Build/check report for BioC 3.22 annotations - BUILD results for EpiTxDb.Mm.mm10 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"	4858
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.Mm.mm10 on nebbiolo2

To the developers/maintainers of the EpiTxDb.Mm.mm10 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.Mm.mm10

Version: 0.99.6

Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data EpiTxDb.Mm.mm10

StartedAt: 2025-11-19 05:56:34 -0500 (Wed, 19 Nov 2025)

EndedAt: 2025-11-19 05:57:34 -0500 (Wed, 19 Nov 2025)

EllapsedTime: 60.3 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 EpiTxDb.Mm.mm10
###
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* checking for file ‘EpiTxDb.Mm.mm10/DESCRIPTION’ ... OK
* preparing ‘EpiTxDb.Mm.mm10’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘EpiTxDb.Mm.mm10.Rmd’ using rmarkdown

Quitting from EpiTxDb.Mm.mm10.Rmd:37-40 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! failed to load resource
  name: AH78918
  title: EpiTxDb tRNAdb for Mus musculus mm10
  reason: Corrupt Cache: resource id
  See AnnotationHub's TroubleshootingTheHubs vignette section on corrupt cache
  cache: /home/biocbuild/.cache/R/AnnotationHub
  reason: ℹ In argument: `rpath = unname(bfcrpath(x, rids = rids))`.
Caused by error in `bfcrpath()`:
! all(rids %in% bfcrid(x)) is not TRUE
---
Backtrace:
     ▆
  1. └─EpiTxDb.Mm.mm10::EpiTxDb.Mm.mm10.tRNAdb()
  2.   └─EpiTxDb.Mm.mm10:::.load_resource(version = version, type = "tRNAdb")
  3.     ├─ah[[id]]
  4.     └─ah[[id]]
  5.       └─AnnotationHub (local) .local(x, i, j = j, ...)
  6.         └─AnnotationHub:::.Hub_get1(...)
  7.           └─base::tryCatch(...)
  8.             └─base (local) tryCatchList(expr, classes, parentenv, handlers)
  9.               └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 10.                 └─value[[3L]](cond)
 11.                   └─base::tryCatch(...)
 12.                     └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 13.                       └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 14.                         └─value[[3L]](cond)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'EpiTxDb.Mm.mm10.Rmd' failed with diagnostics:
failed to load resource
  name: AH78918
  title: EpiTxDb tRNAdb for Mus musculus mm10
  reason: Corrupt Cache: resource id
  See AnnotationHub's TroubleshootingTheHubs vignette section on corrupt cache
  cache: /home/biocbuild/.cache/R/AnnotationHub
  reason: ℹ In argument: `rpath = unname(bfcrpath(x, rids = rids))`.
Caused by error in `bfcrpath()`:
! all(rids %in% bfcrid(x)) is not TRUE
--- failed re-building ‘EpiTxDb.Mm.mm10.Rmd’

SUMMARY: processing the following file failed:
  ‘EpiTxDb.Mm.mm10.Rmd’

Error: Vignette re-building failed.
Execution halted