| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-11-27 12:04 -0500 (Thu, 27 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4876 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.2 Patched (2025-11-05 r88990) -- "[Not] Part in a Rumble" | 4656 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble" | 4602 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4668 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 260/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BulkSignalR 1.2.1 (landing page) Jean-Philippe Villemin
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
| kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | ERROR | skipped | ||||||||||
|
To the developers/maintainers of the BulkSignalR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BulkSignalR.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: BulkSignalR |
| Version: 1.2.1 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data BulkSignalR |
| StartedAt: 2025-11-24 20:29:51 -0500 (Mon, 24 Nov 2025) |
| EndedAt: 2025-11-24 20:32:12 -0500 (Mon, 24 Nov 2025) |
| EllapsedTime: 141.7 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data BulkSignalR
###
##############################################################################
##############################################################################
* checking for file ‘BulkSignalR/DESCRIPTION’ ... OK
* preparing ‘BulkSignalR’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘BulkSignalR-Configure.Rmd’ using rmarkdown
Warning: The vignette title specified in \VignetteIndexEntry{} is different from the title in the YAML metadata. The former is "BulkSignalR-Configure", and the latter is "BulkSignalR : </br> Inference of ligand-receptor interactions from bulk data or spatial transcriptomics". If that is intentional, you may set options(rmarkdown.html_vignette.check_title = FALSE) to suppress this check.
--- finished re-building ‘BulkSignalR-Configure.Rmd’
--- re-building ‘BulkSignalR-Differential.Rmd’ using rmarkdown
--- finished re-building ‘BulkSignalR-Differential.Rmd’
--- re-building ‘BulkSignalR-Main.Rmd’ using rmarkdown
2025-11-24 20:31:45.478 R[23184:71789755] XType: Using static font registry.
Quitting from BulkSignalR-Main.Rmd:547-581 [mouse]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! Request to g:Profiler failed (HTTP 500). The service may be temporarily unavailable.
If the issue persists, please contact biit.support@ut.ee with a reproducible example.
---
Backtrace:
▆
1. └─BulkSignalR::findOrthoGenes(from_organism = "mmusculus", from_values = rownames(bodyMap.mouse))
2. └─orthogene::convert_orthologs(...)
3. └─orthogene::map_orthologs(...)
4. └─orthogene:::map_orthologs_gprofiler(...)
5. └─gprofiler2::gorth(...)
6. └─gprofiler2::gprofiler_request(url, body)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'BulkSignalR-Main.Rmd' failed with diagnostics:
Request to g:Profiler failed (HTTP 500). The service may be temporarily unavailable.
If the issue persists, please contact biit.support@ut.ee with a reproducible example.
--- failed re-building ‘BulkSignalR-Main.Rmd’
SUMMARY: processing the following file failed:
‘BulkSignalR-Main.Rmd’
Error: Vignette re-building failed.
Execution halted