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This page was generated on 2025-10-16 11:40 -0400 (Thu, 16 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4833
merida1macOS 12.7.6 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4614
kjohnson1macOS 13.7.5 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4555
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4586
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 1484/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OmnipathR 3.16.2  (landing page)
Denes Turei
Snapshot Date: 2025-10-13 13:40 -0400 (Mon, 13 Oct 2025)
git_url: https://git.bioconductor.org/packages/OmnipathR
git_branch: RELEASE_3_21
git_last_commit: e923fc4
git_last_commit_date: 2025-08-30 05:55:56 -0400 (Sat, 30 Aug 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.6 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.7.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for OmnipathR on kjohnson1

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: 3.16.2
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_3.16.2.tar.gz
StartedAt: 2025-10-15 06:25:21 -0400 (Wed, 15 Oct 2025)
EndedAt: 2025-10-15 06:38:45 -0400 (Wed, 15 Oct 2025)
EllapsedTime: 804.0 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_3.16.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/OmnipathR.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* 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 13.7.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OmnipathR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OmnipathR’ version ‘3.16.2’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 35 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘OmnipathR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking whether startup messages can be suppressed ... NOTE
[2025-10-15 06:25:55] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-15 06:25:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-15 06:25:55] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-10-15 06:25:55] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-10-15 06:25:55] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-10-13
[2025-10-15 06:25:55] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-10-13 19:23:32 UTC; unix
[2025-10-15 06:25:55] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.16.2
[2025-10-15 06:25:55] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-10-15 06:25:56] [INFO]    [OmnipathR] Session info: [version=R version 4.5.1 Patched (2025-06-14 r88325); os=macOS Ventura 13.7.5; system=aarch64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-10-15; pandoc=3.6.4 @ /opt/homebrew/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto]
[2025-10-15 06:25:56] [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=70.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-10-15 06:25:56] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.3(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 2.2.0(2025-10-13); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.16.2(2025-10-13); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.3.3(2025-05-29); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.3(2025-08-20); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.2(2025-09-08); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.53(2025-08-19); XML 3.99-0.19(2025-08-22); xml2 1.4.0(2025-08-20); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-10-15 06:25:56] [INFO]    [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: 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
[2025-10-15 06:25:56] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-10-15 06:25:56] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-10-15 06:25:56] [TRACE]   [OmnipathR] Contains 1 files.
[2025-10-15 06:25:56] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-10-15 06:25:56] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-15 06:25:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-15 06:25:56] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-10-15 06:25:56] [TRACE]   [OmnipathR] Pandoc version: `3.6.4`.
[2025-10-15 06:25:56] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-10-15 06:25:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-15 06:25:57] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-10-15 06:25:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-15 06:25:57] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-10-15 06:25:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-15 06:25:57] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-10-15 06:25:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-15 06:25:57] [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
[2025-10-15 06:26:18] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-15 06:26:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-15 06:26:18] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-10-15 06:26:18] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-10-15 06:26:18] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-10-13
[2025-10-15 06:26:18] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-10-13 19:23:32 UTC; unix
[2025-10-15 06:26:18] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.16.2
[2025-10-15 06:26:18] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-10-15 06:26:19] [INFO]    [OmnipathR] Session info: [version=R version 4.5.1 Patched (2025-06-14 r88325); os=macOS Ventura 13.7.5; system=aarch64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-10-15; pandoc=3.6.4 @ /opt/homebrew/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto]
[2025-10-15 06:26:19] [INFO]    [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; 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=70.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-10-15 06:26:19] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.3(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 2.2.0(2025-10-13); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.16.2(2025-10-13); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.3.3(2025-05-29); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.3(2025-08-20); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.2(2025-09-08); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.53(2025-08-19); XML 3.99-0.19(2025-08-22); xml2 1.4.0(2025-08-20); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-10-15 06:26:19] [INFO]    [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: aarch64-apple-darwin23.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2025-10-15 06:26:19] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-10-15 06:26:19] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-10-15 06:26:19] [TRACE]   [OmnipathR] Contains 1 files.
[2025-10-15 06:26:19] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-10-15 06:26:20] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-15 06:26:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-15 06:26:20] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-10-15 06:26:20] [TRACE]   [OmnipathR] Pandoc version: `3.6.4`.
[2025-10-15 06:26:20] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-10-15 06:26:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-15 06:26:20] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-10-15 06:26:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-15 06:26:20] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-10-15 06:26:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-15 06:26:20] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-10-15 06:26:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-15 06:26:20] [TRACE]   [OmnipathR] Cache locked: FALSE
* 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                111.192  0.232 111.700
curated_ligrec_stats                  35.139  3.892  48.678
omnipath-interactions                 31.987  3.365  38.150
filter_extra_attrs                    26.693  7.951  36.967
extra_attrs_to_cols                   16.585  2.141  19.713
nichenet_gr_network_omnipath          16.173  1.672  18.103
extra_attr_values                     13.878  2.478  17.643
go_annot_download                     14.797  0.939  15.418
with_extra_attrs                      12.602  1.966  15.061
pivot_annotations                     12.252  0.877  13.382
giant_component                       12.077  0.852  13.274
nichenet_signaling_network_omnipath   11.407  1.156  12.910
has_extra_attrs                        9.415  1.701  11.791
omnipath_for_cosmos                    9.906  0.921  31.068
extra_attrs                            8.661  1.959  11.226
filter_by_resource                     9.858  0.517  10.894
translate_ids_multi                    9.500  0.773  27.181
static_table                           7.771  0.551   8.280
filter_intercell                       7.516  0.468   8.160
curated_ligand_receptor_interactions   6.449  1.077   8.569
find_all_paths                         6.211  0.392   6.671
print_interactions                     5.834  0.543   6.915
signed_ptms                            5.329  0.230   5.748
ensembl_id_mapping_table               2.710  0.206  20.641
all_uniprots                           1.634  0.273  18.705
kegg_conv                              1.530  0.239  12.099
uniprot_full_id_mapping_table          1.116  0.308  13.926
translate_ids                          1.139  0.234  11.064
kegg_rm_prefix                         0.864  0.092   5.573
kegg_link                              0.824  0.106   6.062
* 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-3.21-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-arm64/Resources/library’
* installing *source* package ‘OmnipathR’ ...
** this is package ‘OmnipathR’ version ‘3.16.2’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
[2025-10-13 15:23:48] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-13 15:23:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-13 15:23:48] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-10-13 15:23:48] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-10-13 15:23:48] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-10-13
[2025-10-13 15:23:48] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-10-13 19:23:32 UTC; unix
[2025-10-13 15:23:48] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.16.2
[2025-10-13 15:23:48] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-10-13 15:23:49] [INFO]    [OmnipathR] Session info: [version=R version 4.5.1 Patched (2025-06-14 r88325); os=macOS Ventura 13.7.5; system=aarch64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-10-13; pandoc=3.6.4 @ /opt/homebrew/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto]
[2025-10-13 15:23:50] [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=8.6.13; 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=70.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-10-13 15:23:50] [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 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.3(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 2.2.0(2025-10-13); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.16.2(2025-10-13); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.3.3(2025-05-29); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.3(2025-08-20); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.2(2025-09-08); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.53(2025-08-19); XML 3.99-0.19(2025-08-22); xml2 1.4.0(2025-08-20); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-10-13 15:23:50] [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
[2025-10-13 15:23:50] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-10-13 15:23:50] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-10-13 15:23:50] [TRACE]   [OmnipathR] Contains 1 files.
[2025-10-13 15:23:50] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-10-13 15:23:50] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-13 15:23:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-13 15:23:50] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-10-13 15:23:50] [TRACE]   [OmnipathR] Pandoc version: `3.6.4`.
[2025-10-13 15:23:50] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-10-13 15:23:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-13 15:23:50] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-10-13 15:23:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-13 15:23:50] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-10-13 15:23:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-13 15:23:50] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-10-13 15:23:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-13 15:23:50] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2025-10-13 15:23:52] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-13 15:23:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-13 15:23:52] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-10-13 15:23:52] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-10-13 15:23:52] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-10-13
[2025-10-13 15:23:52] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-10-13 19:23:32 UTC; unix
[2025-10-13 15:23:52] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.16.2
[2025-10-13 15:23:52] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-10-13 15:23:53] [INFO]    [OmnipathR] Session info: [version=R version 4.5.1 Patched (2025-06-14 r88325); os=macOS Ventura 13.7.5; system=aarch64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-10-13; pandoc=3.6.4 @ /opt/homebrew/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto]
[2025-10-13 15:23:53] [INFO]    [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.44 2024-06-07; ICU=70.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-10-13 15:23:54] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.3(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 2.2.0(2025-10-13); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.16.2(2025-10-13); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.3.3(2025-05-29); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.3(2025-08-20); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.2(2025-09-08); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.53(2025-08-19); XML 3.99-0.19(2025-08-22); xml2 1.4.0(2025-08-20); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-10-13 15:23:54] [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
[2025-10-13 15:23:54] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-10-13 15:23:54] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-10-13 15:23:54] [TRACE]   [OmnipathR] Contains 1 files.
[2025-10-13 15:23:54] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-10-13 15:23:54] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-13 15:23:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-13 15:23:54] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-10-13 15:23:54] [TRACE]   [OmnipathR] Pandoc version: `3.6.4`.
[2025-10-13 15:23:54] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-10-13 15:23:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-13 15:23:54] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-10-13 15:23:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-13 15:23:54] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-10-13 15:23:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-13 15:23:54] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-10-13 15:23:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-13 15:23:54] [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 Patched (2025-06-14 r88325) -- "Great Square Root"
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)
[2025-10-15 06:38:05] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-15 06:38:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-15 06:38:05] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-10-15 06:38:05] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-10-15 06:38:05] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-10-13
[2025-10-15 06:38:05] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-10-13 19:23:32 UTC; unix
[2025-10-15 06:38:05] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.16.2
[2025-10-15 06:38:05] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-10-15 06:38:06] [INFO]    [OmnipathR] Session info: [version=R version 4.5.1 Patched (2025-06-14 r88325); os=macOS Ventura 13.7.5; system=aarch64, darwin20; ui=X11; language=C; collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-10-15; pandoc=3.6.4 @ /opt/homebrew/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto]
[2025-10-15 06:38:06] [INFO]    [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; 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=70.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-10-15 06:38:07] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); brio 1.1.5(2024-04-24); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.3(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 2.2.0(2025-10-13); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.16.2(2025-10-13); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.3.3(2025-05-29); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.3(2025-08-20); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.2(2025-09-08); testthat 3.2.3(2025-01-13); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.53(2025-08-19); XML 3.99-0.19(2025-08-22); xml2 1.4.0(2025-08-20); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-10-15 06:38:07] [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
[2025-10-15 06:38:07] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-10-15 06:38:07] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-10-15 06:38:07] [TRACE]   [OmnipathR] Contains 21 files.
[2025-10-15 06:38:07] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-10-15 06:38:07] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-15 06:38:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-15 06:38:07] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-10-15 06:38:07] [TRACE]   [OmnipathR] Pandoc version: `3.6.4`.
[2025-10-15 06:38:07] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-10-15 06:38:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-15 06:38:07] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-10-15 06:38:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-15 06:38:07] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-10-15 06:38:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-15 06:38:07] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-10-15 06:38:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-15 06:38:07] [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 
 14.945   2.009  20.646 

Example timings

OmnipathR.Rcheck/OmnipathR-Ex.timings

nameusersystemelapsed
OmnipathR000
all_uniprot_acs0.0150.0030.019
all_uniprots 1.634 0.27318.705
ancestors0.0080.0010.009
annotated_network1.2070.1211.675
annotation_categories111.192 0.232111.700
annotation_resources0.0650.0080.279
annotations0.5830.0570.757
biomart_query1.2680.1412.205
bioplex10.0130.0030.024
bioplex20.0120.0020.024
bioplex30.0140.0020.022
bioplex_all0.0120.0020.018
bioplex_hct116_10.0120.0020.020
bma_motif_es0.7040.0771.158
bma_motif_vs0.2190.0300.313
chalmers_gem0.0100.0020.012
chalmers_gem_id_mapping_table0.0090.0020.012
chalmers_gem_id_type0.0030.0010.003
chalmers_gem_metabolites0.0100.0020.012
chalmers_gem_network0.0100.0020.012
chalmers_gem_raw0.0100.0020.012
chalmers_gem_reactions0.0090.0010.011
common_name0.0420.0030.045
complex_genes0.7640.0670.950
complex_resources0.0680.0070.132
complexes0.1850.0170.409
consensuspathdb_download000
consensuspathdb_raw_table0.0080.0020.009
cosmos_pkn000
curated_ligand_receptor_interactions6.4491.0778.569
curated_ligrec_stats35.139 3.89248.678
database_summary1.1230.1471.364
descendants0.0090.0020.011
ensembl_dataset0.0140.0010.015
ensembl_id_mapping_table 2.710 0.20620.641
ensembl_id_type0.0020.0000.003
ensembl_name0.0760.0050.082
ensembl_organisms0.1780.0220.203
ensembl_organisms_raw0.1260.0190.147
ensembl_orthology0.0000.0010.000
enzsub_graph2.2510.1742.759
enzsub_resources0.0620.0090.139
enzyme_substrate1.0700.0621.188
evex_download0.0100.0020.012
evidences0.0000.0010.000
extra_attr_values13.878 2.47817.643
extra_attrs 8.661 1.95911.226
extra_attrs_to_cols16.585 2.14119.713
filter_by_resource 9.858 0.51710.894
filter_extra_attrs26.693 7.95136.967
filter_intercell7.5160.4688.160
filter_intercell_network0.0170.0030.020
find_all_paths6.2110.3926.671
from_evidences0.0000.0000.001
get_db0.0000.0000.001
get_ontology_db0.0100.0020.013
giant_component12.077 0.85213.274
go_annot_download14.797 0.93915.418
go_annot_slim0.0000.0010.001
go_ontology_download0.0090.0020.010
guide2pharma_download0.0080.0020.010
harmonizome_download0.0070.0020.009
has_extra_attrs 9.415 1.70111.791
hmdb_id_mapping_table0.0090.0020.013
hmdb_id_type0.0030.0010.004
hmdb_metabolite_fields0.0010.0010.000
hmdb_protein_fields0.0000.0010.001
hmdb_table0.0100.0020.013
homologene_download0.0080.0020.010
homologene_raw0.0240.0030.029
homologene_uniprot_orthology0.0100.0020.012
hpo_download3.3920.3324.858
htridb_download0.0110.0020.014
id_translation_resources0.0000.0010.000
id_types0.0560.0100.071
inbiomap_download000
inbiomap_raw000
interaction_datasets0.7010.1030.870
interaction_graph0.4140.0500.530
interaction_resources0.0660.0150.136
interaction_types0.0950.0100.108
intercell0.8910.1351.113
intercell_categories0.6360.0900.791
intercell_consensus_filter1.0630.1651.270
intercell_generic_categories0.0480.0090.058
intercell_network0.0100.0020.013
intercell_resources0.0670.0160.152
intercell_summary0.0620.0230.088
is_ontology_id000
is_swissprot0.0340.0060.044
is_trembl0.0320.0060.041
is_uniprot0.0120.0020.015
kegg_api_templates0.0010.0020.004
kegg_conv 1.530 0.23912.099
kegg_databases0.0000.0010.001
kegg_ddi0.7490.0952.461
kegg_find0.7510.0982.760
kegg_info0.0110.0030.015
kegg_link0.8240.1066.062
kegg_list0.7390.0891.996
kegg_open0.0100.0020.012
kegg_operations0.0000.0010.000
kegg_organism_codes0.0240.0670.094
kegg_organisms0.0280.0070.040
kegg_pathway_annotations000
kegg_pathway_download0.0110.0020.015
kegg_pathway_list0.0090.0020.011
kegg_pathways_download0.0000.0010.000
kegg_picture1.2620.0603.413
kegg_process0.0120.0020.017
kegg_query0.0040.0000.005
kegg_request0.0690.0100.085
kegg_rm_prefix0.8640.0925.573
latin_name0.0830.0050.093
load_db0.0810.0140.101
metalinksdb_sqlite1.0400.2061.471
metalinksdb_table0.1880.0380.258
metalinksdb_tables0.0120.0040.019
ncbi_taxid0.0570.0060.065
nichenet_build_model0.0000.0000.001
nichenet_expression_data0.0050.0020.007
nichenet_gr_network0.0140.0030.018
nichenet_gr_network_evex0.0060.0010.008
nichenet_gr_network_harmonizome0.0090.0020.011
nichenet_gr_network_htridb0.0080.0030.011
nichenet_gr_network_omnipath16.173 1.67218.103
nichenet_gr_network_pathwaycommons0.0090.0020.012
nichenet_gr_network_regnetwork0.0080.0010.010
nichenet_gr_network_remap0.0080.0020.010
nichenet_gr_network_trrust0.0080.0020.011
nichenet_ligand_activities0.0000.0010.000
nichenet_ligand_target_links0.0010.0010.001
nichenet_ligand_target_matrix0.0000.0010.000
nichenet_lr_network0.0250.0050.031
nichenet_lr_network_guide2pharma0.0100.0020.012
nichenet_lr_network_omnipath0.0260.0050.031
nichenet_lr_network_ramilowski0.0520.0020.054
nichenet_main0.0000.0010.000
nichenet_networks0.0380.0110.049
nichenet_optimization0.0010.0000.000
nichenet_remove_orphan_ligands0.0260.0050.032
nichenet_results_dir0.0010.0010.001
nichenet_signaling_network0.0270.0060.033
nichenet_signaling_network_cpdb0.0090.0020.011
nichenet_signaling_network_evex0.0080.0010.010
nichenet_signaling_network_harmonizome0.0080.0020.010
nichenet_signaling_network_inbiomap000
nichenet_signaling_network_omnipath11.407 1.15612.910
nichenet_signaling_network_pathwaycommons0.0110.0020.015
nichenet_signaling_network_vinayagam0.0100.0030.014
nichenet_test000
nichenet_workarounds000
obo_parser0.1760.0220.387
oma_code0.0510.0040.058
oma_organisms0.0920.0140.114
oma_pairwise0.0120.0030.014
oma_pairwise_genesymbols0.0120.0030.015
oma_pairwise_translated0.0110.0020.013
omnipath-interactions31.987 3.36538.150
omnipath_cache_autoclean000
omnipath_cache_clean0.0130.0060.020
omnipath_cache_clean_db0.1120.0380.196
omnipath_cache_download_ready0.6410.1960.862
omnipath_cache_filter_versions0.1190.0440.168
omnipath_cache_get0.1120.0350.152
omnipath_cache_key0.0020.0010.003
omnipath_cache_latest_or_new0.1130.0250.143
omnipath_cache_load0.4550.0490.747
omnipath_cache_move_in0.1200.0400.172
omnipath_cache_remove0.0790.0260.111
omnipath_cache_save0.1340.0350.183
omnipath_cache_search0.0000.0000.001
omnipath_cache_set_ext0.0880.0300.127
omnipath_cache_update_status0.1090.0300.144
omnipath_cache_wipe000
omnipath_config_path0.0010.0010.001
omnipath_for_cosmos 9.906 0.92131.068
omnipath_load_config0.0010.0000.000
omnipath_log0.0000.0000.001
omnipath_logfile0.0020.0010.003
omnipath_msg0.0060.0020.009
omnipath_query3.9140.2534.289
omnipath_reset_config0.0000.0000.001
omnipath_save_config000
omnipath_set_cachedir0.0310.0070.040
omnipath_set_console_loglevel0.0040.0000.005
omnipath_set_logfile_loglevel0.0030.0000.005
omnipath_set_loglevel0.0020.0000.002
omnipath_show_db0.0760.0200.103
omnipath_unlock_cache_db0.0000.0000.001
only_from000
ontology_ensure_id0.0010.0000.000
ontology_ensure_name0.0000.0010.001
ontology_name_id0.0000.0000.001
organism_for0.0560.0060.067
pathwaycommons_download0.0000.0000.001
pivot_annotations12.252 0.87713.382
preppi_download0.0000.0010.001
preppi_filter0.0000.0000.001
print_bma_motif_es0.5170.0830.675
print_bma_motif_vs0.1360.0190.237
print_interactions5.8340.5436.915
print_path_es1.0110.1271.469
print_path_vs2.3600.3213.178
pubmed_open4.3770.3064.908
query_info0.4440.0590.580
ramilowski_download0.0000.0010.001
ramp_id_mapping_table0.0000.0000.001
ramp_id_type0.0030.0010.004
ramp_sqlite000
ramp_table0.0010.0000.000
ramp_tables000
regnetwork_directions0.0000.0000.001
regnetwork_download0.0000.0000.001
relations_list_to_table0.0960.0220.134
relations_table_to_graph0.0010.0000.000
relations_table_to_list0.0830.0200.133
remap_dorothea_download0.0010.0000.001
remap_filtered0.0000.0000.001
remap_tf_target_download0.0000.0010.001
resource_info0.4500.0820.582
resources0.0540.0080.133
resources_colname0.9440.0751.094
resources_in3.7930.2604.151
show_network000
signed_ptms5.3290.2305.748
simplify_intercell_network0.0010.0000.001
static_table7.7710.5518.280
static_tables0.0680.0180.105
stitch_actions0.0000.0000.001
stitch_links0.0000.0010.001
stitch_network0.0000.0000.001
stitch_remove_prefixes0.0090.0020.012
swap_relations0.0920.0210.119
swissprots_only0.0430.0050.049
tfcensus_download0.6450.1210.863
translate_ids 1.139 0.23411.064
translate_ids_multi 9.500 0.77327.181
trembls_only0.0450.0030.053
trrust_download0.0010.0000.001
uniprot_full_id_mapping_table 1.116 0.30813.926
uniprot_genesymbol_cleanup0.0000.0010.000
uniprot_id_mapping_table0.0010.0010.001
uniprot_id_type0.0020.0010.003
uniprot_idmapping_id_types0.5240.0520.740
unique_intercell_network0.0010.0000.001
unnest_evidences0.0000.0000.001
uploadlists_id_type0.0030.0000.003
vinayagam_download0.0010.0000.001
walk_ontology_tree0.0010.0000.002
with_extra_attrs12.602 1.96615.061
with_references0.8940.0751.090
zenodo_download0.0020.0000.002