Build/check report for BioC 3.23 annotations - BUILD results for EpiTxDb.Hs.hg38 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"	4865
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 EpiTxDb.Hs.hg38 on nebbiolo1

To the developers/maintainers of the EpiTxDb.Hs.hg38 package:
- 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.Hs.hg38

Version: 0.99.7

Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data EpiTxDb.Hs.hg38

StartedAt: 2025-11-26 06:01:35 -0500 (Wed, 26 Nov 2025)

EndedAt: 2025-11-26 06:02:37 -0500 (Wed, 26 Nov 2025)

EllapsedTime: 62.0 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.Hs.hg38
###
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* checking for file ‘EpiTxDb.Hs.hg38/DESCRIPTION’ ... OK
* preparing ‘EpiTxDb.Hs.hg38’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘EpiTxDb.Hs.hg38.Rmd’ using rmarkdown

Quitting from EpiTxDb.Hs.hg38.Rmd:74-88 [unnamed-chunk-6]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `get_seqtype_conversion_lookup()`:
! Biostrings internal error, please report
---
Backtrace:
    ▆
 1. └─Modstrings::ModRNAStringSet(...)
 2.   ├─Biostrings:::XStringSet(...)
 3.   └─Biostrings:::XStringSet(...)
 4.     └─Biostrings:::.charToXStringSet(...)
 5.       ├─Biostrings::make_XStringSet_from_strings(...)
 6.       └─Modstrings (local) make_XStringSet_from_strings(...)
 7.         ├─methods::callNextMethod()
 8.         └─Biostrings (local) .nextMethod(x0 = x0, strings = strings, start = start, width = width)
 9.           └─Biostrings::get_seqtype_conversion_lookup("B", seqtype(x0))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'EpiTxDb.Hs.hg38.Rmd' failed with diagnostics:
Biostrings internal error, please report
--- failed re-building ‘EpiTxDb.Hs.hg38.Rmd’

SUMMARY: processing the following file failed:
  ‘EpiTxDb.Hs.hg38.Rmd’

Error: Vignette re-building failed.
Execution halted