Build/check report for BioC 3.22 - BUILD results for RCAS on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
kjohnson3	macOS 13.7.7 Ventura	arm64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4637
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 RCAS on kjohnson3

To the developers/maintainers of the RCAS package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RCAS.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: RCAS

Version: 1.35.0

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

StartedAt: 2025-10-26 17:40:16 -0400 (Sun, 26 Oct 2025)

EndedAt: 2025-10-26 17:41:26 -0400 (Sun, 26 Oct 2025)

EllapsedTime: 69.8 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 RCAS
###
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* checking for file ‘RCAS/DESCRIPTION’ ... OK
* preparing ‘RCAS’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘RCAS.metaAnalysis.vignette.Rmd’ using rmarkdown
Warning: The vignette title specified in \VignetteIndexEntry{} is different from the title in the YAML metadata. The former is "How to do meta-analysis of multiple samples", and the latter is "How to do meta-analysis of CLIP-seq peaks from multiple samples with RCAS". If that is intentional, you may set options(rmarkdown.html_vignette.check_title = FALSE) to suppress this check.
--- finished re-building ‘RCAS.metaAnalysis.vignette.Rmd’

--- re-building ‘RCAS.vignette.Rmd’ using rmarkdown
2025-10-26 17:40:40.490 R[53637:550969894] XType: Using static font registry.
Error in x$.self$finalize() : attempt to apply non-function
Warning: call dbDisconnect() when finished working with a connection

Quitting from RCAS.vignette.Rmd:222-229 [motif_analysis]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! Bioconductor version cannot be validated; no internet connection?  See
  #troubleshooting section in vignette
---
Backtrace:
     ▆
  1. └─RCAS::runMotifDiscovery(...)
  2.   └─RCAS::extractSequences(queryRegions, genomeVersion)
  3.     └─RCAS::checkSeqDb(genomeVersion)
  4.       └─BSgenome::available.genomes()
  5.         └─BSgenome:::get_data_annotation_contrib_url(type)
  6.           ├─utils::contrib.url(BiocManager::repositories()["BioCann"], type = type)
  7.           └─BiocManager::repositories()
  8.             └─BiocManager:::.version_validate(version)
  9.               ├─base::ifelse(.is_CRAN_check(), .message(txt), .stop(txt))
 10.               └─BiocManager:::.stop(txt)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'RCAS.vignette.Rmd' failed with diagnostics:
Bioconductor version cannot be validated; no internet connection?  See
  #troubleshooting section in vignette
--- failed re-building ‘RCAS.vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘RCAS.vignette.Rmd’

Error: Vignette re-building failed.
Execution halted