Multiple platform build/check report for BioC 3.22 - BUILD results for factR on lconway

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"	4864
lconway	macOS 12.7.1 Monterey	x86_64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4652
kjohnson3	macOS 13.7.7 Ventura	arm64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4597
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4586
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 factR on lconway

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

Version: 1.11.0

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

StartedAt: 2025-10-10 17:09:24 -0400 (Fri, 10 Oct 2025)

EndedAt: 2025-10-10 17:12:29 -0400 (Fri, 10 Oct 2025)

EllapsedTime: 185.2 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 factR
###
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* checking for file ‘factR/DESCRIPTION’ ... OK
* preparing ‘factR’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘factR.Rmd’ using rmarkdown
2025-10-10 17:09:55.698 R[85170:508180906] XType: com.apple.fonts is not accessible.
2025-10-10 17:09:55.699 R[85170:508180906] XType: XTFontStaticRegistry is enabled.
trying URL 'ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M25/gencode.vM25.annotation.gtf.gz'
Content type 'unknown' length 28542432 bytes (27.2 MB)
==================================================

Quitting from factR.Rmd:318-320 [viewafterCDS]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `h()`:
! error in evaluating the argument 'args' in selecting a method for function 'do.call': object 'ccds' not found
---
Backtrace:
    ▆
 1. ├─factR::viewTranscripts(custom_new_CDS.gtf, "Zfr")
 2. │ ├─BiocGenerics::do.call(...)
 3. │ └─base::lapply(...)
 4. │   └─factR (local) FUN(X[[i]], ...)
 5. │     ├─base::suppressWarnings(...)
 6. │     │ └─base::withCallingHandlers(...)
 7. │     └─wiggleplotr::plotTranscripts(...)
 8. └─base::.handleSimpleError(...)
 9.   └─base (local) h(simpleError(msg, call))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'factR.Rmd' failed with diagnostics:
error in evaluating the argument 'args' in selecting a method for function 'do.call': object 'ccds' not found
--- failed re-building ‘factR.Rmd’

SUMMARY: processing the following file failed:
  ‘factR.Rmd’

Error: Vignette re-building failed.
Execution halted