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diaparim puriney

cnvworkshop's Issues

dependencies=TRUE in Dockerfile

Should be resolved by 88d11f9, but adding issue here to be sure.

Can test with:

docker run -it ludwigg/cnvworkshop:latest R -e 'rcmdcheck::rcmdcheck(args = c("--no-manual"), error_on = "error", check_dir = "check")'

Output is:

E  creating vignettes (41.5s)
   --- re-building ‘Geistlinger_CNVWorkshop.Rmd’ using rmarkdown
   Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
   Quitting from lines 113-123 (Geistlinger_CNVWorkshop.Rmd)
   Error: processing vignette 'Geistlinger_CNVWorkshop.Rmd' failed with diagnostics:
   there is no package called 'BSgenome.Btaurus.UCSC.bosTau6.masked'
   --- failed re-building ‘Geistlinger_CNVWorkshop.Rmd’

   SUMMARY: processing the following file failed:
     ‘Geistlinger_CNVWorkshop.Rmd’

   Error: Vignette re-building failed.
   Execution halted
Error in proc$get_built_file() : Build process failed
Calls: <Anonymous> ... build_package -> with_envvar -> force -> <Anonymous>
Execution halted

Operation timed out after 300192 milliseconds with 0 out of 0 bytes received

I'm seeing this locally on wallabe4 in Docker, haven't tested yet on the Cloud. Do you see this too, @lgeistlinger @shbrief @LiNk-NY?

Quitting from lines 835-847 (Geistlinger_CNVWorkshop.Rmd)
  Error: processing vignette 'Geistlinger_CNVWorkshop.Rmd' failed with diagnostics:
  Operation timed out after 300192 milliseconds with 0 out of 0 bytes received
  --- failed re-building ‘Geistlinger_CNVWorkshop.Rmd’

  SUMMARY: processing the following file failed:
    ‘Geistlinger_CNVWorkshop.Rmd’

  Error: Vignette re-building failed.
  Execution halted
Error in proc$get_built_file() : Build process failed
Calls: <Anonymous> ... build_package -> with_envvar -> force -> <Anonymous>
Execution halted

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