Multiple platform build/check report for BioC 3.20 - BUILD results for methodical on palomino8

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4744
palomino8	Windows Server 2022 Datacenter	x64	4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"	4487
merida1	macOS 12.7.5 Monterey	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4515
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4467
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 palomino8

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: 1.2.0

Command: chmod a+r methodical -R && F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data methodical

StartedAt: 2024-12-19 20:06:02 -0500 (Thu, 19 Dec 2024)

EndedAt: 2024-12-19 20:07:27 -0500 (Thu, 19 Dec 2024)

EllapsedTime: 84.1 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

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###
### Running command:
###
###   chmod a+r methodical -R && F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe 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
You do not have sufficient privilege to perform this operation.
You do not have sufficient privilege to perform this operation.

Quitting from lines 51-56 [unnamed-chunk-3] (calculating_methylation_transcription_correlations.Rmd)
Error: processing vignette 'calculating_methylation_transcription_correlations.Rmd' failed with diagnostics:
directory
  "F:\biocbuild\bbs-3.20-bioc\tmpdir\Rtmp4KsUW2/mcrpc_wgbs_hg38_chr11"
  does not seem to contain an HDF5-based SummarizedExperiment object
  previously saved with saveHDF5SummarizedExperiment()
--- failed re-building 'calculating_methylation_transcription_correlations.Rmd'

--- re-building 'identifying_tmrs.Rmd' using rmarkdown

Quitting from lines 68-82 [unnamed-chunk-4] (identifying_tmrs.Rmd)
Error: processing vignette 'identifying_tmrs.Rmd' failed with diagnostics:
unused arguments (expand_upstream = 5000, expand_downstream = 5000)
--- failed re-building 'identifying_tmrs.Rmd'

--- re-building 'working_with_meth_rses.Rmd' using rmarkdown

Quitting from lines 46-48 [unnamed-chunk-2] (working_with_meth_rses.Rmd)
Error: processing vignette 'working_with_meth_rses.Rmd' failed with diagnostics:
F:\biocbuild\bbs-3.20-bioc\tmpdir\Rtmp4KsUW2/mcrpc_wgbs_hg38_chr11 already exists but it does not contain a HDF5 SummarizedExperiment
--- failed re-building 'working_with_meth_rses.Rmd'

SUMMARY: processing the following files failed:
  'calculating_methylation_transcription_correlations.Rmd'
  'identifying_tmrs.Rmd' 'working_with_meth_rses.Rmd'

Error: Vignette re-building failed.
Execution halted