Back to Multiple platform build/check report for BioC 3.23:   simplified   long
ABCDEFGHIJKLMN[O]PQRSTUVWXYZ

This page was generated on 2025-12-22 11:35 -0500 (Mon, 22 Dec 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_64R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" 4878
kjohnson3macOS 13.7.7 Venturaarm64R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" 4593
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 1491/2332HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OmnipathR 3.19.5  (landing page)
Denes Turei
Snapshot Date: 2025-12-21 13:40 -0500 (Sun, 21 Dec 2025)
git_url: https://git.bioconductor.org/packages/OmnipathR
git_branch: devel
git_last_commit: f5182b3
git_last_commit_date: 2025-12-10 07:50:10 -0500 (Wed, 10 Dec 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  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


CHECK results for OmnipathR on kjohnson3

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: 3.19.5
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings OmnipathR_3.19.5.tar.gz
StartedAt: 2025-12-21 21:11:33 -0500 (Sun, 21 Dec 2025)
EndedAt: 2025-12-21 21:25:26 -0500 (Sun, 21 Dec 2025)
EllapsedTime: 832.8 seconds
RetCode: 0
Status:   OK  
CheckDir: OmnipathR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings OmnipathR_3.19.5.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/OmnipathR.Rcheck’
* using R Under development (unstable) (2025-11-04 r88984)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OmnipathR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OmnipathR’ version ‘3.19.5’
* 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
[2025-12-21 21:11:49] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-21 21:11:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-21 21:11:49] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-12-21 21:11:49] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-12-21 21:11:49] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-12-21
[2025-12-21 21:11:49] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2025-12-21 20:05:25 UTC; unix
[2025-12-21 21:11:49] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.19.5
[2025-12-21 21:11:49] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23
[2025-12-21 21:11:50] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2025-11-04 r88984); os=macOS Ventura 13.7.8; system=aarch64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-12-21; pandoc=3.1.12.3 @ /opt/homebrew/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2025-12-21 21:11:50] [INFO]    [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; zstd=1.5.5; PCRE=10.44 2024-06-07; ICU=70.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/lib/libR.dylib; readline=5.2; BLAS=/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-12-21 21:11:50] [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 0.6.39(2025-11-19); 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 0.5.9(2025-12-04); httr 1.4.7(2023-08-15); httr2 1.2.2(2025-12-08); igraph 2.2.1(2025-10-27); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.4(2025-08-27); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.19.5(2025-12-21); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.0(2025-11-04); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.1.0.8.1(2025-12-08); readr 2.1.6(2025-11-14); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.5(2025-11-30); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.0(2025-06-08); tidyr 1.3.2(2025-12-19); 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 0.55(2025-12-16); XML 3.99-0.20(2025-11-08); xml2 1.5.1(2025-12-01); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2025-12-21 21:11:50] [INFO]    [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: aarch64-apple-darwin23.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2025-12-21 21:11:50] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-12-21 21:11:50] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-12-21 21:11:50] [TRACE]   [OmnipathR] Contains 1 files.
[2025-12-21 21:11:50] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-12-21 21:11:50] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-21 21:11:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-21 21:11:50] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-12-21 21:11:50] [TRACE]   [OmnipathR] Pandoc version: `3.1.12.3`.
[2025-12-21 21:11:50] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-12-21 21:11:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-21 21:11:50] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-12-21 21:11:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-21 21:11:50] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-12-21 21:11:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-21 21:11:50] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-12-21 21:11:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-21 21:11:50] [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
[2025-12-21 21:12:04] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-21 21:12:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-21 21:12:04] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-12-21 21:12:04] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-12-21 21:12:04] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-12-21
[2025-12-21 21:12:04] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2025-12-21 20:05:25 UTC; unix
[2025-12-21 21:12:04] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.19.5
[2025-12-21 21:12:04] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23
[2025-12-21 21:12:04] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2025-11-04 r88984); os=macOS Ventura 13.7.8; system=aarch64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-12-21; pandoc=3.1.12.3 @ /opt/homebrew/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2025-12-21 21:12:04] [INFO]    [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; zstd=1.5.5; PCRE=10.44 2024-06-07; ICU=70.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/lib/libR.dylib; readline=5.2; BLAS=/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-12-21 21:12:05] [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 0.6.39(2025-11-19); 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 0.5.9(2025-12-04); httr 1.4.7(2023-08-15); httr2 1.2.2(2025-12-08); igraph 2.2.1(2025-10-27); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.4(2025-08-27); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.19.5(2025-12-21); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.0(2025-11-04); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.1.0.8.1(2025-12-08); readr 2.1.6(2025-11-14); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.5(2025-11-30); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.0(2025-06-08); tidyr 1.3.2(2025-12-19); 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 0.55(2025-12-16); XML 3.99-0.20(2025-11-08); xml2 1.5.1(2025-12-01); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2025-12-21 21:12:05] [INFO]    [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: aarch64-apple-darwin23.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2025-12-21 21:12:05] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-12-21 21:12:05] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-12-21 21:12:05] [TRACE]   [OmnipathR] Contains 1 files.
[2025-12-21 21:12:05] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-12-21 21:12:05] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-21 21:12:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-21 21:12:05] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-12-21 21:12:05] [TRACE]   [OmnipathR] Pandoc version: `3.1.12.3`.
[2025-12-21 21:12:05] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-12-21 21:12:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-21 21:12:05] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-12-21 21:12:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-21 21:12:05] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-12-21 21:12:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-21 21:12:05] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-12-21 21:12:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-21 21:12:05] [TRACE]   [OmnipathR] Cache locked: FALSE
cosmos_ksn: no visible binding for global variable ‘enzyme_genesymbol’
patch_httr2_keep_handle: no visible binding for global variable
  ‘handle’
patch_httr2_keep_handle: no visible global function definition for
  ‘ORIGINAL’
Undefined global functions or variables:
  ORIGINAL enzyme_genesymbol handle
* 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
annotation_categories                41.045  0.083  44.037
curated_ligrec_stats                 16.980  2.591  98.235
omnipath-interactions                13.980  1.288  52.491
filter_extra_attrs                   10.311  4.764  42.309
nichenet_gr_network_omnipath          8.874  0.863  14.086
all_uniprots                          7.956  1.073  30.458
extra_attrs_to_cols                   6.576  1.746  11.105
uniprot_organisms                     6.829  0.980  17.680
go_annot_download                     7.061  0.503   8.695
giant_component                       6.286  0.585  16.996
extra_attr_values                     5.069  1.549  14.707
with_extra_attrs                      5.441  1.163  16.716
nichenet_signaling_network_omnipath   5.415  0.646  12.402
pivot_annotations                     5.236  0.411  20.509
omnipath_for_cosmos                   4.673  0.404  25.275
translate_ids_multi                   4.530  0.362  22.505
extra_attrs                           3.557  1.259   7.249
filter_by_resource                    3.995  0.332   8.253
filter_intercell                      4.046  0.281  11.219
has_extra_attrs                       2.894  1.080   9.832
curated_ligand_receptor_interactions  2.860  0.684  16.543
print_interactions                    3.138  0.264   9.844
find_all_paths                        2.796  0.239   5.672
ensembl_id_mapping_table              1.764  0.231  20.677
kegg_conv                             0.601  0.086  11.143
translate_ids                         0.521  0.105  10.357
kinasephos                            0.477  0.091  18.980
metalinksdb_sqlite                    0.437  0.126   9.737
uniprot_full_id_mapping_table         0.440  0.094  12.325
kegg_rm_prefix                        0.327  0.039   5.436
kegg_link                             0.311  0.047   6.247
* 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-3.23-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/4.6-arm64/Resources/library’
* installing *source* package ‘OmnipathR’ ...
** this is package ‘OmnipathR’ version ‘3.19.5’
** 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
[2025-12-21 15:05:30] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-21 15:05:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-21 15:05:30] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-12-21 15:05:30] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-12-21 15:05:30] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-12-21
[2025-12-21 15:05:30] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2025-12-21 20:05:25 UTC; unix
[2025-12-21 15:05:30] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.19.5
[2025-12-21 15:05:30] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23
[2025-12-21 15:05:31] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2025-11-04 r88984); os=macOS Ventura 13.7.8; system=aarch64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-12-21; pandoc=3.1.12.3 @ /opt/homebrew/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2025-12-21 15:05:31] [INFO]    [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; zstd=1.5.5; PCRE=10.44 2024-06-07; ICU=70.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/lib/libR.dylib; readline=5.2; BLAS=/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-12-21 15:05:31] [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 0.6.39(2025-11-19); 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 0.5.9(2025-12-04); httr 1.4.7(2023-08-15); httr2 1.2.2(2025-12-08); igraph 2.2.1(2025-10-27); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.4(2025-08-27); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.19.5(2025-12-21); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.0(2025-11-04); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.1.0.8.1(2025-12-08); readr 2.1.6(2025-11-14); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.5(2025-11-30); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.0(2025-06-08); tidyr 1.3.2(2025-12-19); 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 0.55(2025-12-16); XML 3.99-0.20(2025-11-08); xml2 1.5.1(2025-12-01); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2025-12-21 15:05:31] [INFO]    [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: aarch64-apple-darwin23.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2025-12-21 15:05:31] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-12-21 15:05:31] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-12-21 15:05:31] [TRACE]   [OmnipathR] Contains 1 files.
[2025-12-21 15:05:31] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-12-21 15:05:31] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-21 15:05:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-21 15:05:31] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-12-21 15:05:31] [TRACE]   [OmnipathR] Pandoc version: `3.1.12.3`.
[2025-12-21 15:05:31] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-12-21 15:05:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-21 15:05:31] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-12-21 15:05:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-21 15:05:31] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-12-21 15:05:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-21 15:05:31] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-12-21 15:05:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-21 15:05:31] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2025-12-21 15:05:32] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-21 15:05:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-21 15:05:32] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-12-21 15:05:32] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-12-21 15:05:32] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-12-21
[2025-12-21 15:05:32] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2025-12-21 20:05:25 UTC; unix
[2025-12-21 15:05:32] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.19.5
[2025-12-21 15:05:32] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23
[2025-12-21 15:05:32] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2025-11-04 r88984); os=macOS Ventura 13.7.8; system=aarch64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-12-21; pandoc=3.1.12.3 @ /opt/homebrew/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2025-12-21 15:05:32] [INFO]    [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; zstd=1.5.5; PCRE=10.44 2024-06-07; ICU=70.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/lib/libR.dylib; readline=5.2; BLAS=/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-12-21 15:05:32] [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 0.6.39(2025-11-19); 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 0.5.9(2025-12-04); httr 1.4.7(2023-08-15); httr2 1.2.2(2025-12-08); igraph 2.2.1(2025-10-27); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.4(2025-08-27); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.19.5(2025-12-21); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.0(2025-11-04); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.1.0.8.1(2025-12-08); readr 2.1.6(2025-11-14); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.5(2025-11-30); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.0(2025-06-08); tidyr 1.3.2(2025-12-19); 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 0.55(2025-12-16); XML 3.99-0.20(2025-11-08); xml2 1.5.1(2025-12-01); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2025-12-21 15:05:32] [INFO]    [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: aarch64-apple-darwin23.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2025-12-21 15:05:32] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-12-21 15:05:32] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-12-21 15:05:32] [TRACE]   [OmnipathR] Contains 1 files.
[2025-12-21 15:05:32] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-12-21 15:05:32] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-21 15:05:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-21 15:05:32] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-12-21 15:05:32] [TRACE]   [OmnipathR] Pandoc version: `3.1.12.3`.
[2025-12-21 15:05:32] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-12-21 15:05:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-21 15:05:32] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-12-21 15:05:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-21 15:05:32] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-12-21 15:05:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-21 15:05:32] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-12-21 15:05:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-21 15:05:32] [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 Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> #!/usr/bin/env Rscript
> 
> #
> #  This file is part of the `OmnipathR` R package
> #
> #  Copyright
> #  2018-2024
> #  Saez Lab, Uniklinik RWTH Aachen, Heidelberg University
> #
> #  File author(s): Alberto Valdeolivas
> #                  Dénes Türei (turei.denes@gmail.com)
> #                  Attila Gábor
> #
> #  Distributed under the MIT (Expat) License.
> #  See accompanying file `LICENSE` or find a copy at
> #      https://directory.fsf.org/wiki/License:Expat
> #
> #  Website: https://r.omnipathdb.org/
> #  Git repo: https://github.com/saezlab/OmnipathR
> #
> 
> 
> library(testthat)
> library(OmnipathR)
[2025-12-21 21:24:17] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-21 21:24:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-21 21:24:17] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-12-21 21:24:18] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-12-21 21:24:18] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-12-21
[2025-12-21 21:24:18] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2025-12-21 20:05:25 UTC; unix
[2025-12-21 21:24:18] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.19.5
[2025-12-21 21:24:18] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23
[2025-12-21 21:24:18] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2025-11-04 r88984); os=macOS Ventura 13.7.8; system=aarch64, darwin20; ui=X11; language=C; collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-12-21; pandoc=3.1.12.3 @ /opt/homebrew/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2025-12-21 21:24:18] [INFO]    [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; zstd=1.5.5; PCRE=10.44 2024-06-07; ICU=70.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/lib/libR.dylib; readline=5.2; BLAS=/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-12-21 21:24:18] [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 0.6.39(2025-11-19); 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 0.5.9(2025-12-04); httr 1.4.7(2023-08-15); httr2 1.2.2(2025-12-08); igraph 2.2.1(2025-10-27); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.4(2025-08-27); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.19.5(2025-12-21); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.0(2025-11-04); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.1.0.8.1(2025-12-08); readr 2.1.6(2025-11-14); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.5(2025-11-30); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); testthat 3.3.1(2025-11-25); tibble 3.3.0(2025-06-08); tidyr 1.3.2(2025-12-19); 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 0.55(2025-12-16); XML 3.99-0.20(2025-11-08); xml2 1.5.1(2025-12-01); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2025-12-21 21:24:18] [INFO]    [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: aarch64-apple-darwin23.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2025-12-21 21:24:18] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-12-21 21:24:18] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-12-21 21:24:18] [TRACE]   [OmnipathR] Contains 22 files.
[2025-12-21 21:24:18] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-12-21 21:24:18] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-21 21:24:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-21 21:24:18] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-12-21 21:24:18] [TRACE]   [OmnipathR] Pandoc version: `3.1.12.3`.
[2025-12-21 21:24:18] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-12-21 21:24:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-21 21:24:18] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-12-21 21:24:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-21 21:24:18] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-12-21 21:24:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-21 21:24:18] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-12-21 21:24:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-21 21:24:18] [TRACE]   [OmnipathR] Cache locked: FALSE
> 
> test_check('OmnipathR')
[ FAIL 0 | WARN 11 | SKIP 0 | PASS 38 ]

[ FAIL 0 | WARN 11 | SKIP 0 | PASS 38 ]
> 
> proc.time()
   user  system elapsed 
 17.062   2.297  61.062 

Example timings

OmnipathR.Rcheck/OmnipathR-Ex.timings

nameusersystemelapsed
OmnipathR000
all_uniprot_acs0.0040.0000.005
all_uniprots 7.956 1.07330.458
ancestors0.0030.0000.003
annotated_network0.6050.0723.907
annotation_categories41.045 0.08344.037
annotation_resources0.0270.0050.666
annotations0.2630.0281.230
biomart_query0.6190.1003.838
bioplex10.0030.0010.003
bioplex20.0030.0010.004
bioplex30.0030.0010.017
bioplex_all0.0030.0010.008
bioplex_hct116_10.0030.0010.005
bma_motif_es0.2740.0401.398
bma_motif_vs0.0910.0160.675
chalmers_gem0.0060.0010.008
chalmers_gem_id_mapping_table0.0060.0020.007
chalmers_gem_id_type0.0010.0000.002
chalmers_gem_metabolites0.0050.0010.006
chalmers_gem_network0.0030.0010.007
chalmers_gem_raw0.0030.0010.005
chalmers_gem_reactions0.0050.0020.007
common_name0.0480.0040.097
complex_genes0.3300.0372.034
complex_resources0.0220.0040.595
complexes0.0820.0110.749
consensuspathdb_download000
consensuspathdb_raw_table0.0070.0010.009
cosmos_pkn000
curated_ligand_receptor_interactions 2.860 0.68416.543
curated_ligrec_stats16.980 2.59198.235
database_summary1.1870.1413.987
descendants0.0080.0010.011
ensembl_dataset0.0260.0010.038
ensembl_id_mapping_table 1.764 0.23120.677
ensembl_id_type0.0000.0000.001
ensembl_name0.2400.0080.258
ensembl_organisms0.0380.0090.077
ensembl_organisms_raw0.0400.0100.117
ensembl_orthology0.0000.0000.001
enzsub_graph0.9200.0793.810
enzsub_resources0.0210.0040.621
enzyme_substrate0.4170.0301.141
evex_download0.0030.0010.004
evidences000
extra_attr_values 5.069 1.54914.707
extra_attrs3.5571.2597.249
extra_attrs_to_cols 6.576 1.74611.105
filter_by_resource3.9950.3328.253
filter_extra_attrs10.311 4.76442.309
filter_intercell 4.046 0.28111.219
filter_intercell_network0.0090.0030.044
find_all_paths2.7960.2395.672
from_evidences0.0000.0000.001
get_db0.0000.0000.001
get_ontology_db0.0080.0010.017
giant_component 6.286 0.58516.996
go_annot_download7.0610.5038.695
go_annot_slim0.0000.0000.001
go_ontology_download0.0030.0010.003
guide2pharma_download0.0020.0000.003
harmonizome_download0.0030.0010.023
has_extra_attrs2.8941.0809.832
hmdb_id_mapping_table0.0040.0010.008
hmdb_id_type0.0010.0010.001
hmdb_metabolite_fields0.0000.0000.001
hmdb_protein_fields0.0000.0010.000
hmdb_table0.0030.0010.005
homologene_download0.0020.0010.004
homologene_raw0.0230.0020.049
homologene_uniprot_orthology0.0030.0010.004
hpo_download1.3540.1242.093
htridb_download0.0070.0010.009
id_translation_resources0.0000.0000.001
id_types0.0320.0040.036
inbiomap_download000
inbiomap_raw000
interaction_datasets0.3580.0400.964
interaction_graph0.1630.0160.875
interaction_resources0.0250.0050.639
interaction_types0.0310.0040.041
intercell0.4960.0661.618
intercell_categories0.2880.0420.804
intercell_consensus_filter0.6890.0793.014
intercell_generic_categories0.0320.0040.053
intercell_network0.0030.0010.012
intercell_resources0.0220.0050.632
intercell_summary0.0320.0100.061
is_ontology_id000
is_swissprot0.0390.0060.084
is_trembl0.0220.0030.032
is_uniprot0.0040.0010.006
kegg_api_templates0.0000.0010.002
kegg_conv 0.601 0.08611.143
kegg_databases000
kegg_ddi0.2570.0361.917
kegg_find0.2600.0311.897
kegg_info0.0030.0010.004
kegg_link0.3110.0476.247
kegg_list0.2970.0371.476
kegg_open0.0030.0010.014
kegg_operations000
kegg_organism_codes0.0080.0250.077
kegg_organisms0.0080.0020.020
kegg_pathway_annotations000
kegg_pathway_download0.0020.0000.004
kegg_pathway_list0.0030.0010.018
kegg_pathways_download000
kegg_picture0.5200.0254.124
kegg_process0.0070.0020.026
kegg_query0.0030.0000.002
kegg_request0.0270.0050.081
kegg_rm_prefix0.3270.0395.436
kinasephos 0.477 0.09118.980
latin_name0.0950.0040.146
load_db0.0270.0080.079
metalinksdb_sqlite0.4370.1269.737
metalinksdb_table0.0970.0180.187
metalinksdb_tables0.0080.0020.035
ncbi_taxid0.0970.0050.137
nichenet_build_model0.0000.0000.001
nichenet_expression_data0.0040.0010.017
nichenet_gr_network0.0090.0020.042
nichenet_gr_network_evex0.0040.0020.032
nichenet_gr_network_harmonizome0.0030.0000.020
nichenet_gr_network_htridb0.0030.0010.014
nichenet_gr_network_omnipath 8.874 0.86314.086
nichenet_gr_network_pathwaycommons0.0040.0010.027
nichenet_gr_network_regnetwork0.0040.0010.016
nichenet_gr_network_remap0.0030.0010.019
nichenet_gr_network_trrust0.0030.0010.007
nichenet_ligand_activities0.0000.0010.001
nichenet_ligand_target_links0.0010.0000.001
nichenet_ligand_target_matrix000
nichenet_lr_network0.0090.0030.030
nichenet_lr_network_guide2pharma0.0040.0010.013
nichenet_lr_network_omnipath0.0100.0040.040
nichenet_lr_network_ramilowski0.0250.0010.038
nichenet_main0.0000.0010.001
nichenet_networks0.0210.0060.075
nichenet_optimization0.0010.0000.000
nichenet_remove_orphan_ligands0.0130.0030.056
nichenet_results_dir000
nichenet_signaling_network0.0110.0030.081
nichenet_signaling_network_cpdb0.0030.0010.004
nichenet_signaling_network_evex0.0030.0010.005
nichenet_signaling_network_harmonizome0.0030.0010.011
nichenet_signaling_network_inbiomap0.0010.0000.000
nichenet_signaling_network_omnipath 5.415 0.64612.402
nichenet_signaling_network_pathwaycommons0.0030.0010.006
nichenet_signaling_network_vinayagam0.0030.0000.005
nichenet_test000
nichenet_workarounds0.0000.0000.001
obo_parser0.0400.0180.540
oma_code0.0540.0050.098
oma_organisms0.0320.0120.085
oma_pairwise0.0290.0010.031
oma_pairwise_genesymbols0.0060.0000.014
oma_pairwise_translated0.0040.0010.014
omnipath-interactions13.980 1.28852.491
omnipath_cache_autoclean0.0010.0010.000
omnipath_cache_clean0.0060.0020.007
omnipath_cache_clean_db0.0670.0140.083
omnipath_cache_download_ready0.2210.0660.532
omnipath_cache_filter_versions0.0320.0130.153
omnipath_cache_get0.0240.0070.067
omnipath_cache_key000
omnipath_cache_latest_or_new0.0210.0070.095
omnipath_cache_load0.2140.0252.857
omnipath_cache_move_in0.0640.0160.151
omnipath_cache_remove0.0290.0110.106
omnipath_cache_save0.0460.0130.156
omnipath_cache_search0.0000.0000.001
omnipath_cache_set_ext0.0240.0100.076
omnipath_cache_update_status0.0260.0090.076
omnipath_cache_wipe000
omnipath_config_path0.0000.0000.001
omnipath_for_cosmos 4.673 0.40425.275
omnipath_load_config0.0000.0010.000
omnipath_log000
omnipath_logfile000
omnipath_msg0.0010.0010.005
omnipath_query2.1790.1282.421
omnipath_reset_config000
omnipath_save_config000
omnipath_set_cachedir0.0090.0030.040
omnipath_set_console_loglevel0.0010.0010.001
omnipath_set_logfile_loglevel0.0010.0000.002
omnipath_set_loglevel0.0000.0000.001
omnipath_show_db0.0190.0060.045
omnipath_unlock_cache_db0.0000.0010.000
only_from000
ontology_ensure_id0.0010.0000.000
ontology_ensure_name000
ontology_name_id000
organism_for0.0640.0040.085
pathwaycommons_download0.0010.0000.005
pivot_annotations 5.236 0.41120.509
preppi_download0.0010.0010.001
preppi_filter0.0010.0010.001
print_bma_motif_es0.2820.0391.103
print_bma_motif_vs0.0610.0090.680
print_interactions3.1380.2649.844
print_path_es0.3820.0342.164
print_path_vs1.1190.1484.377
pubmed_open1.7960.1142.319
query_info0.2030.0140.517
ramilowski_download000
ramp_id_mapping_table0.0010.0000.001
ramp_id_type0.0000.0000.001
ramp_sqlite000
ramp_table000
ramp_tables000
recon3d0.0010.0000.000
recon3d_raw000
recon3d_raw_vmh0.0000.0010.000
regnetwork_directions0.0010.0000.001
regnetwork_download000
relations_list_to_table0.0310.0120.408
relations_table_to_graph000
relations_table_to_list0.0240.0110.134
remap_dorothea_download000
remap_filtered0.0000.0000.001
remap_tf_target_download0.0010.0000.000
resource_info0.2260.0370.564
resources0.0180.0030.584
resources_colname0.5810.0342.730
resources_in1.8050.0892.229
show_network000
signed_ptms2.0170.1093.815
simplify_intercell_network0.0000.0000.005
static_table3.1350.1794.646
static_tables0.0360.0090.059
stitch_actions000
stitch_links0.0000.0000.001
stitch_network0.0000.0000.001
stitch_remove_prefixes0.0020.0000.003
swap_relations0.0470.0160.242
swissprots_only0.0740.0040.078
tfcensus_download0.2960.0360.560
translate_ids 0.521 0.10510.357
translate_ids_multi 4.530 0.36222.505
trembls_only0.0540.0040.113
trrust_download0.0000.0000.001
uniprot_full_id_mapping_table 0.440 0.09412.325
uniprot_genesymbol_cleanup000
uniprot_id_mapping_table000
uniprot_id_type0.0010.0000.002
uniprot_idmapping_id_types0.2430.0291.042
uniprot_organisms 6.829 0.98017.680
unique_intercell_network000
unnest_evidences000
uploadlists_id_type0.0010.0000.009
vinayagam_download0.0010.0000.000
walk_ontology_tree0.0000.0000.006
with_extra_attrs 5.441 1.16316.716
with_references0.4170.0492.179
zenodo_download0.0010.0000.001