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This page was generated on 2025-11-19 06:45 -0500 (Wed, 19 Nov 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4858
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Package 22/49HostnameOS / ArchINSTALLBUILDCHECK
EpiTxDb.Sc.sacCer3 0.99.5  (landing page)
Felix G.M. Ernst
Snapshot Date: 2025-11-19 05:45 -0500 (Wed, 19 Nov 2025)
git_url: https://git.bioconductor.org/packages/EpiTxDb.Sc.sacCer3
git_branch: RELEASE_3_22
git_last_commit: bf65d31
git_last_commit_date: 2021-01-14 10:52:42 -0500 (Thu, 14 Jan 2021)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    ERROR  skipped

BUILD results for EpiTxDb.Sc.sacCer3 on nebbiolo2

To the developers/maintainers of the EpiTxDb.Sc.sacCer3 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.Sc.sacCer3
Version: 0.99.5
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data EpiTxDb.Sc.sacCer3
StartedAt: 2025-11-19 05:56:40 -0500 (Wed, 19 Nov 2025)
EndedAt: 2025-11-19 05:57:40 -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:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data EpiTxDb.Sc.sacCer3
###
##############################################################################
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* checking for file ‘EpiTxDb.Sc.sacCer3/DESCRIPTION’ ... OK
* preparing ‘EpiTxDb.Sc.sacCer3’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘EpiTxDb.Sc.sacCer3.Rmd’ using rmarkdown

Quitting from EpiTxDb.Sc.sacCer3.Rmd:37-40 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! failed to load resource
  name: AH78920
  title: EpiTxDb tRNAdb for Saccharomyces cerevisiae sacCer3
  reason: Corrupt Cache: resource id
  See AnnotationHub's TroubleshootingTheHubs vignette section on corrupt cache
  cache: /home/biocbuild/.cache/R/AnnotationHub
  reason: error in evaluating the argument 'table' in selecting a method for function 'match': ℹ In argument: `rpath = unname(bfcrpath(x, rids = rids))`.
Caused by error in `.sql_get_field()`:
! all(id %in% .get_all_rids(bfc)) is not TRUE
---
Backtrace:
     ▆
  1. └─EpiTxDb.Sc.sacCer3::EpiTxDb.Sc.sacCer3.tRNAdb()
  2.   └─EpiTxDb.Sc.sacCer3:::.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.Sc.sacCer3.Rmd' failed with diagnostics:
failed to load resource
  name: AH78920
  title: EpiTxDb tRNAdb for Saccharomyces cerevisiae sacCer3
  reason: Corrupt Cache: resource id
  See AnnotationHub's TroubleshootingTheHubs vignette section on corrupt cache
  cache: /home/biocbuild/.cache/R/AnnotationHub
  reason: error in evaluating the argument 'table' in selecting a method for function 'match': ℹ In argument: `rpath = unname(bfcrpath(x, rids = rids))`.
Caused by error in `.sql_get_field()`:
! all(id %in% .get_all_rids(bfc)) is not TRUE
--- failed re-building ‘EpiTxDb.Sc.sacCer3.Rmd’

SUMMARY: processing the following file failed:
  ‘EpiTxDb.Sc.sacCer3.Rmd’

Error: Vignette re-building failed.
Execution halted