Build/check report for BioC 3.23 - BUILD results for EpiTxDb on nebbiolo1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.3 LTS)	x86_64	R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"	4821
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BUILD results for EpiTxDb on nebbiolo1

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

Version: 1.23.0

Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data EpiTxDb

StartedAt: 2025-11-07 17:28:10 -0500 (Fri, 07 Nov 2025)

EndedAt: 2025-11-07 17:31:13 -0500 (Fri, 07 Nov 2025)

EllapsedTime: 183.2 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data EpiTxDb
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* checking for file ‘EpiTxDb/DESCRIPTION’ ... OK
* preparing ‘EpiTxDb’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘EpiTxDb-creation.Rmd’ using rmarkdown

Quitting from EpiTxDb-creation.Rmd:54-65 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `h()`:
! error in evaluating the argument 'table' in selecting a method for function '%in%': error in evaluating the argument 'x' in selecting a method for function 'shortName': Biostrings internal error, please report
---
Backtrace:
     ▆
  1. ├─EpiTxDb::makeEpiTxDbFromGRanges(...)
  2. │ └─EpiTxDb::makeEpiTxDb(...)
  3. │   └─EpiTxDb:::.makeEpiTxDb_normarg_modifications(modifications)
  4. │     ├─as.character(modifications$mod_type) %in% ...
  5. │     ├─Modstrings::shortName(ModRNAString())
  6. │     └─Modstrings::ModRNAString()
  7. │       ├─Biostrings:::XString("ModRNA", x, start = start, width = nchar)
  8. │       └─Biostrings:::XString("ModRNA", x, start = start, width = nchar)
  9. │         └─Biostrings:::.charToXString(seqtype, x, start, end, width)
 10. │           ├─Biostrings::make_XString_from_string(...)
 11. │           └─Modstrings (local) make_XString_from_string(x0, string, start(solved_SEW), width(solved_SEW))
 12. │             ├─methods::callNextMethod()
 13. │             └─Biostrings (local) .nextMethod(x0 = x0, string = string, start = start, width = width)
 14. │               └─Biostrings::get_seqtype_conversion_lookup("B", seqtype(x0))
 15. │                 └─base::stop("Biostrings internal error, please report")
 16. ├─base::.handleSimpleError(...)
 17. │ └─base (local) h(simpleError(msg, call))
 18. └─base::.handleSimpleError(...)
 19.   └─base (local) h(simpleError(msg, call))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'EpiTxDb-creation.Rmd' failed with diagnostics:
error in evaluating the argument 'table' in selecting a method for function '%in%': error in evaluating the argument 'x' in selecting a method for function 'shortName': Biostrings internal error, please report
--- failed re-building ‘EpiTxDb-creation.Rmd’

--- re-building ‘EpiTxDb.Rmd’ using rmarkdown
--- finished re-building ‘EpiTxDb.Rmd’

SUMMARY: processing the following file failed:
  ‘EpiTxDb-creation.Rmd’

Error: Vignette re-building failed.
Execution halted