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

To the developers/maintainers of the excluderanges 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: excluderanges

Version: 0.99.10

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

StartedAt: 2025-11-19 05:56:42 -0500 (Wed, 19 Nov 2025)

EndedAt: 2025-11-19 05:57:07 -0500 (Wed, 19 Nov 2025)

EllapsedTime: 25.2 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 excluderanges
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* checking for file ‘excluderanges/DESCRIPTION’ ... OK
* preparing ‘excluderanges’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘excluderanges.Rmd’ using rmarkdown

Quitting from excluderanges.Rmd:135-146 [allhg38excluderanges]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! failed to load resource
  name: AH107307
  title: hg38.Boyle.hg38-Excludable.v2
  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 `bfcrpath()`:
! all(rids %in% bfcrid(x)) is not TRUE
---
Backtrace:
     ▆
  1. ├─query_data[["AH107307"]]
  2. └─query_data[["AH107307"]]
  3.   └─AnnotationHub (local) .local(x, i, j = j, ...)
  4.     └─AnnotationHub:::.Hub_get1(...)
  5.       └─base::tryCatch(...)
  6.         └─base (local) tryCatchList(expr, classes, parentenv, handlers)
  7.           └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
  8.             └─value[[3L]](cond)
  9.               └─base::tryCatch(...)
 10.                 └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 11.                   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 12.                     └─value[[3L]](cond)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'excluderanges.Rmd' failed with diagnostics:
failed to load resource
  name: AH107307
  title: hg38.Boyle.hg38-Excludable.v2
  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 `bfcrpath()`:
! all(rids %in% bfcrid(x)) is not TRUE
--- failed re-building ‘excluderanges.Rmd’

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

Error: Vignette re-building failed.
Execution halted