| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-06-28 12:10 -0400 (Sat, 28 Jun 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4775 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4517 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4559 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4500 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4499 |
| 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 1469/2310 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| OmnipathR 3.17.0 (landing page) Denes Turei
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | ERROR | skipped | skipped | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | ERROR | 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: 3.17.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings OmnipathR_3.17.0.tar.gz |
| StartedAt: 2025-06-27 22:14:05 -0400 (Fri, 27 Jun 2025) |
| EndedAt: 2025-06-27 22:28:22 -0400 (Fri, 27 Jun 2025) |
| EllapsedTime: 856.8 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_3.17.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/OmnipathR.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OmnipathR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OmnipathR’ version ‘3.17.0’
* 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
[2025-06-27 22:14:43] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-06-27 22:14:43] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-06-27 22:14:43] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-06-27 22:14:43] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-06-27 22:14:43] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-06-27
[2025-06-27 22:14:43] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-06-27 19:10:26 UTC; unix
[2025-06-27 22:14:43] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.0
[2025-06-27 22:14:43] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-06-27 22:14:44] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-06-27; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto]
[2025-06-27 22:14:44] [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]
[2025-06-27 22:14:44] [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 2.3.2(2024-07-29); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 6.4.0(2025-06-22); 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 1.1.2(2025-03-26); igraph 2.1.4(2025-01-23); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); memoise 2.0.1(2021-11-26); OmnipathR 3.17.0(2025-06-27); pillar 1.10.2(2025-04-05); 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 1.0.4(2025-02-05); 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 1.0.14(2025-01-12); 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 2.4.1(2025-06-08); 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 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-06-27 22:14:44] [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
[2025-06-27 22:14:44] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-06-27 22:14:44] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-06-27 22:14:44] [TRACE] [OmnipathR] Contains 1 files.
[2025-06-27 22:14:44] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-06-27 22:14:44] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-06-27 22:14:44] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-06-27 22:14:44] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-06-27 22:14:44] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-06-27 22:14:44] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-06-27 22:14:44] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-06-27 22:14:44] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-06-27 22:14:44] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-06-27 22:14:44] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-06-27 22:14:44] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-06-27 22:14:44] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-06-27 22:14:44] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-06-27 22:14:44] [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
[2025-06-27 22:15:09] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-06-27 22:15:09] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-06-27 22:15:09] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-06-27 22:15:09] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-06-27 22:15:09] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-06-27
[2025-06-27 22:15:09] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-06-27 19:10:26 UTC; unix
[2025-06-27 22:15:09] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.0
[2025-06-27 22:15:09] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-06-27 22:15:10] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-06-27; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto]
[2025-06-27 22:15:10] [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]
[2025-06-27 22:15:11] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 6.4.0(2025-06-22); 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 1.1.2(2025-03-26); igraph 2.1.4(2025-01-23); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); memoise 2.0.1(2021-11-26); OmnipathR 3.17.0(2025-06-27); pillar 1.10.2(2025-04-05); 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 1.0.4(2025-02-05); 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 1.0.14(2025-01-12); 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 2.4.1(2025-06-08); 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 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-06-27 22:15:11] [INFO] [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: x86_64-apple-darwin22.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2025-06-27 22:15:11] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-06-27 22:15:11] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-06-27 22:15:11] [TRACE] [OmnipathR] Contains 1 files.
[2025-06-27 22:15:11] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-06-27 22:15:11] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-06-27 22:15:11] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-06-27 22:15:11] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-06-27 22:15:11] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-06-27 22:15:11] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-06-27 22:15:11] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-06-27 22:15:11] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-06-27 22:15:11] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-06-27 22:15:11] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-06-27 22:15:11] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-06-27 22:15:11] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-06-27 22:15:11] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-06-27 22:15:11] [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: omnipath_for_cosmos
> ### Title: OmniPath PPI for the COSMOS PKN
> ### Aliases: omnipath_for_cosmos
>
> ### ** Examples
>
> op_cosmos <- omnipath_for_cosmos()
[2025-06-27 22:27:07] [INFO] [OmnipathR] OmniPath network for COSMOS PKN; datasets: omnipath; resources: all; interaction types: post-translational (PPI); organism: Human.
[2025-06-27 22:27:07] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-06-27 22:27:07] [TRACE] [OmnipathR] Arguments for OmniPath query: [organisms=9606,query_type=interactions]
[2025-06-27 22:27:07] [TRACE] [OmnipathR] Organism(s): 9606
[2025-06-27 22:27:07] [TRACE] [OmnipathR] Orthology targets:
[2025-06-27 22:27:07] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-06-27 22:27:07] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-06-27 22:27:07] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-06-27 22:27:07] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-06-27 22:27:07] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-06-27 22:27:07] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-06-27 22:27:07] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-06-27 22:27:07] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-06-27 22:27:07] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-06-27 22:27:07] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2025-06-27 22:27:07] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.33324s from omnipathdb.org (47 Kb/s); Redirect: 0s, DNS look up: 0.001268s, Connection: 0.002294s, Pretransfer: 0.168302s, First byte at: 0.332897s
[2025-06-27 22:27:07] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 28 Jun 2025 02:27:07 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Sat, 28 Jun 2025 03:27:07 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-06-27 22:27:10] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-06-27 22:27:10] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-06-27 22:27:10] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-06-27 22:27:10] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-06-27 22:27:10] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-06-27 22:27:10] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`.
[2025-06-27 22:27:10] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2025-06-27 22:27:10] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2025-06-27 22:27:10] [INFO] [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1]
[2025-06-27 22:27:10] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-06-27 22:27:10] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-06-27 22:27:11] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`.
[2025-06-27 22:27:14] [SUCCESS] [OmnipathR] Downloaded 81529 interactions.
[2025-06-27 22:27:14] [TRACE] [OmnipathR] ID translation table: from `uniprot` to `genesymbol`, using Ensembl BioMart.
[2025-06-27 22:27:14] [TRACE] [OmnipathR] Creating ID mapping table from `uniprotswissprot` to `external_gene_name`, for organism hsapiens
[2025-06-27 22:27:14] [TRACE] [OmnipathR] BioMart query: <?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE Query>
<Query virtualSchemaName="default" formatter="TSV" header="0" uniqueRows="0" count="" datasetConfigVersion="0.6" completionStamp="1" >
<Dataset name="hsapiens_gene_ensembl" interface="default" >
<Attribute name="uniprotswissprot"/>
<Attribute name="external_gene_name"/>
</Dataset>
</Query>
[2025-06-27 22:27:14] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2025-06-27 22:27:14] [TRACE] [OmnipathR] Looking up in cache: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`.
[2025-06-27 22:27:14] [INFO] [OmnipathR] Cache record does not exist: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`
[2025-06-27 22:27:14] [TRACE] [OmnipathR] Could not find in cache, initiating download: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`.
[2025-06-27 22:27:14] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-06-27 22:27:14] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-06-27 22:27:14] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-06-27 22:27:14] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-06-27 22:27:14] [INFO] [OmnipathR] Cache item `d8282bd9b4260cbc5a0923f1eff00b1534d7f081` version 1: status changed from `unknown` to `started`.
[2025-06-27 22:27:14] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/d8282bd9b4260cbc5a0923f1eff00b1534d7f081-1.rds`.
[2025-06-27 22:27:14] [INFO] [OmnipathR] Retrieving URL: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`
[2025-06-27 22:27:14] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-06-27 22:27:14] [TRACE] [OmnipathR] Attempt 1/3: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`
[2025-06-27 22:27:14] [TRACE] [OmnipathR] Preparing httr2 request to URL `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`.
[2025-06-27 22:27:14] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-06-27 22:27:14] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-06-27 22:27:14] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-06-27 22:27:14] [TRACE] [OmnipathR] Sending HTTP request.
[2025-06-27 22:27:15] [TRACE] [OmnipathR] HTTP 200 (OK)
[2025-06-27 22:27:15] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2025-06-27 22:27:15] [TRACE] [OmnipathR] Downloaded 1014 bytes in 0.18706s from www.ensembl.org (5.3 Kb/s); Redirect: 0s, DNS look up: 0.024535s, Connection: 0.10359s, Pretransfer: 0.103655s, First byte at: 0.18692s
[2025-06-27 22:27:15] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; X-GitHub-Request-Id: 778B:177D32:A7A2AD:A8B02E:685F0360; Server: GitHub.com; X-Cache-Hits: 2; Vary: Accept-Encoding; Cache-Control: no-cache, no-store, must-revalidate; x-proxy-cache: MISS; X-Cache: HIT; Content-Type: text/html; charset=utf-8; X-Fastly-Request-ID: 632474f1888fdabb1c8a873acc61fc251264631b; Content-Encoding: gzip; Date: Sat, 28 Jun 2025 02:27:15 GMT; Expires: 0; X-Served-By: cache-lcy-eglc8600053-LCY; Pragma: no-cache; X-Timer: S1751077635.224402,VS0,VE0; Access-Control-Allow-Origin: *; Accept-Ranges: bytes; ETag: W/"681dc811-8aa"; Via: 1.1 varnish; Connection: keep-alive; Age: 61; Content-Length: 1014
[2025-06-27 22:27:15] [TRACE] [OmnipathR] Response headers: [X-GitHub-Request-Id=778B:177D32:A7A2AD:A8B02E:685F0360,Server=GitHub.com,X-Cache-Hits=2,Vary=Accept-Encoding,Cache-Control=no-cache, no-store, must-revalidate,x-proxy-cache=MISS,X-Cache=HIT,Content-Type=text/html; charset=utf-8,X-Fastly-Request-ID=632474f1888fdabb1c8a873acc61fc251264631b,Content-Encoding=gzip,Date=Sat, 28 Jun 2025 02:27:15 GMT,Expires=0,X-Served-By=cache-lcy-eglc8600053-LCY,Pragma=no-cache,X-Timer=S1751077635.224402,VS0,VE0,Access-Control-Allow-Origin=*,Accept-Ranges=bytes,ETag=W/"681dc811-8aa",Via=1.1 varnish,Connection=keep-alive,Age=61,Content-Length=1014]
[2025-06-27 22:27:15] [TRACE] [OmnipathR] Calling reader callback on response.
[2025-06-27 22:27:15] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/d8282bd9b4260cbc5a0923f1eff00b1534d7f081-1.rds`.
[2025-06-27 22:27:15] [INFO] [OmnipathR] Download ready [key=d8282bd9b4260cbc5a0923f1eff00b1534d7f081, version=1]
[2025-06-27 22:27:15] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-06-27 22:27:15] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-06-27 22:27:15] [INFO] [OmnipathR] Cache item `d8282bd9b4260cbc5a0923f1eff00b1534d7f081` version 1: status changed from `started` to `ready`.
[2025-06-27 22:27:15] [WARN] [OmnipathR] BioMart: missing success flag, data might be incomplete or contain error message!
[2025-06-27 22:27:15] [WARN] [OmnipathR] <html>
[2025-06-27 22:27:15] [WARN] [OmnipathR] <head>
[2025-06-27 22:27:15] [WARN] [OmnipathR] <title>Service unavailable</title>
[2025-06-27 22:27:15] [WARN] [OmnipathR] <meta name="robots" content="noindex">
[2025-06-27 22:27:15] [WARN] [OmnipathR] <base href="//status.ensembl.org">
[2025-06-27 22:27:15] [WARN] [OmnipathR] <style>
[2025-06-27 22:27:15] [WARN] [OmnipathR] html,
[2025-06-27 22:27:15] [WARN] [OmnipathR] body {
[2025-06-27 22:27:15] [WARN] [OmnipathR] padding: 0;
[2025-06-27 22:27:15] [WARN] [OmnipathR] margin: 0;
[2025-06-27 22:27:15] [WARN] [OmnipathR] height: 100%;
[2025-06-27 22:27:15] [WARN] [OmnipathR] }
[2025-06-27 22:27:15] [WARN] [OmnipathR] body {
[2025-06-27 22:27:15] [WARN] [OmnipathR] display: grid;
[2025-06-27 22:27:15] [WARN] [OmnipathR] grid-template-rows: [header] auto [main] 1fr [footer] auto;
[2025-06-27 22:27:15] [WARN] [OmnipathR] font-family: Luxi Sans, Helvetica, Arial, Geneva, sans-serif;
[2025-06-27 22:27:15] [WARN] [OmnipathR] font-size: 90%;
[2025-06-27 22:27:15] [WARN] [OmnipathR] }
[2025-06-27 22:27:15] [WARN] [OmnipathR] h1 {
[2025-06-27 22:27:15] [WARN] [OmnipathR] font-size: 1.5rem;
[2025-06-27 22:27:15] [WARN] [OmnipathR] }
[2025-06-27 22:27:15] [WARN] [OmnipathR] h2 {
[2025-06-27 22:27:15] [WARN] [OmnipathR] font-size: 1.2rem;
[2025-06-27 22:27:15] [WARN] [OmnipathR] }
[2025-06-27 22:27:15] [WARN] [OmnipathR] h3 {
[2025-06-27 22:27:15] [WARN] [OmnipathR] font-size: 1.1rem;
[2025-06-27 22:27:15] [WARN] [OmnipathR] }
[2025-06-27 22:27:15] [WARN] [OmnipathR] header {
[2025-06-27 22:27:15] [WARN] [OmnipathR] grid-row: header;
[2025-06-27 22:27:15] [WARN] [OmnipathR] padding: 5px;
[2025-06-27 22:27:15] [WARN] [OmnipathR] height: 60px;
[2025-06-27 22:27:15] [WARN] [OmnipathR] background-color: #333366;
[2025-06-27 22:27:15] [WARN] [OmnipathR] }
[2025-06-27 22:27:15] [WARN] [OmnipathR] header img {
[2025-06-27 22:27:15] [WARN] [OmnipathR] width: 185px;
[2025-06-27 22:27:15] [WARN] [OmnipathR] height: 45px
[2025-06-27 22:27:15] [WARN] [OmnipathR] }
[2025-06-27 22:27:15] [WARN] [OmnipathR] main {
[2025-06-27 22:27:15] [WARN] [OmnipathR] grid-row: main;
[2025-06-27 22:27:15] [WARN] [OmnipathR] padding: 20px;
[2025-06-27 22:27:15] [WARN] [OmnipathR] }
[2025-06-27 22:27:15] [WARN] [OmnipathR] .mirrors {
[2025-06-27 22:27:15] [WARN] [OmnipathR] border: solid 1px #ccc;
[2025-06-27 22:27:15] [WARN] [OmnipathR] margin-top: 20px;
[2025-06-27 22:27:15] [WARN] [OmnipathR] padding: 10px;
[2025-06-27 22:27:15] [WARN] [OmnipathR] }
[2025-06-27 22:27:15] [WARN] [OmnipathR] footer {
[2025-06-27 22:27:15] [WARN] [OmnipathR] grid-row: footer;
[2025-06-27 22:27:15] [WARN] [OmnipathR] padding: 0 20px;
[2025-06-27 22:27:15] [WARN] [OmnipathR] }
[2025-06-27 22:27:15] [WARN] [OmnipathR] </style>
[2025-06-27 22:27:15] [WARN] [OmnipathR] </head>
[2025-06-27 22:27:15] [WARN] [OmnipathR] <body>
[2025-06-27 22:27:15] [WARN] [OmnipathR] <header>
[2025-06-27 22:27:15] [WARN] [OmnipathR] <img src="/e-ensembl.png" alt="ensembl-logo" />
[2025-06-27 22:27:15] [WARN] [OmnipathR] </header>
[2025-06-27 22:27:15] [WARN] [OmnipathR] <main>
[2025-06-27 22:27:15] [WARN] [OmnipathR] <h1>Server Status</h1>
[2025-06-27 22:27:15] [WARN] [OmnipathR] <p>
[2025-06-27 22:27:15] [WARN] [OmnipathR] <img src="/exclamation_alert.png" alt="[!]" style="float:left;padding:0 10px;width:100px;height:89px" />
[2025-06-27 22:27:15] [WARN] [OmnipathR] The Ensembl web service you requested is temporarily unavailable.
[2025-06-27 22:27:15] [WARN] [OmnipathR] We are working to restore the service as soon as possible, and apologise for any inconvenience caused.
[2025-06-27 22:27:15] [WARN] [OmnipathR] </p>
[2025-06-27 22:27:15] [WARN] [OmnipathR] <p>For all enquiries, please <a href="https://www.ensembl.info/contact-us/">contact our HelpDesk</a>.</p>
[2025-06-27 22:27:15] [WARN] [OmnipathR] <div class="mirrors">
[2025-06-27 22:27:15] [WARN] [OmnipathR] <h3>Ensembl mirrors</h3>
[2025-06-27 22:27:15] [WARN] [OmnipathR] We now also manage two mirrors of the Ensembl website, hosted in different regions of the Amazon cloud:
[2025-06-27 22:27:15] [WARN] [OmnipathR] <ul>
[2025-06-27 22:27:15] [WARN] [OmnipathR] <li><a href="https://useast.ensembl.org/index.html?redirect=no">useast.ensembl.org</a></li>
[2025-06-27 22:27:15] [WARN] [OmnipathR] <li><a href="https://asia.ensembl.org/index.html?redirect=no">asia.ensembl.org</a></li>
[2025-06-27 22:27:15] [WARN] [OmnipathR] </ul>
[2025-06-27 22:27:15] [WARN] [OmnipathR] These will be available while the main service is unavailable, although please note that some of the
[2025-06-27 22:27:15] [WARN] [OmnipathR] facilities on these mirror may not be fully functional as they rely on resources hosted at our main
[2025-06-27 22:27:15] [WARN] [OmnipathR] data centre.
[2025-06-27 22:27:15] [WARN] [OmnipathR] </div>
[2025-06-27 22:27:15] [WARN] [OmnipathR] </main>
[2025-06-27 22:27:15] [WARN] [OmnipathR] <footer>
[2025-06-27 22:27:15] [WARN] [OmnipathR] <p>© 2025 EMBL-EBI</p>
[2025-06-27 22:27:15] [WARN] [OmnipathR] </footer>
[2025-06-27 22:27:15] [WARN] [OmnipathR] </body>
[2025-06-27 22:27:15] [WARN] [OmnipathR] </html>
[2025-06-27 22:27:15] [SUCCESS] [OmnipathR] www.ensembl.org: downloaded 81 records
Error in `set_names()`:
! The size of `nm` (2) must be compatible with the size of `x` (1).
Backtrace:
▆
1. ├─OmnipathR::omnipath_for_cosmos()
2. │ └─... %T>% ...
3. ├─dplyr::bind_rows(...)
4. │ └─rlang::list2(...)
5. ├─OmnipathR::translate_ids_multi(...)
6. │ └─source_cols %>% seq_along %>% ...
7. ├─purrr::reduce(...)
8. │ └─purrr:::reduce_impl(.x, .f, ..., .init = .init, .dir = .dir)
9. │ └─OmnipathR (local) fn(out, elt, ...)
10. │ └─OmnipathR::translate_ids(...)
11. │ └─... %>% ...
12. ├─purrr::reduce2(...)
13. │ └─purrr:::reduce2_impl(.x, .y, .f, ..., .init = .init, .left = TRUE)
14. │ └─OmnipathR (local) .f(out, .x[[x_i]], .y[[y_i]], ...)
15. │ ├─... %>% ...
16. │ └─OmnipathR:::id_translation_table(...)
17. │ └─OmnipathR::ensembl_id_mapping_table(...)
18. │ └─... %>% trim_and_distinct
19. ├─OmnipathR:::ensure_character(., From, To)
20. │ └─d %>% mutate(across(c(!!!cols), as.character))
21. ├─dplyr::mutate(., across(c(!!!cols), as.character))
22. ├─OmnipathR:::trim_and_distinct(.)
23. │ └─d %>% mutate(across(everything(), str_trim)) %>% distinct
24. ├─dplyr::distinct(.)
25. ├─dplyr::mutate(., across(everything(), str_trim))
26. ├─rlang::set_names(., c("From", "To"))
27. └─rlang::abort(message = message)
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
annotation_categories 55.777 0.332 57.971
filter_extra_attrs 39.903 13.300 78.428
curated_ligrec_stats 38.069 15.081 120.588
omnipath-interactions 29.453 2.933 56.377
extra_attrs_to_cols 13.689 10.091 27.331
extra_attr_values 16.959 3.194 33.737
nichenet_gr_network_omnipath 15.681 1.730 19.916
go_annot_download 13.870 1.543 14.029
extra_attrs 10.544 2.199 19.711
nichenet_signaling_network_omnipath 11.354 1.131 14.894
has_extra_attrs 9.153 2.960 12.244
giant_component 10.573 1.181 14.742
filter_by_resource 8.424 1.309 18.473
curated_ligand_receptor_interactions 6.725 1.224 16.959
filter_intercell 5.908 0.881 11.130
find_all_paths 6.266 0.485 6.876
enzsub_graph 2.682 0.845 9.040
ensembl_id_mapping_table 1.422 1.876 14.444
all_uniprots 1.622 0.244 13.874
kegg_conv 1.378 0.191 12.694
metalinksdb_sqlite 1.010 0.342 15.677
kegg_picture 0.904 0.054 5.198
kegg_rm_prefix 0.768 0.096 5.344
kegg_link 0.696 0.141 6.178
* 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-3.22-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 ‘3.17.0’ ** 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 [2025-06-27 15:10:39] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-06-27 15:10:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-06-27 15:10:39] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-06-27 15:10:39] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-06-27 15:10:39] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-06-27 [2025-06-27 15:10:39] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-06-27 19:10:26 UTC; unix [2025-06-27 15:10:39] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.0 [2025-06-27 15:10:39] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22 [2025-06-27 15:10:40] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-06-27; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto] [2025-06-27 15:10:41] [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] [2025-06-27 15:10:41] [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 2.3.2(2024-07-29); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 6.4.0(2025-06-22); 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 1.1.2(2025-03-26); igraph 2.1.4(2025-01-23); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); memoise 2.0.1(2021-11-26); OmnipathR 3.17.0(2025-06-27); pillar 1.10.2(2025-04-05); 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 1.0.4(2025-02-05); 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 1.0.14(2025-01-12); 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 2.4.1(2025-06-08); 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 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13) [2025-06-27 15:10:41] [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 [2025-06-27 15:10:41] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-06-27 15:10:41] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-06-27 15:10:41] [TRACE] [OmnipathR] Contains 1 files. [2025-06-27 15:10:41] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-06-27 15:10:41] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-06-27 15:10:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-06-27 15:10:41] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-06-27 15:10:41] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-06-27 15:10:41] [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). [2025-06-27 15:10:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-06-27 15:10:41] [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). [2025-06-27 15:10:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-06-27 15:10:41] [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). [2025-06-27 15:10:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-06-27 15:10:41] [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). [2025-06-27 15:10:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-06-27 15:10:41] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2025-06-27 15:10:43] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-06-27 15:10:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-06-27 15:10:43] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-06-27 15:10:43] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-06-27 15:10:43] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-06-27 [2025-06-27 15:10:43] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-06-27 19:10:26 UTC; unix [2025-06-27 15:10:43] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.0 [2025-06-27 15:10:43] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22 [2025-06-27 15:10:44] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-06-27; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto] [2025-06-27 15:10:44] [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] [2025-06-27 15:10:44] [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 2.3.2(2024-07-29); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 6.4.0(2025-06-22); 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 1.1.2(2025-03-26); igraph 2.1.4(2025-01-23); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); memoise 2.0.1(2021-11-26); OmnipathR 3.17.0(2025-06-27); pillar 1.10.2(2025-04-05); 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 1.0.4(2025-02-05); 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 1.0.14(2025-01-12); 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 2.4.1(2025-06-08); 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 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13) [2025-06-27 15:10:44] [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 [2025-06-27 15:10:44] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-06-27 15:10:44] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-06-27 15:10:44] [TRACE] [OmnipathR] Contains 1 files. [2025-06-27 15:10:44] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-06-27 15:10:44] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-06-27 15:10:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-06-27 15:10:44] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-06-27 15:10:44] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-06-27 15:10:44] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-06-27 15:10:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-06-27 15:10:44] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-06-27 15:10:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-06-27 15:10:45] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-06-27 15:10:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-06-27 15:10:45] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-06-27 15:10:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-06-27 15:10:45] [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 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'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)
[2025-06-27 22:27:21] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-06-27 22:27:21] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-06-27 22:27:21] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-06-27 22:27:21] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-06-27 22:27:21] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-06-27
[2025-06-27 22:27:21] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-06-27 19:10:26 UTC; unix
[2025-06-27 22:27:21] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.0
[2025-06-27 22:27:21] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-06-27 22:27:22] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=C; collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-06-27; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto]
[2025-06-27 22:27:22] [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]
[2025-06-27 22:27:23] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); brio 1.1.5(2024-04-24); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 6.4.0(2025-06-22); 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 1.1.2(2025-03-26); igraph 2.1.4(2025-01-23); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); memoise 2.0.1(2021-11-26); OmnipathR 3.17.0(2025-06-27); pillar 1.10.2(2025-04-05); 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 1.0.4(2025-02-05); 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 1.0.14(2025-01-12); 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 2.4.1(2025-06-08); 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 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-06-27 22:27:23] [INFO] [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: x86_64-apple-darwin22.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2025-06-27 22:27:23] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-06-27 22:27:23] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-06-27 22:27:23] [TRACE] [OmnipathR] Contains 3 files.
[2025-06-27 22:27:23] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-06-27 22:27:23] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-06-27 22:27:23] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-06-27 22:27:23] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-06-27 22:27:23] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-06-27 22:27:23] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-06-27 22:27:23] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-06-27 22:27:23] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-06-27 22:27:23] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-06-27 22:27:23] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-06-27 22:27:23] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-06-27 22:27:23] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-06-27 22:27:23] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-06-27 22:27:23] [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
15.930 2.609 45.281
OmnipathR.Rcheck/OmnipathR-Ex.timings
| name | user | system | elapsed | |
| OmnipathR | 0.001 | 0.001 | 0.001 | |
| all_uniprot_acs | 0.021 | 0.003 | 0.025 | |
| all_uniprots | 1.622 | 0.244 | 13.874 | |
| ancestors | 0.010 | 0.002 | 0.012 | |
| annotated_network | 1.215 | 0.132 | 4.428 | |
| annotation_categories | 55.777 | 0.332 | 57.971 | |
| annotation_resources | 0.063 | 0.009 | 0.596 | |
| annotations | 0.534 | 0.053 | 1.451 | |
| biomart_query | 1.235 | 0.187 | 2.287 | |
| bioplex1 | 0.011 | 0.002 | 0.012 | |
| bioplex2 | 0.010 | 0.002 | 0.012 | |
| bioplex3 | 0.010 | 0.002 | 0.012 | |
| bioplex_all | 0.010 | 0.001 | 0.012 | |
| bioplex_hct116_1 | 0.011 | 0.002 | 0.013 | |
| bma_motif_es | 0.601 | 0.077 | 1.598 | |
| bma_motif_vs | 0.189 | 0.027 | 0.706 | |
| chalmers_gem | 0.011 | 0.002 | 0.014 | |
| chalmers_gem_id_mapping_table | 0.009 | 0.001 | 0.011 | |
| chalmers_gem_id_type | 0.002 | 0.000 | 0.002 | |
| chalmers_gem_metabolites | 0.009 | 0.002 | 0.010 | |
| chalmers_gem_network | 0.009 | 0.002 | 0.011 | |
| chalmers_gem_raw | 0.010 | 0.002 | 0.011 | |
| chalmers_gem_reactions | 0.010 | 0.001 | 0.011 | |
| common_name | 0.035 | 0.004 | 0.040 | |
| complex_genes | 0.654 | 0.064 | 2.458 | |
| complex_resources | 0.060 | 0.007 | 0.660 | |
| complexes | 0.169 | 0.017 | 0.733 | |
| consensuspathdb_download | 0.001 | 0.000 | 0.000 | |
| consensuspathdb_raw_table | 0.011 | 0.002 | 0.014 | |
| cosmos_pkn | 0 | 0 | 0 | |
| curated_ligand_receptor_interactions | 6.725 | 1.224 | 16.959 | |
| curated_ligrec_stats | 38.069 | 15.081 | 120.588 | |
| database_summary | 1.793 | 0.822 | 4.002 | |
| descendants | 0.012 | 0.008 | 0.018 | |
| ensembl_dataset | 0.013 | 0.008 | 0.020 | |
| ensembl_id_mapping_table | 1.422 | 1.876 | 14.444 | |
| ensembl_id_type | 0.003 | 0.001 | 0.004 | |
| ensembl_name | 0.077 | 0.021 | 0.106 | |
| ensembl_organisms | 0.208 | 0.119 | 0.345 | |
| ensembl_organisms_raw | 0.179 | 0.153 | 0.312 | |
| ensembl_orthology | 0.000 | 0.000 | 0.001 | |
| enzsub_graph | 2.682 | 0.845 | 9.040 | |
| enzsub_resources | 0.077 | 0.008 | 0.680 | |
| enzyme_substrate | 1.450 | 0.075 | 2.809 | |
| evex_download | 0.013 | 0.002 | 0.017 | |
| evidences | 0 | 0 | 0 | |
| extra_attr_values | 16.959 | 3.194 | 33.737 | |
| extra_attrs | 10.544 | 2.199 | 19.711 | |
| extra_attrs_to_cols | 13.689 | 10.091 | 27.331 | |
| filter_by_resource | 8.424 | 1.309 | 18.473 | |
| filter_extra_attrs | 39.903 | 13.300 | 78.428 | |
| filter_intercell | 5.908 | 0.881 | 11.130 | |
| filter_intercell_network | 0.021 | 0.004 | 0.025 | |
| find_all_paths | 6.266 | 0.485 | 6.876 | |
| from_evidences | 0.000 | 0.001 | 0.001 | |
| get_db | 0.001 | 0.000 | 0.000 | |
| get_ontology_db | 0.012 | 0.002 | 0.014 | |
| giant_component | 10.573 | 1.181 | 14.742 | |
| go_annot_download | 13.870 | 1.543 | 14.029 | |
| go_annot_slim | 0.001 | 0.001 | 0.000 | |
| go_ontology_download | 0.012 | 0.002 | 0.014 | |
| guide2pharma_download | 0.011 | 0.002 | 0.013 | |
| harmonizome_download | 0.010 | 0.002 | 0.012 | |
| has_extra_attrs | 9.153 | 2.960 | 12.244 | |
| hmdb_id_mapping_table | 0.011 | 0.002 | 0.013 | |
| hmdb_id_type | 0.002 | 0.001 | 0.003 | |
| hmdb_metabolite_fields | 0.000 | 0.001 | 0.002 | |
| hmdb_protein_fields | 0.000 | 0.000 | 0.001 | |
| hmdb_table | 0.011 | 0.002 | 0.013 | |
| homologene_download | 0.011 | 0.002 | 0.013 | |
| homologene_raw | 0.023 | 0.003 | 0.028 | |
| homologene_uniprot_orthology | 0.011 | 0.002 | 0.013 | |
| hpo_download | 2.707 | 0.418 | 3.219 | |
| htridb_download | 0.014 | 0.002 | 0.016 | |
| id_translation_resources | 0.001 | 0.000 | 0.001 | |
| id_types | 0.068 | 0.012 | 0.080 | |
| inbiomap_download | 0.000 | 0.000 | 0.001 | |
| inbiomap_raw | 0 | 0 | 0 | |
| interaction_datasets | 0.674 | 0.085 | 0.991 | |
| interaction_graph | 0.399 | 0.032 | 1.034 | |
| interaction_resources | 0.089 | 0.010 | 0.865 | |
| interaction_types | 0.050 | 0.007 | 0.058 | |
| intercell | 0.733 | 0.105 | 1.310 | |
| intercell_categories | 0.601 | 0.083 | 0.913 | |
| intercell_consensus_filter | 1.460 | 0.171 | 3.111 | |
| intercell_generic_categories | 0.055 | 0.008 | 0.064 | |
| intercell_network | 0.011 | 0.002 | 0.014 | |
| intercell_resources | 0.065 | 0.008 | 0.631 | |
| intercell_summary | 0.059 | 0.019 | 0.078 | |
| is_ontology_id | 0.000 | 0.000 | 0.001 | |
| is_swissprot | 0.035 | 0.004 | 0.040 | |
| is_trembl | 0.034 | 0.005 | 0.039 | |
| is_uniprot | 0.011 | 0.002 | 0.013 | |
| kegg_api_templates | 0.002 | 0.003 | 0.004 | |
| kegg_conv | 1.378 | 0.191 | 12.694 | |
| kegg_databases | 0.000 | 0.001 | 0.000 | |
| kegg_ddi | 0.605 | 0.077 | 1.958 | |
| kegg_find | 0.606 | 0.070 | 2.101 | |
| kegg_info | 0.011 | 0.002 | 0.013 | |
| kegg_link | 0.696 | 0.141 | 6.178 | |
| kegg_list | 0.623 | 0.092 | 1.688 | |
| kegg_open | 0.012 | 0.001 | 0.013 | |
| kegg_operations | 0.000 | 0.000 | 0.001 | |
| kegg_organism_codes | 0.026 | 0.059 | 0.085 | |
| kegg_organisms | 0.027 | 0.007 | 0.033 | |
| kegg_pathway_annotations | 0.000 | 0.001 | 0.000 | |
| kegg_pathway_download | 0.009 | 0.002 | 0.011 | |
| kegg_pathway_list | 0.012 | 0.002 | 0.014 | |
| kegg_pathways_download | 0 | 0 | 0 | |
| kegg_picture | 0.904 | 0.054 | 5.198 | |
| kegg_process | 0.022 | 0.003 | 0.024 | |
| kegg_query | 0.008 | 0.001 | 0.009 | |
| kegg_request | 0.070 | 0.009 | 0.081 | |
| kegg_rm_prefix | 0.768 | 0.096 | 5.344 | |
| latin_name | 0.076 | 0.007 | 0.085 | |
| load_db | 0.107 | 0.022 | 0.128 | |
| metalinksdb_sqlite | 1.010 | 0.342 | 15.677 | |
| metalinksdb_table | 0.261 | 0.044 | 0.306 | |
| metalinksdb_tables | 0.020 | 0.006 | 0.026 | |
| ncbi_taxid | 0.068 | 0.006 | 0.075 | |
| nichenet_build_model | 0 | 0 | 0 | |
| nichenet_expression_data | 0.010 | 0.001 | 0.012 | |
| nichenet_gr_network | 0.031 | 0.005 | 0.037 | |
| nichenet_gr_network_evex | 0.010 | 0.002 | 0.012 | |
| nichenet_gr_network_harmonizome | 0.010 | 0.002 | 0.012 | |
| nichenet_gr_network_htridb | 0.010 | 0.002 | 0.011 | |
| nichenet_gr_network_omnipath | 15.681 | 1.730 | 19.916 | |
| nichenet_gr_network_pathwaycommons | 0.011 | 0.001 | 0.013 | |
| nichenet_gr_network_regnetwork | 0.010 | 0.002 | 0.011 | |
| nichenet_gr_network_remap | 0.010 | 0.002 | 0.013 | |
| nichenet_gr_network_trrust | 0.010 | 0.002 | 0.012 | |
| nichenet_ligand_activities | 0 | 0 | 0 | |
| nichenet_ligand_target_links | 0 | 0 | 0 | |
| nichenet_ligand_target_matrix | 0 | 0 | 0 | |
| nichenet_lr_network | 0.031 | 0.005 | 0.037 | |
| nichenet_lr_network_guide2pharma | 0.012 | 0.001 | 0.013 | |
| nichenet_lr_network_omnipath | 0.033 | 0.005 | 0.037 | |
| nichenet_lr_network_ramilowski | 0.011 | 0.001 | 0.013 | |
| nichenet_main | 0 | 0 | 0 | |
| nichenet_networks | 0.057 | 0.012 | 0.069 | |
| nichenet_optimization | 0 | 0 | 0 | |
| nichenet_remove_orphan_ligands | 0.066 | 0.009 | 0.074 | |
| nichenet_results_dir | 0.000 | 0.000 | 0.001 | |
| nichenet_signaling_network | 0.031 | 0.005 | 0.037 | |
| nichenet_signaling_network_cpdb | 0.009 | 0.002 | 0.011 | |
| nichenet_signaling_network_evex | 0.011 | 0.002 | 0.013 | |
| nichenet_signaling_network_harmonizome | 0.010 | 0.002 | 0.012 | |
| nichenet_signaling_network_inbiomap | 0.000 | 0.001 | 0.000 | |
| nichenet_signaling_network_omnipath | 11.354 | 1.131 | 14.894 | |
| nichenet_signaling_network_pathwaycommons | 0.012 | 0.002 | 0.015 | |
| nichenet_signaling_network_vinayagam | 0.012 | 0.002 | 0.014 | |
| nichenet_test | 0.000 | 0.001 | 0.000 | |
| nichenet_workarounds | 0 | 0 | 0 | |
| obo_parser | 0.119 | 0.025 | 0.179 | |
| oma_code | 0.040 | 0.004 | 0.044 | |
| oma_organisms | 0.093 | 0.018 | 0.111 | |
| oma_pairwise | 0.011 | 0.002 | 0.014 | |
| oma_pairwise_genesymbols | 0.011 | 0.002 | 0.014 | |
| oma_pairwise_translated | 0.011 | 0.002 | 0.014 | |
| omnipath-interactions | 29.453 | 2.933 | 56.377 | |
| omnipath_cache_autoclean | 0.000 | 0.000 | 0.001 | |
| omnipath_cache_clean | 0.013 | 0.005 | 0.018 | |
| omnipath_cache_clean_db | 0.136 | 0.024 | 0.162 | |
| omnipath_cache_download_ready | 0.562 | 0.136 | 0.826 | |
| omnipath_cache_filter_versions | 0.102 | 0.026 | 0.142 | |
| omnipath_cache_get | 0.088 | 0.020 | 0.111 | |
| omnipath_cache_key | 0.001 | 0.000 | 0.002 | |
| omnipath_cache_latest_or_new | 0.063 | 0.015 | 0.078 | |
| omnipath_cache_load | 0.523 | 0.047 | 3.301 | |
| omnipath_cache_move_in | 0.166 | 0.041 | 0.224 | |
| omnipath_cache_remove | 0.132 | 0.027 | 0.173 | |
| omnipath_cache_save | 0.169 | 0.033 | 0.262 | |
| omnipath_cache_search | 0.001 | 0.000 | 0.001 | |
| omnipath_cache_set_ext | 0.087 | 0.023 | 0.122 | |
| omnipath_cache_update_status | 0.094 | 0.020 | 0.116 | |
| omnipath_cache_wipe | 0 | 0 | 0 | |
| omnipath_config_path | 0.000 | 0.000 | 0.001 | |