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

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

Version: 1.11.1

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

StartedAt: 2025-10-10 18:53:44 -0400 (Fri, 10 Oct 2025)

EndedAt: 2025-10-10 18:57:38 -0400 (Fri, 10 Oct 2025)

EllapsedTime: 234.0 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data RgnTX
###
##############################################################################
##############################################################################


* checking for file ‘RgnTX/DESCRIPTION’ ... OK
* preparing ‘RgnTX’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘RgnTX.Rmd’ using rmarkdown
2025-10-10 18:56:26.041 R[62108:509475314] XType: com.apple.fonts is not accessible.
2025-10-10 18:56:26.042 R[62108:509475314] XType: XTFontStaticRegistry is enabled.

Quitting from RgnTX.Rmd:738-757 [unnamed-chunk-30]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! subscript contains invalid names
---
Backtrace:
     ▆
  1. ├─cds.tx0[trans.ids]
  2. └─cds.tx0[trans.ids]
  3.   ├─methods::callNextMethod(x = x, i = i)
  4.   │ └─base::eval(call, callEnv)
  5.   │   └─base::eval(call, callEnv)
  6.   └─S4Vectors (local) .nextMethod(x = x, i = i)
  7.     └─S4Vectors:::subset_along_ROWS(x, i, drop = drop)
  8.       ├─S4Vectors::extractROWS(x, i)
  9.       └─GenomicRanges (local) extractROWS(x, i)
 10.         └─IRanges (local) METHOD(x, i)
 11.           └─S4Vectors::normalizeSingleBracketSubscript(i, x, as.NSBS = TRUE)
 12.             ├─S4Vectors::NSBS(...)
 13.             └─S4Vectors::NSBS(...)
 14.               └─S4Vectors:::.subscript_error("subscript contains invalid ", what)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'RgnTX.Rmd' failed with diagnostics:
subscript contains invalid names
--- failed re-building ‘RgnTX.Rmd’

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

Error: Vignette re-building failed.
Execution halted