Multiple platform build/check report for BioC 3.22 - BUILD results for methodical on taishan

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"	4902
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 taishan

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results

Summary

Package: methodical

Version: 1.6.0

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

StartedAt: 2025-11-11 03:04:35 -0000 (Tue, 11 Nov 2025)

EndedAt: 2025-11-11 03:06:05 -0000 (Tue, 11 Nov 2025)

EllapsedTime: 90.0 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

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### Running command:
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###   /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data 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

Quitting from calculating_methylation_transcription_correlations.Rmd:50-57 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `TumourMethData::download_meth_dataset()`:
! H5 file cannot be found
---
Backtrace:
    ▆
 1. └─TumourMethData::download_meth_dataset(dataset = "mcrpc_wgbs_hg38_chr11")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'calculating_methylation_transcription_correlations.Rmd' failed with diagnostics:
H5 file cannot be found
--- failed re-building ‘calculating_methylation_transcription_correlations.Rmd’

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

Quitting from working_with_meth_rses.Rmd:46-49 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `TumourMethData::download_meth_dataset()`:
! H5 file cannot be found
---
Backtrace:
    ▆
 1. └─TumourMethData::download_meth_dataset(dataset = "mcrpc_wgbs_hg38_chr11")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'working_with_meth_rses.Rmd' failed with diagnostics:
H5 file cannot be found
--- failed re-building ‘working_with_meth_rses.Rmd’

SUMMARY: processing the following files failed:
  ‘calculating_methylation_transcription_correlations.Rmd’
  ‘working_with_meth_rses.Rmd’

Error: Vignette re-building failed.
Execution halted