Multiple platform build/check report for BioC 3.23 - BUILD results for AnnotationHub on lconway

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"	4826
lconway	macOS 12.7.6 Monterey	x86_64	R Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences"	4561
kjohnson3	macOS 13.7.7 Ventura	arm64	R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"	4562
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 AnnotationHub on lconway

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

Version: 4.1.0

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data AnnotationHub

StartedAt: 2025-11-17 16:05:51 -0500 (Mon, 17 Nov 2025)

EndedAt: 2025-11-17 16:26:54 -0500 (Mon, 17 Nov 2025)

EllapsedTime: 1263.0 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data AnnotationHub
###
##############################################################################
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* checking for file ‘AnnotationHub/DESCRIPTION’ ... OK
* preparing ‘AnnotationHub’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘AnnotationHub-HOWTO.Rmd’ using rmarkdown

Quitting from AnnotationHub-HOWTO.Rmd:310-313 [unnamed-chunk-23]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! failed to load resource
  name: AH57960
  title: clinvar_20160203.vcf.gz
  reason: 1 resources failed to download
---
Backtrace:
     ▆
  1. ├─ah[["AH57960"]]
  2. └─ah[["AH57960"]]
  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 'AnnotationHub-HOWTO.Rmd' failed with diagnostics:
failed to load resource
  name: AH57960
  title: clinvar_20160203.vcf.gz
  reason: 1 resources failed to download
--- failed re-building ‘AnnotationHub-HOWTO.Rmd’

--- re-building ‘AnnotationHub.Rmd’ using rmarkdown
--- finished re-building ‘AnnotationHub.Rmd’

--- re-building ‘TroubleshootingTheHubs.Rmd’ using rmarkdown
--- finished re-building ‘TroubleshootingTheHubs.Rmd’

SUMMARY: processing the following file failed:
  ‘AnnotationHub-HOWTO.Rmd’

Error: Vignette re-building failed.
Execution halted