Build/check report for BioC 3.22 - BUILD results for epigraHMM on nebbiolo2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"	4893
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BUILD results for epigraHMM on nebbiolo2

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

Version: 1.18.0

Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 epigraHMM

StartedAt: 2026-03-24 17:25:05 -0400 (Tue, 24 Mar 2026)

EndedAt: 2026-03-24 17:29:55 -0400 (Tue, 24 Mar 2026)

EllapsedTime: 290.2 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 epigraHMM
###
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* checking for file ‘epigraHMM/DESCRIPTION’ ... OK
* preparing ‘epigraHMM’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘epigraHMM.Rmd’ using rmarkdown

Quitting from epigraHMM.Rmd:255-283 [data_peak_consensus]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `h()`:
! error in evaluating the argument 'table' in selecting a method for function '%in%': 
---
Backtrace:
     ▆
  1. ├─epigraHMM::epigraHMMDataSetFromBam(...)
  2. │ └─epigraHMM:::getGap(gapTrack, genome, genomeList[["seqinfo"]])
  3. │   ├─rtracklayer::ucscTableQuery(session, table = "gap")
  4. │   └─rtracklayer::ucscTableQuery(session, table = "gap")
  5. │     ├─rtracklayer::ucscTableQuery(genome(x), ...)
  6. │     └─rtracklayer::ucscTableQuery(genome(x), ...)
  7. │       └─rtracklayer (local) .local(x, ...)
  8. │         ├─rtracklayer::`tableName<-`(`*tmp*`, check = check, value = table)
  9. │         └─rtracklayer::`tableName<-`(`*tmp*`, check = check, value = table)
 10. │           └─rtracklayer (local) .local(x, ..., value = value)
 11. │             └─rtracklayer:::normArgTable(value, x)
 12. │               ├─name %in% tableNames(query)
 13. │               ├─rtracklayer::tableNames(query)
 14. │               └─rtracklayer::tableNames(query)
 15. │                 └─rtracklayer (local) .local(object, ...)
 16. │                   ├─restfulr::read(url$list$tracks, genome = genome, trackLeavesOnly = 1)
 17. │                   └─restfulr::read(url$list$tracks, genome = genome, trackLeavesOnly = 1)
 18. │                     ├─base::tryCatch(...)
 19. │                     │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 20. │                     │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 21. │                     │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
 22. │                     └─x@protocol$read(x, cacheInfo)
 23. │                       └─restfulr:::handleResponse(content, reader, cache.info, x@errorHandler)
 24. │                         └─restfulr (local) errorHandler(responseError)
 25. │                           └─base::stop(response$statusMessage)
 26. └─base::.handleSimpleError(`<fn>`, "", base::quote(errorHandler(responseError)))
 27.   └─base (local) h(simpleError(msg, call))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'epigraHMM.Rmd' failed with diagnostics:
error in evaluating the argument 'table' in selecting a method for function '%in%': 
--- failed re-building ‘epigraHMM.Rmd’

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

Error: Vignette re-building failed.
Execution halted