| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-08-28 11:40 -0400 (Thu, 28 Aug 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4824 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4604 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4545 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4579 |
| 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 1484/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| OmnipathR 3.16.1 (landing page) Denes Turei
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
| kunpeng2 | 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: 3.16.1 |
| 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_3.16.1.tar.gz |
| StartedAt: 2025-08-26 07:22:32 -0400 (Tue, 26 Aug 2025) |
| EndedAt: 2025-08-26 07:45:36 -0400 (Tue, 26 Aug 2025) |
| EllapsedTime: 1383.6 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: OmnipathR.Rcheck |
| Warnings: NA |
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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_3.16.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/OmnipathR.Rcheck’
* using R version 4.5.1 RC (2025-06-05 r88288)
* 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 ‘3.16.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 35 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable. Move as many as possible to Suggests and
use conditionally.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘OmnipathR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking whether startup messages can be suppressed ... NOTE
[2025-08-26 07:23:34] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-26 07:23:34] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-26 07:23:34] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-08-26 07:23:34] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-08-26 07:23:34] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-08-25
[2025-08-26 07:23:34] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-08-25 19:14:24 UTC; unix
[2025-08-26 07:23:34] [INFO] [OmnipathR] Package `OmnipathR` version: 3.16.1
[2025-08-26 07:23:34] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-08-26 07:23:35] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 RC (2025-06-05 r88288); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-08-26; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto]
[2025-08-26 07:23:35] [INFO] [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.44 2024-06-07; ICU=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-08-26 07:23:36] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.4(2025-06-18); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.1.4(2025-01-23); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.3(2025-08-20); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); memoise 2.0.1(2021-11-26); OmnipathR 3.16.1(2025-08-25); pillar 1.11.0(2025-07-04); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.3.3(2025-05-29); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.4.3(2025-08-20); rvest 1.0.4(2024-02-12); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.53(2025-08-19); XML 3.99-0.19(2025-08-22); xml2 1.4.0(2025-08-20); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-08-26 07:23:36] [INFO] [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: x86_64-apple-darwin22.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2025-08-26 07:23:36] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-08-26 07:23:36] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-08-26 07:23:36] [TRACE] [OmnipathR] Contains 1 files.
[2025-08-26 07:23:36] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-08-26 07:23:36] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-26 07:23:36] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-26 07:23:36] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-08-26 07:23:36] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-08-26 07:23:36] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-08-26 07:23:36] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-26 07:23:36] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-08-26 07:23:36] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-26 07:23:36] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-08-26 07:23:36] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-26 07:23:36] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-08-26 07:23:36] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-26 07:23:36] [TRACE] [OmnipathR] Cache locked: FALSE
It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
[2025-08-26 07:24:24] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-26 07:24:24] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-26 07:24:24] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-08-26 07:24:24] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-08-26 07:24:24] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-08-25
[2025-08-26 07:24:24] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-08-25 19:14:24 UTC; unix
[2025-08-26 07:24:24] [INFO] [OmnipathR] Package `OmnipathR` version: 3.16.1
[2025-08-26 07:24:24] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-08-26 07:24:25] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 RC (2025-06-05 r88288); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-08-26; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto]
[2025-08-26 07:24:26] [INFO] [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.44 2024-06-07; ICU=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-08-26 07:24:26] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.4(2025-06-18); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.1.4(2025-01-23); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.3(2025-08-20); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); memoise 2.0.1(2021-11-26); OmnipathR 3.16.1(2025-08-25); pillar 1.11.0(2025-07-04); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.3.3(2025-05-29); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.4.3(2025-08-20); rvest 1.0.4(2024-02-12); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.53(2025-08-19); XML 3.99-0.19(2025-08-22); xml2 1.4.0(2025-08-20); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-08-26 07:24:26] [INFO] [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: x86_64-apple-darwin22.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2025-08-26 07:24:26] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-08-26 07:24:26] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-08-26 07:24:26] [TRACE] [OmnipathR] Contains 1 files.
[2025-08-26 07:24:26] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-08-26 07:24:26] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-26 07:24:26] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-26 07:24:26] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-08-26 07:24:26] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-08-26 07:24:26] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-08-26 07:24:26] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-26 07:24:26] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-08-26 07:24:26] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-26 07:24:26] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-08-26 07:24:26] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-26 07:24:26] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-08-26 07:24:26] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-26 07:24:26] [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 ... ERROR
Running examples in ‘OmnipathR-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: organism_for
> ### Title: Make sure the resource supports the organism and it has the ID
> ### Aliases: organism_for
>
> ### ** Examples
>
> organism_for(10116, 'chalmers-gem')
Error in organism_for(10116, "chalmers-gem") :
Organism `10116` (common_name: `Norway rat - BN/NHsdMcwi`; common_name: `Norway rat - BN/NHsdMcwi`) is not supported by resource `chalmers-gem`. Supported organisms: Human, Mouse, Rat, Zebrafish, Drosophila melanogaster (Fruit fly), Caenorhabditis elegans (PRJNA13758), Caenorhabditis elegans (Nematode, N2).
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
annotation_categories 96.355 0.391 99.140
filter_extra_attrs 70.651 19.657 160.331
curated_ligrec_stats 68.886 7.486 140.098
omnipath-interactions 63.535 5.161 84.376
extra_attrs_to_cols 37.921 6.132 57.629
extra_attr_values 35.271 6.321 59.488
nichenet_gr_network_omnipath 35.991 2.821 41.846
nichenet_signaling_network_omnipath 25.980 2.023 29.008
extra_attrs 20.206 5.112 29.790
giant_component 22.932 1.980 27.442
has_extra_attrs 20.097 4.716 39.990
go_annot_download 21.178 2.552 35.570
filter_by_resource 21.119 1.306 35.762
omnipath_for_cosmos 18.293 1.299 35.243
find_all_paths 13.773 0.828 18.680
curated_ligand_receptor_interactions 12.163 2.063 21.302
filter_intercell 11.042 1.082 12.819
omnipath_query 9.383 0.413 10.593
hpo_download 4.771 0.693 15.517
enzsub_graph 4.863 0.346 6.918
database_summary 3.191 0.408 6.318
all_uniprots 2.375 0.394 21.824
ensembl_id_mapping_table 2.283 0.293 11.498
kegg_conv 2.184 0.295 8.624
biomart_query 1.864 0.283 9.213
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 2 NOTEs
See
‘/Users/biocbuild/bbs-3.21-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 ‘3.16.1’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location [2025-08-25 15:14:46] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-25 15:14:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-25 15:14:46] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-08-25 15:14:46] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-08-25 15:14:46] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-08-25 [2025-08-25 15:14:46] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-08-25 19:14:24 UTC; unix [2025-08-25 15:14:46] [INFO] [OmnipathR] Package `OmnipathR` version: 3.16.1 [2025-08-25 15:14:46] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21 [2025-08-25 15:14:47] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 RC (2025-06-05 r88288); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-08-25; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto] [2025-08-25 15:14:47] [INFO] [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.44 2024-06-07; ICU=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1] [2025-08-25 15:14:48] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.4(2025-06-18); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.1.4(2025-01-23); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.3(2025-08-20); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); memoise 2.0.1(2021-11-26); OmnipathR 3.16.1(2025-08-25); pillar 1.11.0(2025-07-04); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.3.3(2025-05-29); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.4.3(2025-08-20); rvest 1.0.4(2024-02-12); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.53(2025-08-19); XML 3.99-0.19(2025-08-22); xml2 1.4.0(2025-08-20); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13) [2025-08-25 15:14:48] [INFO] [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: x86_64-apple-darwin22.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE [2025-08-25 15:14:48] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-08-25 15:14:48] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-08-25 15:14:48] [TRACE] [OmnipathR] Contains 1 files. [2025-08-25 15:14:48] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-08-25 15:14:48] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-25 15:14:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-25 15:14:48] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-08-25 15:14:48] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-08-25 15:14:48] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-08-25 15:14:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-25 15:14:48] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-08-25 15:14:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-25 15:14:48] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-08-25 15:14:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-25 15:14:48] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-08-25 15:14:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-25 15:14:48] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2025-08-25 15:14:51] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-25 15:14:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-25 15:14:51] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-08-25 15:14:51] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-08-25 15:14:51] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-08-25 [2025-08-25 15:14:51] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-08-25 19:14:24 UTC; unix [2025-08-25 15:14:51] [INFO] [OmnipathR] Package `OmnipathR` version: 3.16.1 [2025-08-25 15:14:51] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21 [2025-08-25 15:14:52] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 RC (2025-06-05 r88288); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-08-25; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto] [2025-08-25 15:14:52] [INFO] [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.44 2024-06-07; ICU=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1] [2025-08-25 15:14:52] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.4(2025-06-18); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.1.4(2025-01-23); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.3(2025-08-20); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); memoise 2.0.1(2021-11-26); OmnipathR 3.16.1(2025-08-25); pillar 1.11.0(2025-07-04); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.3.3(2025-05-29); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.4.3(2025-08-20); rvest 1.0.4(2024-02-12); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.53(2025-08-19); XML 3.99-0.19(2025-08-22); xml2 1.4.0(2025-08-20); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13) [2025-08-25 15:14:52] [INFO] [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: x86_64-apple-darwin22.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE [2025-08-25 15:14:52] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-08-25 15:14:52] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-08-25 15:14:52] [TRACE] [OmnipathR] Contains 1 files. [2025-08-25 15:14:52] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-08-25 15:14:52] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-25 15:14:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-25 15:14:52] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-08-25 15:14:52] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-08-25 15:14:52] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-08-25 15:14:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-25 15:14:52] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-08-25 15:14:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-25 15:14:52] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-08-25 15:14:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-25 15:14:52] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-08-25 15:14:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-25 15:14:52] [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 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'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)
[2025-08-26 07:44:20] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-26 07:44:20] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-26 07:44:20] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-08-26 07:44:20] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-08-26 07:44:20] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-08-25
[2025-08-26 07:44:20] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-08-25 19:14:24 UTC; unix
[2025-08-26 07:44:20] [INFO] [OmnipathR] Package `OmnipathR` version: 3.16.1
[2025-08-26 07:44:20] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-08-26 07:44:21] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 RC (2025-06-05 r88288); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=C; collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-08-26; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto]
[2025-08-26 07:44:21] [INFO] [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.44 2024-06-07; ICU=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-08-26 07:44:22] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); brio 1.1.5(2024-04-24); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.4(2025-06-18); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.1.4(2025-01-23); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.3(2025-08-20); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); memoise 2.0.1(2021-11-26); OmnipathR 3.16.1(2025-08-25); pillar 1.11.0(2025-07-04); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.3.3(2025-05-29); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.4.3(2025-08-20); rvest 1.0.4(2024-02-12); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); testthat 3.2.3(2025-01-13); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.53(2025-08-19); XML 3.99-0.19(2025-08-22); xml2 1.4.0(2025-08-20); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-08-26 07:44:22] [INFO] [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: x86_64-apple-darwin22.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2025-08-26 07:44:22] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-08-26 07:44:22] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-08-26 07:44:22] [TRACE] [OmnipathR] Contains 3 files.
[2025-08-26 07:44:22] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-08-26 07:44:22] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-26 07:44:22] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-26 07:44:22] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-08-26 07:44:22] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-08-26 07:44:22] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-08-26 07:44:22] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-26 07:44:22] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-08-26 07:44:22] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-26 07:44:22] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-08-26 07:44:22] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-26 07:44:22] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-08-26 07:44:22] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-26 07:44:22] [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
27.729 3.437 51.693
OmnipathR.Rcheck/OmnipathR-Ex.timings
| name | user | system | elapsed | |
| OmnipathR | 0.000 | 0.001 | 0.001 | |
| all_uniprot_acs | 0.039 | 0.005 | 0.043 | |
| all_uniprots | 2.375 | 0.394 | 21.824 | |
| ancestors | 0.019 | 0.003 | 0.021 | |
| annotated_network | 1.925 | 0.196 | 4.129 | |
| annotation_categories | 96.355 | 0.391 | 99.140 | |
| annotation_resources | 0.133 | 0.014 | 0.657 | |
| annotations | 0.790 | 0.082 | 1.823 | |
| biomart_query | 1.864 | 0.283 | 9.213 | |
| bioplex1 | 0.020 | 0.003 | 0.023 | |
| bioplex2 | 0.020 | 0.003 | 0.024 | |
| bioplex3 | 0.020 | 0.003 | 0.024 | |
| bioplex_all | 0.020 | 0.004 | 0.023 | |
| bioplex_hct116_1 | 0.020 | 0.003 | 0.022 | |
| bma_motif_es | 0.970 | 0.101 | 1.958 | |
| bma_motif_vs | 0.374 | 0.042 | 0.921 | |
| chalmers_gem | 0.020 | 0.003 | 0.022 | |
| chalmers_gem_id_mapping_table | 0.020 | 0.003 | 0.063 | |
| chalmers_gem_id_type | 0.004 | 0.001 | 0.005 | |
| chalmers_gem_metabolites | 0.019 | 0.003 | 0.023 | |
| chalmers_gem_network | 0.019 | 0.002 | 0.022 | |
| chalmers_gem_raw | 0.021 | 0.003 | 0.030 | |
| chalmers_gem_reactions | 0.021 | 0.004 | 0.034 | |
| common_name | 0.060 | 0.006 | 0.064 | |
| complex_genes | 1.071 | 0.100 | 2.274 | |
| complex_resources | 0.125 | 0.011 | 0.650 | |
| complexes | 0.286 | 0.024 | 0.818 | |
| consensuspathdb_download | 0.001 | 0.001 | 0.001 | |
| consensuspathdb_raw_table | 0.019 | 0.003 | 0.021 | |
| cosmos_pkn | 0 | 0 | 0 | |
| curated_ligand_receptor_interactions | 12.163 | 2.063 | 21.302 | |
| curated_ligrec_stats | 68.886 | 7.486 | 140.098 | |
| database_summary | 3.191 | 0.408 | 6.318 | |
| descendants | 0.019 | 0.004 | 0.022 | |
| ensembl_dataset | 0.021 | 0.003 | 0.023 | |
| ensembl_id_mapping_table | 2.283 | 0.293 | 11.498 | |
| ensembl_id_type | 0.005 | 0.001 | 0.006 | |
| ensembl_name | 0.114 | 0.011 | 0.145 | |
| ensembl_organisms | 0.324 | 0.049 | 0.416 | |
| ensembl_organisms_raw | 0.287 | 0.047 | 0.387 | |
| ensembl_orthology | 0.000 | 0.002 | 0.002 | |
| enzsub_graph | 4.863 | 0.346 | 6.918 | |
| enzsub_resources | 0.129 | 0.013 | 0.617 | |
| enzyme_substrate | 2.865 | 0.142 | 4.363 | |
| evex_download | 0.019 | 0.004 | 0.029 | |
| evidences | 0.001 | 0.001 | 0.001 | |
| extra_attr_values | 35.271 | 6.321 | 59.488 | |
| extra_attrs | 20.206 | 5.112 | 29.790 | |
| extra_attrs_to_cols | 37.921 | 6.132 | 57.629 | |
| filter_by_resource | 21.119 | 1.306 | 35.762 | |
| filter_extra_attrs | 70.651 | 19.657 | 160.331 | |
| filter_intercell | 11.042 | 1.082 | 12.819 | |
| filter_intercell_network | 0.044 | 0.006 | 0.070 | |
| find_all_paths | 13.773 | 0.828 | 18.680 | |
| from_evidences | 0.000 | 0.001 | 0.001 | |
| get_db | 0.001 | 0.000 | 0.001 | |
| get_ontology_db | 0.021 | 0.003 | 0.045 | |
| giant_component | 22.932 | 1.980 | 27.442 | |
| go_annot_download | 21.178 | 2.552 | 35.570 | |
| go_annot_slim | 0.001 | 0.001 | 0.002 | |
| go_ontology_download | 0.019 | 0.004 | 0.025 | |
| guide2pharma_download | 0.020 | 0.004 | 0.028 | |
| harmonizome_download | 0.020 | 0.004 | 0.025 | |
| has_extra_attrs | 20.097 | 4.716 | 39.990 | |
| hmdb_id_mapping_table | 0.019 | 0.003 | 0.021 | |
| hmdb_id_type | 0.005 | 0.001 | 0.005 | |
| hmdb_metabolite_fields | 0.000 | 0.002 | 0.003 | |
| hmdb_protein_fields | 0.001 | 0.001 | 0.002 | |
| hmdb_table | 0.019 | 0.002 | 0.021 | |
| homologene_download | 0.019 | 0.004 | 0.022 | |
| homologene_raw | 0.039 | 0.007 | 0.161 | |
| homologene_uniprot_orthology | 0.019 | 0.003 | 0.022 | |
| hpo_download | 4.771 | 0.693 | 15.517 | |
| htridb_download | 0.019 | 0.004 | 0.024 | |
| id_translation_resources | 0.000 | 0.001 | 0.002 | |
| id_types | 0.089 | 0.022 | 0.115 | |
| inbiomap_download | 0.000 | 0.001 | 0.001 | |
| inbiomap_raw | 0 | 0 | 0 | |
| interaction_datasets | 1.038 | 0.130 | 2.214 | |
| interaction_graph | 0.769 | 0.049 | 1.955 | |
| interaction_resources | 0.184 | 0.020 | 0.696 | |
| interaction_types | 0.087 | 0.011 | 0.161 | |
| intercell | 1.245 | 0.153 | 2.698 | |
| intercell_categories | 1.044 | 0.163 | 2.214 | |
| intercell_consensus_filter | 2.392 | 0.265 | 4.891 | |
| intercell_generic_categories | 0.089 | 0.012 | 0.124 | |
| intercell_network | 0.021 | 0.004 | 0.086 | |
| intercell_resources | 0.135 | 0.017 | 0.808 | |
| intercell_summary | 0.105 | 0.048 | 0.190 | |
| is_ontology_id | 0.000 | 0.000 | 0.001 | |
| is_swissprot | 0.057 | 0.007 | 0.115 | |
| is_trembl | 0.057 | 0.007 | 0.127 | |
| is_uniprot | 0.021 | 0.003 | 0.024 | |
| kegg_api_templates | 0.003 | 0.008 | 0.011 | |
| kegg_conv | 2.184 | 0.295 | 8.624 | |
| kegg_databases | 0.000 | 0.001 | 0.001 | |
| kegg_ddi | 0.951 | 0.118 | 2.367 | |
| kegg_find | 0.923 | 0.158 | 2.808 | |
| kegg_info | 0.019 | 0.003 | 0.022 | |
| kegg_link | 1.058 | 0.136 | 4.230 | |
| kegg_list | 0.912 | 0.123 | 1.847 | |
| kegg_open | 0.018 | 0.003 | 0.020 | |
| kegg_operations | 0.000 | 0.001 | 0.001 | |
| kegg_organism_codes | 0.066 | 0.185 | 0.257 | |
| kegg_organisms | 0.045 | 0.012 | 0.056 | |
| kegg_pathway_annotations | 0.000 | 0.001 | 0.001 | |
| kegg_pathway_download | 0.019 | 0.003 | 0.022 | |
| kegg_pathway_list | 0.018 | 0.003 | 0.022 | |
| kegg_pathways_download | 0.001 | 0.001 | 0.001 | |
| kegg_picture | 1.142 | 0.079 | 2.643 | |
| kegg_process | 0.034 | 0.004 | 0.038 | |
| kegg_query | 0.016 | 0.001 | 0.017 | |
| kegg_request | 0.120 | 0.014 | 0.133 | |
| kegg_rm_prefix | 1.174 | 0.137 | 3.754 | |
| latin_name | 0.112 | 0.011 | 0.124 | |
| load_db | 0.177 | 0.034 | 0.215 | |
| metalinksdb_sqlite | 1.642 | 0.448 | 3.420 | |
| metalinksdb_table | 0.437 | 0.082 | 0.515 | |
| metalinksdb_tables | 0.035 | 0.008 | 0.043 | |
| ncbi_taxid | 0.114 | 0.012 | 0.128 | |
| nichenet_build_model | 0.000 | 0.001 | 0.001 | |
| nichenet_expression_data | 0.019 | 0.003 | 0.022 | |
| nichenet_gr_network | 0.055 | 0.008 | 0.062 | |
| nichenet_gr_network_evex | 0.020 | 0.003 | 0.024 | |
| nichenet_gr_network_harmonizome | 0.020 | 0.003 | 0.023 | |
| nichenet_gr_network_htridb | 0.019 | 0.004 | 0.024 | |
| nichenet_gr_network_omnipath | 35.991 | 2.821 | 41.846 | |
| nichenet_gr_network_pathwaycommons | 0.020 | 0.003 | 0.022 | |
| nichenet_gr_network_regnetwork | 0.020 | 0.003 | 0.023 | |
| nichenet_gr_network_remap | 0.019 | 0.003 | 0.023 | |
| nichenet_gr_network_trrust | 0.063 | 0.007 | 0.070 | |
| nichenet_ligand_activities | 0.000 | 0.001 | 0.001 | |
| nichenet_ligand_target_links | 0.001 | 0.002 | 0.002 | |
| nichenet_ligand_target_matrix | 0.000 | 0.001 | 0.001 | |
| nichenet_lr_network | 0.057 | 0.008 | 0.065 | |
| nichenet_lr_network_guide2pharma | 0.020 | 0.003 | 0.023 | |
| nichenet_lr_network_omnipath | 0.060 | 0.009 | 0.109 | |
| nichenet_lr_network_ramilowski | 0.019 | 0.003 | 0.023 | |
| nichenet_main | 0.001 | 0.001 | 0.001 | |
| nichenet_networks | 0.096 | 0.019 | 0.147 | |
| nichenet_optimization | 0.001 | 0.000 | 0.001 | |
| nichenet_remove_orphan_ligands | 0.056 | 0.008 | 0.064 | |
| nichenet_results_dir | 0.000 | 0.000 | 0.001 | |
| nichenet_signaling_network | 0.058 | 0.009 | 0.068 | |
| nichenet_signaling_network_cpdb | 0.019 | 0.003 | 0.021 | |
| nichenet_signaling_network_evex | 0.020 | 0.003 | 0.023 | |
| nichenet_signaling_network_harmonizome | 0.019 | 0.003 | 0.022 | |
| nichenet_signaling_network_inbiomap | 0 | 0 | 0 | |
| nichenet_signaling_network_omnipath | 25.980 | 2.023 | 29.008 | |
| nichenet_signaling_network_pathwaycommons | 0.019 | 0.003 | 0.022 | |
| nichenet_signaling_network_vinayagam | 0.018 | 0.003 | 0.022 | |
| nichenet_test | 0.000 | 0.001 | 0.000 | |
| nichenet_workarounds | 0.000 | 0.001 | 0.001 | |
| obo_parser | 0.175 | 0.042 | 0.372 | |
| oma_code | 0.059 | 0.006 | 0.063 | |
| oma_organisms | 0.144 | 0.033 | 0.177 | |
| oma_pairwise | 0.074 | 0.003 | 0.078 | |
| oma_pairwise_genesymbols | 0.020 | 0.003 | 0.023 | |
| oma_pairwise_translated | 0.021 | 0.003 | 0.023 | |
| omnipath-interactions | 63.535 | 5.161 | 84.376 | |
| omnipath_cache_autoclean | 0.001 | 0.001 | 0.001 | |
| omnipath_cache_clean | 0.022 | 0.007 | 0.029 | |
| omnipath_cache_clean_db | 0.302 | 0.045 | 0.346 | |
| omnipath_cache_download_ready | 1.088 | 0.246 | 1.364 | |
| omnipath_cache_filter_versions | 0.228 | 0.049 | 0.301 | |
| omnipath_cache_get | 0.164 | 0.029 | 0.192 | |
| omnipath_cache_key | 0.002 | 0.001 | 0.004 | |
| omnipath_cache_latest_or_new | 0.123 | 0.022 | 0.146 | |
| omnipath_cache_load | 0.910 | 0.065 | 2.027 | |
| omnipath_cache_move_in | 0.304 | 0.070 | 0.379 | |
| omnipath_cache_remove | 0.184 | 0.048 | 0.236 | |
| omnipath_cache_save | 0.302 | 0.043 | 0.470 | |
| omnipath_cache_search | 0.000 | 0.001 | 0.001 | |
| omnipath_cache_set_ext | 0.145 | 0.037 | 0.186 | |
| omnipath_cache_update_status | 0.172 | 0.031 | 0.201 | |
| omnipath_cache_wipe | 0.000 | 0.000 | 0.001 | |
| omnipath_config_path | 0.001 | 0.001 | 0.001 | |
| omnipath_for_cosmos | 18.293 | 1.299 | 35.243 | |
| omnipath_load_config | 0.001 | 0.001 | 0.001 | |
| omnipath_log | 0.001 | 0.000 | 0.001 | |
| omnipath_logfile | 0.003 | 0.001 | 0.005 | |
| omnipath_msg | 0.010 | 0.001 | 0.012 | |
| omnipath_query | 9.383 | 0.413 | 10.593 | |
| 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 | 0.061 | |
| omnipath_set_console_loglevel | 0.007 | 0.001 | 0.008 | |
| omnipath_set_logfile_loglevel | 0.008 | 0.001 | 0.009 | |
| omnipath_set_loglevel | 0.004 | 0.001 | 0.005 | |
| omnipath_show_db | 0.134 | 0.031 | 0.169 | |
| omnipath_unlock_cache_db | 0.000 | 0.000 | 0.001 | |
| only_from | 0.001 | 0.001 | 0.001 | |
| ontology_ensure_id | 0.000 | 0.001 | 0.001 | |
| ontology_ensure_name | 0.000 | 0.001 | 0.001 | |
| ontology_name_id | 0.001 | 0.001 | 0.002 | |