Build/check report for BioC 3.23 - BUILD results for RNAmodR.ML 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"	4818
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BUILD results for RNAmodR.ML on nebbiolo1

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

Version: 1.25.0

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

StartedAt: 2025-11-05 19:41:53 -0500 (Wed, 05 Nov 2025)

EndedAt: 2025-11-05 19:43:40 -0500 (Wed, 05 Nov 2025)

EllapsedTime: 107.1 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 RNAmodR.ML
###
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* checking for file ‘RNAmodR.ML/DESCRIPTION’ ... OK
* preparing ‘RNAmodR.ML’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘RNAmodR.ML.Rmd’ using rmarkdown
[E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/ca93d4a0d1c5c_2521'
[E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/ca93d4f04f68d_2523'
[E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/ca93d2308334c_2525'
[E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/ca93d4a0d1c5c_2521'
[E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/ca93d4f04f68d_2523'
[E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/ca93d2308334c_2525'
[E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/ca93d4a0d1c5c_2521'
[E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/ca93d4a0d1c5c_2521'
[E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/ca93d4f04f68d_2523'
[E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/ca93d4f04f68d_2523'
[E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/ca93d2308334c_2525'
[E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/ca93d2308334c_2525'

Quitting from RNAmodR.ML.Rmd:140-142 [unnamed-chunk-6]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<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. ├─global ModMLExample(files[[1]], annotation, sequences)
  2. │ ├─RNAmodR:::Modifier(...)
  3. │ └─RNAmodR:::Modifier(...)
  4. │   └─RNAmodR:::.new_ModFromCharacter(...)
  5. │     └─RNAmodR:::.new_ModFromSequenceData(className, data, ...)
  6. │       └─RNAmodR:::.Modifier(className, x)
  7. │         ├─methods::new(...)
  8. │         │ ├─methods::initialize(value, ...)
  9. │         │ └─RNAmodR.ML (local) initialize(value, ...)
 10. │         │   ├─methods::callNextMethod()
 11. │         │   └─methods (local) .nextMethod(.Object = .Object, ... = ...)
 12. │         └─RNAmodR:::.norm_mod(proto)
 13. │           └─RNAmodR:::.is_valid_modType(modType, seqtype(x))
 14. │             └─RNAmodR:::.is_valid_RNAmodType(modType)
 15. │               ├─modType %in% Modstrings::shortName(Modstrings::ModRNAString())
 16. │               ├─Modstrings::shortName(Modstrings::ModRNAString())
 17. │               └─Modstrings::ModRNAString()
 18. │                 ├─Biostrings:::XString("ModRNA", x, start = start, width = nchar)
 19. │                 └─Biostrings:::XString("ModRNA", x, start = start, width = nchar)
 20. │                   └─Biostrings:::.charToXString(seqtype, x, start, end, width)
 21. │                     ├─Biostrings::make_XString_from_string(...)
 22. │                     └─Modstrings (local) make_XString_from_string(x0, string, start(solved_SEW), width(solved_SEW))
 23. │                       ├─methods::callNextMethod()
 24. │                       └─Biostrings (local) .nextMethod(x0 = x0, string = string, start = start, width = width)
 25. │                         └─Biostrings::get_seqtype_conversion_lookup("B", seqtype(x0))
 26. │                           └─base::stop("Biostrings internal error, please report")
 27. ├─base::.handleSimpleError(...)
 28. │ └─base (local) h(simpleError(msg, call))
 29. └─base::.handleSimpleError(...)
 30.   └─base (local) h(simpleError(msg, call))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'RNAmodR.ML.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 ‘RNAmodR.ML.Rmd’

SUMMARY: processing the following file failed:
  ‘RNAmodR.ML.Rmd’

Error: Vignette re-building failed.
Execution halted