Denes Turei
| Snapshot Date: 2026-05-06 13:40 -0400 (Wed, 06 May 2026) |
| git_url: https://git.bioconductor.org/packages/OmnipathR |
| git_branch: RELEASE_3_23 |
| git_last_commit: a4e9224 |
| git_last_commit_date: 2026-04-29 06:27:44 -0400 (Wed, 29 Apr 2026) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-05-07 11:36 -0400 (Thu, 07 May 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 RC (2026-04-17 r89917) -- "Because it was There" | 4990 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.6.0 Patched (2026-04-24 r89963) -- "Because it was There" | 4723 |
| 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 1541/2418 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| OmnipathR 4.0.0 (landing page) Denes Turei
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | ERROR | OK | ERROR | ERROR | |||||||||
| See other builds for OmnipathR in R Universe. | ||||||||||||||
|
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: 4.0.0 |
| 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_4.0.0.tar.gz |
| StartedAt: 2026-05-06 21:38:35 -0400 (Wed, 06 May 2026) |
| EndedAt: 2026-05-06 21:38:39 -0400 (Wed, 06 May 2026) |
| EllapsedTime: 4.0 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_4.0.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/OmnipathR.Rcheck’
* using R version 4.6.0 Patched (2026-04-24 r89963)
* using platform: aarch64-apple-darwin23
* R was compiled by
Apple clang version 17.0.0 (clang-1700.3.19.1)
GNU Fortran (GCC) 14.2.0
* running under: macOS Tahoe 26.3.1
* using session charset: UTF-8
* current time: 2026-05-07 01:38:36 UTC
* using option ‘--no-vignettes’
* checking for file ‘OmnipathR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OmnipathR’ version ‘4.0.0’
* 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 ... ERROR
Installation failed.
See ‘/Users/biocbuild/bbs-3.23-bioc/meat/OmnipathR.Rcheck/00install.out’ for details.
* DONE
Status: 1 ERROR
See
‘/Users/biocbuild/bbs-3.23-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/4.6/Resources/library’ * installing *source* package ‘OmnipathR’ ... ** this is package ‘OmnipathR’ version ‘4.0.0’ ** 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 [2026-05-06 15:39:26] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-06 15:39:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-06 15:39:26] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2026-05-06 15:39:26] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2026-05-06 15:39:26] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-05-06 [2026-05-06 15:39:26] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-05-06 19:39:21 UTC; unix [2026-05-06 15:39:26] [INFO] [OmnipathR] Package `OmnipathR` version: 4.0.0 [2026-05-06 15:39:26] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23 Error: package or namespace load failed for ‘OmnipathR’: .onLoad failed in loadNamespace() for 'OmnipathR', details: call: strsplit(info, "\n", useBytes = TRUE)[[1]] error: subscript out of bounds Error: loading failed Execution halted ERROR: loading failed * removing ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR’ * restoring previous ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR’