Multiple platform build/check report for BioC 3.22 - BUILD results for methodical 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"	4615
merida1	macOS 12.7.6 Monterey	x86_64	4.5.2 Patched (2025-11-05 r88990) -- "[Not] Part in a Rumble"	4610
kjohnson1	macOS 13.7.5 Ventura	arm64	4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble"	4598
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4668
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 methodical on nebbiolo2

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

Version: 1.6.0

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

StartedAt: 2025-11-17 21:57:05 -0500 (Mon, 17 Nov 2025)

EndedAt: 2025-11-17 22:21:17 -0500 (Mon, 17 Nov 2025)

EllapsedTime: 1452.3 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 --md5 methodical
###
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* checking for file ‘methodical/DESCRIPTION’ ... OK
* preparing ‘methodical’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘calculating_methylation_transcription_correlations.Rmd’ using rmarkdown
--- finished re-building ‘calculating_methylation_transcription_correlations.Rmd’

--- re-building ‘working_with_meth_rses.Rmd’ using rmarkdown

Quitting from working_with_meth_rses.Rmd:184-200 [unnamed-chunk-7]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! failed to load resource
  name: AH99003
  title: UCSC RepeatMasker annotations (Sep2021) for Human (hg38)
  reason: 1 resources failed to download
---
Backtrace:
     ▆
  1. ├─AnnotationHub::AnnotationHub()[["AH99003"]]
  2. └─AnnotationHub::AnnotationHub()[["AH99003"]]
  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 'working_with_meth_rses.Rmd' failed with diagnostics:
failed to load resource
  name: AH99003
  title: UCSC RepeatMasker annotations (Sep2021) for Human (hg38)
  reason: 1 resources failed to download
--- failed re-building ‘working_with_meth_rses.Rmd’

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

Error: Vignette re-building failed.
Execution halted