08-22 15:11:13] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-08-22 15:11:14] [INFO]    [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); 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=2025-08-22; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto]
[2025-08-22 15:11:14] [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]
[2025-08-22 15:11:14] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(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 1.0.4(2025-06-18); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.1.4(2025-01-23); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.3(2025-08-20); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); memoise 2.0.1(2021-11-26); OmnipathR 3.17.4(2025-08-22); pillar 1.11.0(2025-07-04); 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 2.29(2024-11-04); RSQLite 2.4.3(2025-08-20); rvest 1.0.4(2024-02-12); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); 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)
[2025-08-22 15:11:14] [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
[2025-08-22 15:11:14] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-08-22 15:11:14] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-08-22 15:11:14] [TRACE]   [OmnipathR] Contains 1 files.
[2025-08-22 15:11:14] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-08-22 15:11:14] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-22 15:11:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-22 15:11:14] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-08-22 15:11:14] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-08-22 15:11:14] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-08-22 15:11:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-22 15:11:14] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-08-22 15:11:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-22 15:11:14] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-08-22 15:11:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-22 15:11:14] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-08-22 15:11:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-22 15:11:14] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package keeps a record of temporary installation path
* DONE (OmnipathR)

Tests output

OmnipathR.Rcheck/tests/testthat.Rout


R version 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
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Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
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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)
[2025-08-22 22:45:57] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-22 22:45:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-22 22:45:57] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-08-22 22:45:57] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-08-22 22:45:57] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-08-22
[2025-08-22 22:45:57] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-08-22 19:10:55 UTC; unix
[2025-08-22 22:45:57] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.17.4
[2025-08-22 22:45:57] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-08-22 22:45:58] [INFO]    [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); 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=2025-08-22; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto]
[2025-08-22 22:45:58] [INFO]    [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.44 2024-06-07; ICU=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-08-22 22:45:59] [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 1.0.4(2025-06-18); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.1.4(2025-01-23); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.3(2025-08-20); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); memoise 2.0.1(2021-11-26); OmnipathR 3.17.4(2025-08-22); pillar 1.11.0(2025-07-04); 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 2.29(2024-11-04); RSQLite 2.4.3(2025-08-20); rvest 1.0.4(2024-02-12); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); 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)
[2025-08-22 22:45:59] [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
[2025-08-22 22:45:59] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-08-22 22:45:59] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-08-22 22:45:59] [TRACE]   [OmnipathR] Contains 22 files.
[2025-08-22 22:45:59] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-08-22 22:45:59] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-22 22:45:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-22 22:45:59] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-08-22 22:45:59] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-08-22 22:45:59] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-08-22 22:45:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-22 22:45:59] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-08-22 22:45:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-22 22:45:59] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-08-22 22:45:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-22 22:45:59] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-08-22 22:45:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-22 22:45:59] [TRACE]   [OmnipathR] Cache locked: FALSE
> 
> test_check('OmnipathR')
[ FAIL 0 | WARN 12 | SKIP 0 | PASS 38 ]

[ FAIL 0 | WARN 12 | SKIP 0 | PASS 38 ]
> 
> proc.time()
   user  system elapsed 
 51.494   6.233 101.661 

Example timings

OmnipathR.Rcheck/OmnipathR-Ex.timings

nameusersystemelapsed
OmnipathR000
all_uniprot_acs0.0210.0040.025
all_uniprots27.266 3.09444.989
ancestors0.0110.0010.013
annotated_network1.4600.1374.529
annotation_categories60.932 0.36162.857
annotation_resources0.0660.0090.627
annotations0.6110.0491.468
biomart_query1.4440.2254.542
bioplex10.0110.0020.012
bioplex20.0090.0020.011
bioplex30.0100.0020.013
bioplex_all0.0100.0010.012
bioplex_hct116_10.0090.0020.012
bma_motif_es0.6820.0761.488
bma_motif_vs0.2150.0250.723
chalmers_gem0.0100.0020.012
chalmers_gem_id_mapping_table0.0090.0020.011
chalmers_gem_id_type0.0020.0010.003
chalmers_gem_metabolites0.0100.0020.011
chalmers_gem_network0.0100.0020.011
chalmers_gem_raw0.0090.0010.010
chalmers_gem_reactions0.0100.0020.011
common_name0.1140.0070.121
complex_genes0.7910.0662.463
complex_resources0.0630.0080.654
complexes0.1860.0190.715
consensuspathdb_download000
consensuspathdb_raw_table0.0100.0020.013
cosmos_pkn0.0000.0010.000
curated_ligand_receptor_interactions 7.805 1.27818.222
curated_ligrec_stats 43.198 19.693136.605
database_summary2.1390.2124.634
descendants0.0150.0020.017
ensembl_dataset0.0600.0030.114
ensembl_id_mapping_table 2.305 0.31612.662
ensembl_id_type0.0020.0010.003
ensembl_name0.3220.0780.654
ensembl_organisms0.1700.2350.495
ensembl_organisms_raw0.1560.1711.119
ensembl_orthology0.0000.0020.002
enzsub_graph2.5890.3186.151
enzsub_resources0.0480.0100.642
enzyme_substrate1.0690.2092.236
evex_download0.0090.0020.012
evidences000
extra_attr_values17.683 4.03431.512
extra_attrs10.591 2.23717.596
extra_attrs_to_cols21.457 3.51633.357
filter_by_resource10.746 0.86216.464
filter_extra_attrs42.79312.36868.249
filter_intercell 8.135 0.71715.911
filter_intercell_network0.0240.0040.028
find_all_paths6.9450.5137.578
from_evidences0.0000.0010.000
get_db0.0000.0000.001
get_ontology_db0.0110.0020.013
giant_component12.278 1.26416.320
go_annot_download13.870 1.80514.763
go_annot_slim000
go_ontology_download0.0100.0010.011
guide2pharma_download0.0110.0020.014
harmonizome_download0.0100.0020.012
has_extra_attrs10.331 3.14113.524
hmdb_id_mapping_table0.0110.0020.013
hmdb_id_type0.0020.0000.002
hmdb_metabolite_fields0.0010.0000.002
hmdb_protein_fields0.0010.0000.001
hmdb_table0.0120.0020.013
homologene_download0.0110.0020.013
homologene_raw0.0590.0030.062
homologene_uniprot_orthology0.0120.0020.014
hpo_download3.2000.5233.696
htridb_download0.0110.0020.014
id_translation_resources000
id_types0.0620.0120.076
inbiomap_download0.0010.0000.001
inbiomap_raw0.0000.0000.001
interaction_datasets0.7800.0871.230
interaction_graph0.4560.0391.051
interaction_resources0.1120.0120.710
interaction_types0.0740.0070.081
intercell0.9050.1171.792
intercell_categories0.7260.0911.042
intercell_consensus_filter1.5760.1643.360
intercell_generic_categories0.0880.0090.097
intercell_network0.0100.0020.012
intercell_resources0.0690.0090.665
intercell_summary0.0910.0210.112
is_ontology_id000
is_swissprot0.0620.0060.068
is_trembl0.0670.0050.073
is_uniprot0.0130.0020.014
kegg_api_templates0.0010.0030.004
kegg_conv 1.610 0.21511.531
kegg_databases0.0000.0010.001
kegg_ddi0.6850.0772.047
kegg_find0.6800.0722.230
kegg_info0.0110.0010.012
kegg_link0.7440.1025.884
kegg_list0.6510.0741.660
kegg_open0.0110.0020.012
kegg_operations000
kegg_organism_codes0.0220.0610.084
kegg_organisms0.0270.0070.035
kegg_pathway_annotations000
kegg_pathway_download0.0110.0010.013
kegg_pathway_list0.0090.0010.012
kegg_pathways_download000
kegg_picture 1.053 0.05810.007
kegg_process0.0230.0040.026
kegg_query0.0080.0010.009
kegg_request0.0760.0100.087
kegg_rm_prefix0.8250.1025.587
latin_name0.2480.0100.259
load_db0.1030.0210.126
metalinksdb_sqlite 1.075 0.32710.185
metalinksdb_table0.2630.0480.314
metalinksdb_tables0.0200.0040.024
ncbi_taxid0.2320.0090.242
nichenet_build_model0.0010.0000.000
nichenet_expression_data0.0110.0020.013
nichenet_gr_network0.0280.0050.032
nichenet_gr_network_evex0.0090.0010.011
nichenet_gr_network_harmonizome0.0110.0010.013
nichenet_gr_network_htridb0.0090.0010.011
nichenet_gr_network_omnipath17.598 1.78421.716
nichenet_gr_network_pathwaycommons0.0120.0020.014
nichenet_gr_network_regnetwork0.0110.0020.012
nichenet_gr_network_remap0.0110.0010.013
nichenet_gr_network_trrust0.0110.0020.012
nichenet_ligand_activities0.0010.0000.001
nichenet_ligand_target_links000
nichenet_ligand_target_matrix0.0010.0000.000
nichenet_lr_network0.0320.0060.037
nichenet_lr_network_guide2pharma0.0110.0020.013
nichenet_lr_network_omnipath0.0300.0050.036
nichenet_lr_network_ramilowski0.0100.0020.012
nichenet_main000
nichenet_networks0.0520.0090.061
nichenet_optimization0.0000.0000.001
nichenet_remove_orphan_ligands0.0790.0080.088
nichenet_results_dir0.0000.0000.001
nichenet_signaling_network0.0340.0050.039
nichenet_signaling_network_cpdb0.0110.0020.012
nichenet_signaling_network_evex0.0110.0020.013
nichenet_signaling_network_harmonizome0.0110.0010.013
nichenet_signaling_network_inbiomap000
nichenet_signaling_network_omnipath13.286 1.23516.837
nichenet_signaling_network_pathwaycommons0.0120.0020.013
nichenet_signaling_network_vinayagam0.0120.0020.014
nichenet_test000
nichenet_workarounds000
obo_parser0.1120.0266.260
oma_code0.1330.0050.140
oma_organisms0.1590.0210.181
oma_pairwise0.0120.0020.015
oma_pairwise_genesymbols0.0130.0010.015
oma_pairwise_translated0.0120.0020.013
omnipath-interactions33.756 3.08760.344
omnipath_cache_autoclean000
omnipath_cache_clean0.0080.0030.012
omnipath_cache_clean_db0.1550.0230.179
omnipath_cache_download_ready0.5380.1320.748
omnipath_cache_filter_versions0.1410.0310.186
omnipath_cache_get0.0930.0210.116
omnipath_cache_key0.0020.0000.002
omnipath_cache_latest_or_new0.0690.0150.084
omnipath_cache_load0.5270.0462.891
omnipath_cache_move_in0.1690.0430.226
omnipath_cache_remove0.1150.0300.156
omnipath_cache_save0.2610.0390.342
omnipath_cache_search0.0000.0010.002
omnipath_cache_set_ext0.0920.0230.145
omnipath_cache_update_status0.1000.0210.122
omnipath_cache_wipe000
omnipath_config_path0.0000.0000.001
omnipath_for_cosmos10.310 0.86627.821
omnipath_load_config0.0000.0010.000
omnipath_log000
omnipath_logfile0.0010.0000.002
omnipath_msg0.0050.0010.007
omnipath_query4.1520.2344.396
omnipath_reset_config000
omnipath_save_config0.0000.0010.001
omnipath_set_cachedir0.0310.0050.035
omnipath_set_console_loglevel0.0050.0000.006
omnipath_set_logfile_loglevel0.0030.0000.003
omnipath_set_loglevel0.0020.0000.003
omnipath_show_db0.0760.0140.090
omnipath_unlock_cache_db000
only_from000
ontology_ensure_id0.0000.0000.001
ontology_ensure_name0.0000.0000.001
ontology_name_id0.0010.0000.001
organism_for0.1760.0060.183
pathwaycommons_download0.0010.0000.001
pivot_annotations10.816 1.03719.969
preppi_download0.0010.0000.001
preppi_filter0.0010.0000.002
print_bma_motif_es0.8020.1021.666
print_bma_motif_vs0.1660.0170.701
print_interactions 7.271 0.54911.806
print_path_es0.9260.0772.660
print_path_vs2.8240.2995.688
pubmed_open4.7880.2745.115
query_info0.4480.0300.682
ramilowski_download0.0000.0000.001
ramp_id_mapping_table000
ramp_id_type0.0020.0010.003
ramp_sqlite0.0010.0000.000
ramp_table0.0010.0000.001
ramp_tables0.0010.0000.001
regnetwork_directions0.0010.0000.001
regnetwork_download0.0010.0010.001
relations_list_to_table0.1000.0266.260
relations_table_to_graph0.0010.0000.001
relations_table_to_list0.0830.0180.120
remap_dorothea_download0.0010.0010.001
remap_filtered0.0000.0010.000
remap_tf_target_download0.0000.0010.001
resource_info0.4930.1080.808
resources0.0580.0100.856
resources_colname1.1640.0893.643
resources_in4.3780.2294.629
show_network0.0000.0000.001
signed_ptms5.7960.2966.755
simplify_intercell_network0.0010.0000.001
static_table7.1690.5898.319
static_tables0.0620.0130.086
stitch_actions0.0010.0000.001
stitch_links0.0010.0010.000
stitch_network0.0010.0000.002
stitch_remove_prefixes0.0080.0020.010
swap_relations0.1760.0230.226
swissprots_only0.1300.0050.135
tfcensus_download0.5870.0680.833
translate_ids 1.249 0.18111.093
translate_ids_multi 8.440 0.60916.472
trembls_only0.1280.0050.133
trrust_download0.0000.0010.001
uniprot_full_id_mapping_table 1.217 0.17912.557
uniprot_genesymbol_cleanup0.0000.0010.000
uniprot_id_mapping_table0.0000.0000.001
uniprot_id_type0.0020.0000.002
uniprot_idmapping_id_types0.5180.0651.230
uniprot_organisms22.684 2.89428.595
unique_intercell_network0.0010.0000.001
unnest_evidences000
uploadlists_id_type0.0030.0010.003
vinayagam_download0.0010.0010.001
walk_ontology_tree0.0010.0010.002
with_extra_attrs16.711 3.47622.572
with_references1.0310.1012.610
zenodo_download0.0010.0010.002