Back to Multiple platform build/check report for BioC 3.20:   simplified   long
ABCDEFGHIJKL[M]NOPQRSTUVWXYZ

This page was generated on 2024-05-13 11:38:24 -0400 (Mon, 13 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4663
palomino4Windows Server 2022 Datacenterx644.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 4394
merida1macOS 12.7.4 Montereyx86_644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4425
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4480
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

Package 1191/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
methodical 1.1.0  (landing page)
Richard Heery
Snapshot Date: 2024-05-10 14:05:07 -0400 (Fri, 10 May 2024)
git_url: https://git.bioconductor.org/packages/methodical
git_branch: devel
git_last_commit: 3aab960
git_last_commit_date: 2024-04-30 11:53:36 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    ERROR  skippedskipped
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  
kjohnson1macOS 13.6.6 Ventura / arm64see weekly results here

BUILD results for methodical on palomino4


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: 1.1.0
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: 2024-05-10 19:30:19 -0400 (Fri, 10 May 2024)
EndedAt: 2024-05-10 19:32:22 -0400 (Fri, 10 May 2024)
EllapsedTime: 123.0 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### 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
###
##############################################################################
##############################################################################


* 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  at 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\RtmpwPeLEI/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
--- finished re-building 'identifying_tmrs.Rmd'

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

Quitting from lines  at 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\RtmpwPeLEI/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'
  'working_with_meth_rses.Rmd'

Error: Vignette re-building failed.
Execution halted