Multiple platform build/check report for BioC 3.23 - BUILD results for BulkSignalR on kjohnson3

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"	4783
kjohnson3	macOS 13.7.7 Ventura	arm64	4.6.0 alpha (2026-04-08 r89818)	4701
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*

BUILD results for BulkSignalR on kjohnson3

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.

raw results

Summary

Package: BulkSignalR

Version: 1.3.2

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data BulkSignalR

StartedAt: 2026-04-22 15:55:26 -0400 (Wed, 22 Apr 2026)

EndedAt: 2026-04-22 15:57:06 -0400 (Wed, 22 Apr 2026)

EllapsedTime: 100.1 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data BulkSignalR
###
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* checking for file ‘BulkSignalR/DESCRIPTION’ ... OK
* preparing ‘BulkSignalR’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed 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

Quitting from BulkSignalR-Main.Rmd:547-581 [mouse]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `map_orthologs_gprofiler()`:
! Error : lexical error: invalid char in json text.
          ": "query_1"}, {"converted": NaN, "description": "N/A", "inc
                     (right here) ------^

---
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(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'BulkSignalR-Main.Rmd' failed with diagnostics:
Error : lexical error: invalid char in json text.
          ": "query_1"}, {"converted": NaN, "description": "N/A", "inc
                     (right here) ------^


--- failed re-building ‘BulkSignalR-Main.Rmd’

SUMMARY: processing the following file failed:
  ‘BulkSignalR-Main.Rmd’

Error: Vignette re-building failed.
Execution halted