Denes Turei
| Snapshot Date: 2025-11-17 13:45 -0500 (Mon, 17 Nov 2025) |
| git_url: https://git.bioconductor.org/packages/OmnipathR |
| git_branch: RELEASE_3_22 |
| git_last_commit: 7ab5630 |
| git_last_commit_date: 2025-11-17 12:48:40 -0500 (Mon, 17 Nov 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-11-20 12:05 -0500 (Thu, 20 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4615 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.2 Patched (2025-11-05 r88990) -- "[Not] Part in a Rumble" | 4610 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble" | 4598 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4668 |
| 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 1505/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| OmnipathR 3.18.2 (landing page) Denes Turei
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | ERROR | ||||||||||
|
To the developers/maintainers of the OmnipathR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/OmnipathR.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: OmnipathR |
| Version: 3.18.2 |
| 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_3.18.2.tar.gz |
| StartedAt: 2025-11-18 11:30:39 -0500 (Tue, 18 Nov 2025) |
| EndedAt: 2025-11-18 11:59:59 -0500 (Tue, 18 Nov 2025) |
| EllapsedTime: 1760.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: OmnipathR.Rcheck |
| Warnings: 0 |
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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_3.18.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/OmnipathR.Rcheck’
* using R version 4.5.2 Patched (2025-11-05 r88990)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OmnipathR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OmnipathR’ version ‘3.18.2’
* 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
[2025-11-18 11:31:39] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-18 11:31:39] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-18 11:31:39] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-11-18 11:31:39] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-11-18 11:31:39] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-11-17
[2025-11-18 11:31:39] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2025-11-17 22:02:15 UTC; unix
[2025-11-18 11:31:39] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.2
[2025-11-18 11:31:39] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-11-18 11:31:40] [INFO] [OmnipathR] Session info: [version=R version 4.5.2 Patched (2025-11-05 r88990); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-11-18; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto]
[2025-11-18 11:31:40] [INFO] [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.44 2024-06-07; ICU=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-11-18 11:31:41] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); digest 0.6.38(2025-11-12); dplyr 1.1.4(2023-11-17); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.4(2025-10-17); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.2.1(2025-10-27); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.18.2(2025-11-17); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.0(2025-11-04); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); readr 2.1.6(2025-11-14); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.4(2025-11-10); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.54(2025-10-30); XML 3.99-0.20(2025-11-08); xml2 1.5.0(2025-11-17); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-11-18 11:31:41] [INFO] [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: x86_64-apple-darwin22.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2025-11-18 11:31:41] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-11-18 11:31:41] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-11-18 11:31:41] [TRACE] [OmnipathR] Contains 1 files.
[2025-11-18 11:31:41] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-11-18 11:31:41] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-18 11:31:41] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-18 11:31:41] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-11-18 11:31:41] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-11-18 11:31:41] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-11-18 11:31:41] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-18 11:31:41] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-11-18 11:31:41] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-18 11:31:41] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-11-18 11:31:41] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-18 11:31:41] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-11-18 11:31:41] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-18 11:31:41] [TRACE] [OmnipathR] Cache locked: FALSE
It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
[2025-11-18 11:32:23] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-18 11:32:23] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-18 11:32:23] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-11-18 11:32:23] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-11-18 11:32:23] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-11-17
[2025-11-18 11:32:23] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2025-11-17 22:02:15 UTC; unix
[2025-11-18 11:32:23] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.2
[2025-11-18 11:32:23] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-11-18 11:32:24] [INFO] [OmnipathR] Session info: [version=R version 4.5.2 Patched (2025-11-05 r88990); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-11-18; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto]
[2025-11-18 11:32:24] [INFO] [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.44 2024-06-07; ICU=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-11-18 11:32:24] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); digest 0.6.38(2025-11-12); dplyr 1.1.4(2023-11-17); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.4(2025-10-17); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.2.1(2025-10-27); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.18.2(2025-11-17); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.0(2025-11-04); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); readr 2.1.6(2025-11-14); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.4(2025-11-10); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.54(2025-10-30); XML 3.99-0.20(2025-11-08); xml2 1.5.0(2025-11-17); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-11-18 11:32:24] [INFO] [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: x86_64-apple-darwin22.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2025-11-18 11:32:24] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-11-18 11:32:24] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-11-18 11:32:24] [TRACE] [OmnipathR] Contains 1 files.
[2025-11-18 11:32:24] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-11-18 11:32:25] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-18 11:32:25] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-18 11:32:25] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-11-18 11:32:25] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-11-18 11:32:25] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-11-18 11:32:25] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-18 11:32:25] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-11-18 11:32:25] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-18 11:32:25] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-11-18 11:32:25] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-18 11:32:25] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-11-18 11:32:25] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-18 11:32:25] [TRACE] [OmnipathR] Cache locked: FALSE
cosmos_ksn: no visible binding for global variable ‘enzyme_genesymbol’
Undefined global functions or variables:
enzyme_genesymbol
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
annotation_categories 97.233 0.419 100.801
filter_extra_attrs 72.815 18.763 144.771
curated_ligrec_stats 74.753 7.663 141.721
omnipath-interactions 68.016 5.116 87.848
all_uniprots 50.699 5.143 73.439
uniprot_organisms 42.708 4.492 48.493
extra_attrs_to_cols 39.890 6.469 55.813
extra_attr_values 35.524 6.074 48.342
nichenet_gr_network_omnipath 38.373 2.869 42.320
with_extra_attrs 33.549 5.932 40.143
nichenet_signaling_network_omnipath 27.506 1.902 30.827
extra_attrs 21.576 4.911 32.310
giant_component 24.251 2.012 27.063
has_extra_attrs 20.506 5.118 34.065
filter_by_resource 22.344 1.242 25.573
go_annot_download 20.920 2.606 21.384
omnipath_for_cosmos 20.844 1.432 38.768
pivot_annotations 17.429 1.884 20.863
translate_ids_multi 16.579 0.988 32.945
find_all_paths 15.301 0.792 16.837
print_interactions 15.036 0.972 18.127
curated_ligand_receptor_interactions 12.911 1.965 21.924
signed_ptms 12.886 0.518 15.002
filter_intercell 11.168 1.093 19.073
pubmed_open 10.537 0.494 11.912
omnipath_query 10.054 0.457 10.856
static_table 9.631 0.803 10.970
resources_in 9.927 0.395 11.368
print_path_vs 5.468 0.499 8.085
hpo_download 4.644 0.731 13.325
enzsub_graph 4.973 0.346 6.860
ensembl_id_mapping_table 3.607 0.414 20.864
database_summary 3.251 0.336 5.167
intercell_consensus_filter 2.601 0.269 5.056
kegg_conv 2.429 0.300 9.446
kinasephos 1.846 0.246 19.510
translate_ids 1.830 0.222 11.793
uniprot_full_id_mapping_table 1.780 0.260 13.174
kegg_link 1.275 0.144 5.303
tfcensus_download 0.863 0.110 7.203
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.22-bioc/meat/OmnipathR.Rcheck/00check.log’
for details.
OmnipathR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL OmnipathR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’ * installing *source* package ‘OmnipathR’ ... ** this is package ‘OmnipathR’ version ‘3.18.2’ ** 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 [2025-11-17 17:02:42] [INFO] [OmnipathR] Setting up new cache directory `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-11-17 17:02:42] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-11-17 17:02:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-11-17 17:02:42] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-11-17 17:02:42] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-11-17 17:02:42] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-11-17 [2025-11-17 17:02:42] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2025-11-17 22:02:15 UTC; unix [2025-11-17 17:02:42] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.2 [2025-11-17 17:02:42] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22 [2025-11-17 17:02:45] [INFO] [OmnipathR] Session info: [version=R version 4.5.2 Patched (2025-11-05 r88990); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-11-17; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto] [2025-11-17 17:02:46] [INFO] [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.44 2024-06-07; ICU=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1] [2025-11-17 17:02:46] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); digest 0.6.38(2025-11-12); dplyr 1.1.4(2023-11-17); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.4(2025-10-17); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.2.1(2025-10-27); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.18.2(2025-11-17); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.0(2025-11-04); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); readr 2.1.6(2025-11-14); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.4(2025-11-10); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.54(2025-10-30); XML 3.99-0.20(2025-11-08); xml2 1.5.0(2025-11-17); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13) [2025-11-17 17:02:46] [INFO] [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: x86_64-apple-darwin22.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE [2025-11-17 17:02:46] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-11-17 17:02:46] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-11-17 17:02:46] [TRACE] [OmnipathR] Contains 1 files. [2025-11-17 17:02:46] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-11-17 17:02:46] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-11-17 17:02:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-11-17 17:02:46] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-11-17 17:02:46] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-11-17 17:02:46] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-11-17 17:02:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-11-17 17:02:46] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-11-17 17:02:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-11-17 17:02:46] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-11-17 17:02:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-11-17 17:02:46] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-11-17 17:02:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-11-17 17:02:46] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2025-11-17 17:02:50] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-11-17 17:02:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-11-17 17:02:50] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-11-17 17:02:50] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-11-17 17:02:50] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-11-17 [2025-11-17 17:02:50] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2025-11-17 22:02:15 UTC; unix [2025-11-17 17:02:50] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.2 [2025-11-17 17:02:50] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22 [2025-11-17 17:02:51] [INFO] [OmnipathR] Session info: [version=R version 4.5.2 Patched (2025-11-05 r88990); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-11-17; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto] [2025-11-17 17:02:51] [INFO] [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.44 2024-06-07; ICU=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1] [2025-11-17 17:02:51] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); digest 0.6.38(2025-11-12); dplyr 1.1.4(2023-11-17); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.4(2025-10-17); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.2.1(2025-10-27); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.18.2(2025-11-17); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.0(2025-11-04); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); readr 2.1.6(2025-11-14); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.4(2025-11-10); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.54(2025-10-30); XML 3.99-0.20(2025-11-08); xml2 1.5.0(2025-11-17); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13) [2025-11-17 17:02:51] [INFO] [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: x86_64-apple-darwin22.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE [2025-11-17 17:02:51] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-11-17 17:02:51] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-11-17 17:02:51] [TRACE] [OmnipathR] Contains 1 files. [2025-11-17 17:02:51] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-11-17 17:02:51] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-11-17 17:02:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-11-17 17:02:51] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-11-17 17:02:51] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-11-17 17:02:51] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-11-17 17:02:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-11-17 17:02:51] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-11-17 17:02:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-11-17 17:02:51] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-11-17 17:02:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-11-17 17:02:52] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-11-17 17:02:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-11-17 17:02:52] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package keeps a record of temporary installation path * DONE (OmnipathR)
OmnipathR.Rcheck/tests/testthat.Rout
R version 4.5.2 Patched (2025-11-05 r88990) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
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> #!/usr/bin/env Rscript
>
> #
> # This file is part of the `OmnipathR` R package
> #
> # Copyright
> # 2018-2024
> # Saez Lab, Uniklinik RWTH Aachen, Heidelberg University
> #
> # File author(s): Alberto Valdeolivas
> # Dénes Türei (turei.denes@gmail.com)
> # Attila Gábor
> #
> # Distributed under the MIT (Expat) License.
> # See accompanying file `LICENSE` or find a copy at
> # https://directory.fsf.org/wiki/License:Expat
> #
> # Website: https://r.omnipathdb.org/
> # Git repo: https://github.com/saezlab/OmnipathR
> #
>
>
> library(testthat)
> library(OmnipathR)
[2025-11-18 11:57:32] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-18 11:57:32] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-18 11:57:32] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-11-18 11:57:32] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-11-18 11:57:32] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-11-17
[2025-11-18 11:57:32] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2025-11-17 22:02:15 UTC; unix
[2025-11-18 11:57:32] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.2
[2025-11-18 11:57:32] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-11-18 11:57:33] [INFO] [OmnipathR] Session info: [version=R version 4.5.2 Patched (2025-11-05 r88990); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=C; collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-11-18; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto]
[2025-11-18 11:57:34] [INFO] [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.44 2024-06-07; ICU=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-11-18 11:57:34] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); brio 1.1.5(2024-04-24); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); digest 0.6.38(2025-11-12); dplyr 1.1.4(2023-11-17); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.4(2025-10-17); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.2.1(2025-10-27); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.18.2(2025-11-17); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.0(2025-11-04); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); readr 2.1.6(2025-11-14); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.4(2025-11-10); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); testthat 3.3.0(2025-11-13); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.54(2025-10-30); XML 3.99-0.20(2025-11-08); xml2 1.5.0(2025-11-17); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-11-18 11:57:34] [INFO] [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: x86_64-apple-darwin22.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2025-11-18 11:57:34] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-11-18 11:57:34] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-11-18 11:57:34] [TRACE] [OmnipathR] Contains 22 files.
[2025-11-18 11:57:34] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-11-18 11:57:34] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-18 11:57:34] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-18 11:57:34] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-11-18 11:57:34] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-11-18 11:57:34] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-11-18 11:57:34] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-18 11:57:34] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-11-18 11:57:34] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-18 11:57:34] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-11-18 11:57:34] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-18 11:57:34] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-11-18 11:57:34] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-18 11:57:34] [TRACE] [OmnipathR] Cache locked: FALSE
>
> test_check('OmnipathR')
[ FAIL 0 | WARN 12 | SKIP 0 | PASS 38 ]
[ FAIL 0 | WARN 12 | SKIP 0 | PASS 38 ]
>
> proc.time()
user system elapsed
88.842 10.515 121.165
OmnipathR.Rcheck/OmnipathR-Ex.timings
| name | user | system | elapsed | |
| OmnipathR | 0.001 | 0.001 | 0.002 | |
| all_uniprot_acs | 0.038 | 0.005 | 0.043 | |
| all_uniprots | 50.699 | 5.143 | 73.439 | |
| ancestors | 0.020 | 0.003 | 0.022 | |
| annotated_network | 2.267 | 0.220 | 4.606 | |
| annotation_categories | 97.233 | 0.419 | 100.801 | |
| annotation_resources | 0.134 | 0.021 | 0.798 | |
| annotations | 0.956 | 0.085 | 1.838 | |
| biomart_query | 2.088 | 0.272 | 3.432 | |
| bioplex1 | 0.019 | 0.003 | 0.022 | |
| bioplex2 | 0.019 | 0.003 | 0.022 | |
| bioplex3 | 0.018 | 0.003 | 0.021 | |
| bioplex_all | 0.019 | 0.003 | 0.022 | |
| bioplex_hct116_1 | 0.019 | 0.003 | 0.022 | |
| bma_motif_es | 1.043 | 0.115 | 2.117 | |
| bma_motif_vs | 0.412 | 0.044 | 1.115 | |
| chalmers_gem | 0.018 | 0.003 | 0.021 | |
| chalmers_gem_id_mapping_table | 0.019 | 0.003 | 0.021 | |
| chalmers_gem_id_type | 0.004 | 0.001 | 0.005 | |
| chalmers_gem_metabolites | 0.020 | 0.003 | 0.022 | |
| chalmers_gem_network | 0.019 | 0.002 | 0.022 | |
| chalmers_gem_raw | 0.019 | 0.003 | 0.022 | |
| chalmers_gem_reactions | 0.019 | 0.002 | 0.022 | |
| common_name | 0.202 | 0.012 | 0.214 | |
| complex_genes | 1.189 | 0.111 | 2.590 | |
| complex_resources | 0.132 | 0.016 | 0.749 | |
| complexes | 0.341 | 0.032 | 0.853 | |
| consensuspathdb_download | 0.000 | 0.001 | 0.001 | |
| consensuspathdb_raw_table | 0.020 | 0.004 | 0.024 | |
| cosmos_pkn | 0.000 | 0.001 | 0.001 | |
| curated_ligand_receptor_interactions | 12.911 | 1.965 | 21.924 | |
| curated_ligrec_stats | 74.753 | 7.663 | 141.721 | |
| database_summary | 3.251 | 0.336 | 5.167 | |
| descendants | 0.018 | 0.002 | 0.022 | |
| ensembl_dataset | 0.081 | 0.002 | 0.084 | |
| ensembl_id_mapping_table | 3.607 | 0.414 | 20.864 | |
| ensembl_id_type | 0.004 | 0.001 | 0.006 | |
| ensembl_name | 0.735 | 0.029 | 0.806 | |
| ensembl_organisms | 0.300 | 0.046 | 0.548 | |
| ensembl_organisms_raw | 0.295 | 0.046 | 0.486 | |
| ensembl_orthology | 0.000 | 0.002 | 0.002 | |
| enzsub_graph | 4.973 | 0.346 | 6.860 | |
| enzsub_resources | 0.131 | 0.015 | 0.744 | |
| enzyme_substrate | 2.873 | 0.127 | 3.793 | |
| evex_download | 0.022 | 0.005 | 0.046 | |
| evidences | 0.000 | 0.001 | 0.001 | |
| extra_attr_values | 35.524 | 6.074 | 48.342 | |
| extra_attrs | 21.576 | 4.911 | 32.310 | |
| extra_attrs_to_cols | 39.890 | 6.469 | 55.813 | |
| filter_by_resource | 22.344 | 1.242 | 25.573 | |
| filter_extra_attrs | 72.815 | 18.763 | 144.771 | |
| filter_intercell | 11.168 | 1.093 | 19.073 | |
| filter_intercell_network | 0.039 | 0.006 | 0.046 | |
| find_all_paths | 15.301 | 0.792 | 16.837 | |
| from_evidences | 0.001 | 0.001 | 0.001 | |
| get_db | 0.001 | 0.001 | 0.001 | |
| get_ontology_db | 0.019 | 0.004 | 0.030 | |
| giant_component | 24.251 | 2.012 | 27.063 | |
| go_annot_download | 20.920 | 2.606 | 21.384 | |
| go_annot_slim | 0.001 | 0.001 | 0.001 | |
| go_ontology_download | 0.018 | 0.003 | 0.022 | |
| guide2pharma_download | 0.018 | 0.003 | 0.021 | |
| harmonizome_download | 0.018 | 0.003 | 0.021 | |
| has_extra_attrs | 20.506 | 5.118 | 34.065 | |
| hmdb_id_mapping_table | 0.020 | 0.003 | 0.023 | |
| hmdb_id_type | 0.005 | 0.001 | 0.006 | |
| hmdb_metabolite_fields | 0.001 | 0.002 | 0.002 | |
| hmdb_protein_fields | 0.001 | 0.001 | 0.001 | |
| hmdb_table | 0.023 | 0.004 | 0.072 | |
| homologene_download | 0.118 | 0.005 | 0.218 | |
| homologene_raw | 0.124 | 0.008 | 0.251 | |
| homologene_uniprot_orthology | 0.024 | 0.004 | 0.028 | |
| hpo_download | 4.644 | 0.731 | 13.325 | |
| htridb_download | 0.020 | 0.004 | 0.084 | |
| id_translation_resources | 0.000 | 0.000 | 0.001 | |
| id_types | 0.088 | 0.016 | 0.148 | |
| inbiomap_download | 0.000 | 0.001 | 0.000 | |
| inbiomap_raw | 0.000 | 0.001 | 0.001 | |
| interaction_datasets | 1.156 | 0.129 | 2.509 | |
| interaction_graph | 0.909 | 0.068 | 2.115 | |
| interaction_resources | 0.133 | 0.020 | 0.800 | |
| interaction_types | 0.136 | 0.012 | 0.179 | |
| intercell | 1.413 | 0.171 | 3.201 | |
| intercell_categories | 1.190 | 0.149 | 2.446 | |
| intercell_consensus_filter | 2.601 | 0.269 | 5.056 | |
| intercell_generic_categories | 0.149 | 0.014 | 0.191 | |
| intercell_network | 0.022 | 0.005 | 0.026 | |
| intercell_resources | 0.130 | 0.013 | 0.664 | |
| intercell_summary | 0.159 | 0.054 | 0.320 | |
| is_ontology_id | 0.000 | 0.000 | 0.001 | |
| is_swissprot | 0.112 | 0.009 | 0.200 | |
| is_trembl | 0.114 | 0.010 | 0.238 | |
| is_uniprot | 0.104 | 0.013 | 0.215 | |
| kegg_api_templates | 0.004 | 0.007 | 0.010 | |
| kegg_conv | 2.429 | 0.300 | 9.446 | |
| kegg_databases | 0.001 | 0.001 | 0.001 | |
| kegg_ddi | 1.114 | 0.127 | 3.152 | |
| kegg_find | 1.115 | 0.115 | 3.347 | |
| kegg_info | 0.019 | 0.002 | 0.022 | |
| kegg_link | 1.275 | 0.144 | 5.303 | |
| kegg_list | 1.139 | 0.127 | 2.801 | |
| kegg_open | 0.019 | 0.002 | 0.022 | |
| kegg_operations | 0.001 | 0.001 | 0.001 | |
| kegg_organism_codes | 0.067 | 0.188 | 0.445 | |
| kegg_organisms | 0.048 | 0.012 | 0.060 | |
| kegg_pathway_annotations | 0.000 | 0.000 | 0.001 | |
| kegg_pathway_download | 0.020 | 0.003 | 0.079 | |
| kegg_pathway_list | 0.019 | 0.003 | 0.021 | |
| kegg_pathways_download | 0.001 | 0.001 | 0.001 | |
| kegg_picture | 1.515 | 0.076 | 3.463 | |
| kegg_process | 0.040 | 0.006 | 0.046 | |
| kegg_query | 0.019 | 0.002 | 0.156 | |
| kegg_request | 0.131 | 0.017 | 0.209 | |
| kegg_rm_prefix | 1.361 | 0.151 | 4.817 | |
| kinasephos | 1.846 | 0.246 | 19.510 | |
| latin_name | 0.415 | 0.016 | 0.452 | |
| load_db | 0.182 | 0.039 | 0.255 | |
| metalinksdb_sqlite | 1.861 | 0.457 | 3.722 | |
| metalinksdb_table | 0.466 | 0.094 | 0.579 | |
| metalinksdb_tables | 0.034 | 0.007 | 0.043 | |
| ncbi_taxid | 0.424 | 0.017 | 0.447 | |
| nichenet_build_model | 0.000 | 0.001 | 0.001 | |
| nichenet_expression_data | 0.020 | 0.003 | 0.023 | |
| nichenet_gr_network | 0.056 | 0.009 | 0.065 | |
| nichenet_gr_network_evex | 0.019 | 0.003 | 0.022 | |
| nichenet_gr_network_harmonizome | 0.021 | 0.003 | 0.026 | |
| nichenet_gr_network_htridb | 0.019 | 0.003 | 0.022 | |
| nichenet_gr_network_omnipath | 38.373 | 2.869 | 42.320 | |
| nichenet_gr_network_pathwaycommons | 0.020 | 0.003 | 0.022 | |
| nichenet_gr_network_regnetwork | 0.020 | 0.003 | 0.022 | |
| nichenet_gr_network_remap | 0.020 | 0.003 | 0.022 | |
| nichenet_gr_network_trrust | 0.020 | 0.003 | 0.023 | |
| nichenet_ligand_activities | 0.000 | 0.001 | 0.002 | |
| nichenet_ligand_target_links | 0.001 | 0.002 | 0.003 | |
| nichenet_ligand_target_matrix | 0.000 | 0.001 | 0.001 | |
| nichenet_lr_network | 0.057 | 0.008 | 0.066 | |
| nichenet_lr_network_guide2pharma | 0.021 | 0.003 | 0.022 | |
| nichenet_lr_network_omnipath | 0.059 | 0.008 | 0.070 | |
| nichenet_lr_network_ramilowski | 0.020 | 0.002 | 0.023 | |
| nichenet_main | 0.000 | 0.001 | 0.001 | |
| nichenet_networks | 0.175 | 0.018 | 0.197 | |
| nichenet_optimization | 0.000 | 0.001 | 0.001 | |
| nichenet_remove_orphan_ligands | 0.060 | 0.007 | 0.069 | |
| nichenet_results_dir | 0.000 | 0.001 | 0.001 | |
| nichenet_signaling_network | 0.066 | 0.009 | 0.079 | |
| nichenet_signaling_network_cpdb | 0.020 | 0.003 | 0.023 | |
| nichenet_signaling_network_evex | 0.021 | 0.003 | 0.023 | |
| nichenet_signaling_network_harmonizome | 0.020 | 0.003 | 0.024 | |
| nichenet_signaling_network_inbiomap | 0.001 | 0.001 | 0.001 | |
| nichenet_signaling_network_omnipath | 27.506 | 1.902 | 30.827 | |
| nichenet_signaling_network_pathwaycommons | 0.020 | 0.003 | 0.023 | |
| nichenet_signaling_network_vinayagam | 0.020 | 0.003 | 0.022 | |
| nichenet_test | 0.000 | 0.000 | 0.001 | |
| nichenet_workarounds | 0.000 | 0.001 | 0.000 | |
| obo_parser | 0.187 | 0.065 | 0.421 | |
| oma_code | 0.228 | 0.007 | 0.237 | |
| oma_organisms | 0.138 | 0.027 | 0.164 | |
| oma_pairwise | 0.020 | 0.003 | 0.023 | |
| oma_pairwise_genesymbols | 0.019 | 0.002 | 0.022 | |
| oma_pairwise_translated | 0.019 | 0.003 | 0.023 | |
| omnipath-interactions | 68.016 | 5.116 | 87.848 | |
| omnipath_cache_autoclean | 0.000 | 0.001 | 0.001 | |
| omnipath_cache_clean | 0.020 | 0.007 | 0.028 | |
| omnipath_cache_clean_db | 0.242 | 0.046 | 0.312 | |
| omnipath_cache_download_ready | 1.133 | 0.248 | 1.436 | |
| omnipath_cache_filter_versions | 0.177 | 0.047 | 0.227 | |
| omnipath_cache_get | 0.228 | 0.031 | 0.259 | |
| omnipath_cache_key | 0.002 | 0.001 | 0.003 | |
| omnipath_cache_latest_or_new | 0.117 | 0.022 | 0.141 | |
| omnipath_cache_load | 0.915 | 0.069 | 2.134 | |
| omnipath_cache_move_in | 0.300 | 0.065 | 0.384 | |
| omnipath_cache_remove | 0.187 | 0.042 | 0.233 | |
| omnipath_cache_save | 0.356 | 0.051 | 0.555 | |
| omnipath_cache_search | 0.001 | 0.001 | 0.002 | |
| omnipath_cache_set_ext | 0.148 | 0.038 | 0.188 | |
| omnipath_cache_update_status | 0.150 | 0.027 | 0.177 | |
| omnipath_cache_wipe | 0.000 | 0.001 | 0.001 | |
| omnipath_config_path | 0.001 | 0.000 | 0.001 | |
| omnipath_for_cosmos | 20.844 | 1.432 | 38.768 | |
| omnipath_load_config | 0.000 | 0.001 | 0.001 | |
| omnipath_log | 0.001 | 0.000 | 0.001 | |
| omnipath_logfile | 0.002 | 0.001 | 0.004 | |
| omnipath_msg | 0.011 | 0.002 | 0.012 | |
| omnipath_query | 10.054 | 0.457 | 10.856 | |
| omnipath_reset_config | 0.000 | 0.001 | 0.001 | |
| omnipath_save_config | 0.000 | 0.001 | 0.001 | |
| omnipath_set_cachedir | 0.053 | 0.009 | 0.062 | |
| omnipath_set_console_loglevel | 0.007 | 0.000 | 0.008 | |
| omnipath_set_logfile_loglevel | 0.008 | 0.001 | 0.008 | |
| omnipath_set_loglevel | 0.005 | 0.001 | 0.005 | |
| omnipath_show_db | 0.133 | 0.025 | 0.161 | |
| omnipath_unlock_cache_db | 0.000 | 0.001 | 0.001 | |
| only_from | 0.001 | 0.000 | 0.001 | |
| ontology_ensure_id | 0.001 | 0.001 | 0.002 | |
| ontology_ensure_name | 0.001 | 0.001 | 0.002 | |
| ontology_name_id | 0.001 | 0.001 | 0.003 | |
| organism_for | 0.280 | 0.010 | 0.305 | |
| pathwaycommons_download | 0.001 | 0.001 | 0.003 | |
| pivot_annotations | 17.429 | 1.884 | 20.863 | |
| preppi_download | 0.001 | 0.001 | 0.002 | |
| preppi_filter | 0.002 | 0.001 | 0.002 | |
| print_bma_motif_es | 0.805 | 0.115 | 1.683 | |
| print_bma_motif_vs | 0.308 | 0.033 | 0.933 | |
| print_interactions | 15.036 | 0.972 | 18.127 | |
| print_path_es | 1.287 | 0.106 | 2.369 | |
| print_path_vs | 5.468 | 0.499 | 8.085 | |
| pubmed_open | 10.537 | 0.494 | 11.912 | |
| query_info | 0.602 | 0.046 | 0.973 | |
| ramilowski_download | 0.001 | 0.001 | 0.002 | |
| ramp_id_mapping_table | 0.001 | 0.000 | 0.001 | |
| ramp_id_type | 0.004 | 0.001 | 0.005 | |
| ramp_sqlite | 0.001 | 0.001 | 0.001 | |
| ramp_table | 0.001 | 0.000 | 0.002 | |
| ramp_tables | 0.001 | 0.001 | 0.001 | |
| recon3d | 0.003 | 0.001 | 0.004 | |
| recon3d_raw | 0.001 | 0.001 | 0.002 | |
| recon3d_raw_vmh | 0.001 | 0.000 | 0.002 | |
| regnetwork_directions | 0.001 | 0.001 | 0.002 | |
| regnetwork_download | 0.001 | 0.001 | 0.002 | |
| relations_list_to_table | 0.171 | 0.061 | 0.355 | |
| relations_table_to_graph | 0.000 | 0.001 | 0.001 | |
| relations_table_to_list | 0.133 | 0.052 | 0.208 | |
| remap_dorothea_download | 0.001 | 0.001 | 0.002 | |
| remap_filtered | 0.000 | 0.002 | 0.001 | |
| remap_tf_target_download | 0.001 | 0.001 | 0.001 | |
| resource_info | 0.753 | 0.238 | 1.296 | |
| resources | 0.113 | 0.016 | 0.763 | |
| resources_colname | 1.719 | 0.156 | 2.836 | |
| resources_in | 9.927 | 0.395 | 11.368 | |
| show_network | 0.001 | 0.001 | 0.002 | |
| signed_ptms | 12.886 | 0.518 | 15.002 | |
| simplify_intercell_network | 0.002 | 0.001 | 0.002 | |
| static_table | 9.631 | 0.803 | 10.970 | |
| static_tables | 0.109 | 0.027 | 0.230 | |
| stitch_actions | 0.001 | 0.000 | 0.002 | |
| stitch_links | 0.001 | 0.001 | 0.002 | |
| stitch_network | 0.001 | 0.001 | 0.002 | |
| stitch_remove_prefixes | 0.015 | 0.003 | 0.018 | |
| swap_relations | 0.144 | 0.054 | 0.230 | |
| swissprots_only | 0.208 | 0.009 | 0.216 | |
| tfcensus_download | 0.863 | 0.110 | 7.203 | |
| translate_ids | 1.830 | 0.222 | 11.793 | |
| translate_ids_multi | 16.579 | 0.988 | 32.945 | |
| trembls_only | 0.219 | 0.009 | 0.228 | |
| trrust_download | 0.001 | 0.001 | 0.002 | |
| uniprot_full_id_mapping_table | 1.780 | 0.260 | 13.174 | |
| uniprot_genesymbol_cleanup | 0.001 | 0.001 | 0.001 | |
| uniprot_id_mapping_table | 0.001 | 0.001 | 0.002 | |
| uniprot_id_type | 0.004 | 0.001 | 0.005 | |
| uniprot_idmapping_id_types | 0.740 | 0.100 | 1.394 | |
| uniprot_organisms | 42.708 | 4.492 | 48.493 | |
| unique_intercell_network | 0.002 | 0.001 | 0.002 | |
| unnest_evidences | 0.000 | 0.001 | 0.001 | |
| uploadlists_id_type | 0.003 | 0.000 | 0.003 | |
| vinayagam_download | 0.001 | 0.001 | 0.002 | |
| walk_ontology_tree | 0.003 | 0.001 | 0.003 | |
| with_extra_attrs | 33.549 | 5.932 | 40.143 | |
| with_references | 1.536 | 0.143 | 2.606 | |
| zenodo_download | 0.002 | 0.002 | 0.004 | |