neurogenomics / EpiCompare

Comparison, benchmarking & QC of epigenetic datasets
https://doi.org/doi:10.18129/B9.bioc.EpiCompare
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GHA Windows: ` there is no package called 'TxDb.Hsapiens.UCSC.hg19.knownGene'` #117

Closed bschilder closed 1 year ago

bschilder commented 2 years ago

Not sure why this is happening, but the Windows GitHub Actions virtual env doesn't seem to be able to install the Bioc data package TxDb.Hsapiens.UCSC.hg19.knownGene. This is despite the fact that both the release and devel versions aren't showing any errors on any platforms.

GHA link: https://github.com/neurogenomics/EpiCompare/actions/runs/3177112870/jobs/5177183808#step:21:37

Loading required package: sessioninfo
── R CMD build ─────────────────────────────────────────────────────────────────
* checking for file 'D:\a\EpiCompare\EpiCompare/DESCRIPTION' ... OK
* preparing 'EpiCompare':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
      -----------------------------------
* installing *source* package 'EpiCompare' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : 
  there is no package called 'TxDb.Hsapiens.UCSC.hg19.knownGene'
Calls: <Anonymous> ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
ERROR: lazy loading failed for package 'EpiCompare'
* removing 'C:/Users/RUNNER~1/AppData/Local/Temp/RtmpEFNrca/Rinst121[46](https://github.com/neurogenomics/EpiCompare/actions/runs/3177112870/jobs/5177183808#step:21:47)b3e287d/EpiCompare'
      -----------------------------------
ERROR: package installation failed
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.

My guess is that this will go away with time, but just noting it here to keep aware of it until it's resolved.

bschilder commented 1 year ago

This has since been resolved automatically