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Fix GitHub Action

Open bschilder opened this issue 8 months ago • 8 comments

https://github.com/neurogenomics/MungeSumstats/actions/runs/6652926537/job/18077848264

It seems therworkflows GHA is failing due to the inability get some some resource files:

The downloaded binary packages are in
	/var/folders/3s/vfzpb5r51gs6y328rmlgzm7c0000gn/T//RtmpokJdJw/downloaded_packages
── R CMD build ─────────────────────────────────────────────────────────────────
* checking for file ‘.../DESCRIPTION’ ... OK
* preparing ‘MungeSumstats’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
Error: --- re-building ‘docker.Rmd’ using rmarkdown
--- finished re-building ‘docker.Rmd’
--- re-building ‘MungeSumstats.Rmd’ using rmarkdown
trying URL 'ftp://ftp.ensembl.org/pub/assembly_mapping/homo_sapiens/GRCh37_to_GRCh38.chain.gz'
Content type 'unknown' length 285250 bytes (278 KB)
==================================================
Quitting from lines 660-675 [unnamed-chunk-13] (MungeSumstats.Rmd)
Error: Error: processing vignette 'MungeSumstats.Rmd' failed with diagnostics:
No such file or directory: '/var/folders/3s/vfzpb5r51gs6y328rmm7c0000gn/T//RtmpK6ONEL/file2c69376a9483eduAttainOkbay_standardised.tsv'. Unable to create new file for writing (it does not exist already). Do you have permission to write here, is there space on the disk and does the path exist?
--- failed re-building ‘MungeSumstats.Rmd’
--- re-building ‘OpenGWAS.Rmd’ using rmarkdown
--- finished re-building ‘OpenGWAS.Rmd’
SUMMARY: processing the following file failed:
  ‘MungeSumstats.Rmd’
Error: Error: Vignette re-building failed.
Execution halted
Error: Error in proc$get_built_file() : Build process failed
Calls: <Anonymous> ... build_package -> with_envvar -> force -> <Anonymous>
Execution halted
Error: Process completed with exit code 1.
Run actions/upload-artifact@v3
Warning: No files were found with the provided path: check. No artifacts will be uploaded.

This could be due to one or more of the following:

  • Download limits
  • Security protocols for certain URLs
  • The choice of system downloader (e.g. "libcurl")

bschilder avatar Oct 27 '23 11:10 bschilder