Incomplete or Erroring Workshops

Question

Incomplete or Erroring Workshops

Closed this issue 6 years ago · 5 comments

Dear Workshop Contributors,
@mikelove @lwaldron @PeteHaitch @risserlin
@sa-lee @drisso @zhaleh-safikhani @kstreet13
@lgeistlinger @npcooley @Simon-Coetzee @nturaga
@vobencha

A few items are still unresolved for getting a complete workshop build.

Please check the _bookdown.yml file and the assigned issue for the status of your workshop
Make sure that you are using the appropriate Rmd file for your workshop (there should be no duplicate workshop files)
Ensure that you are modifying the DESCRIPTION file and your package list accordingly so that all dependencies are documented

Best regards,
Marcel

cc: @mtmorgan @lshep

Answer 1 · 2018-07-07T14:23:20.000Z

Hi @LiNk-NY ,

it looks like for a couple of workshops (including ours) the problem is that aroma.light is failing its checks in bioc-devel and hence biocLite won't be able to install it. Any workaround? Or should we ask @HenrikBengtsson to fix it? :)

Answer 2 · 2018-07-07T15:01:35.000Z

The workaround is to install https://cran.r-project.org/src/contrib/Archive/princurve/princurve_1.1-12.tar.gz or GitHub devel branch of princurve. The reason is Issue rcannood/princurve#8.

Answer 3 · 2018-07-07T21:55:45.000Z

It looks like this devel branch of princurve was merged into the master branch, so I'll try just adding dynverse/princurve to the Remotes: .

Answer 4 · 2018-07-09T21:17:39.000Z

We don't need the devel version of princurve. The latest version should be good enough (2.0.4).

Answer 5 · 2018-07-09T23:14:29.000Z

I can confirm that aroma.light passes R CMD check --as-cran with the princurve 2.0.4 that just hit CRAN. I've/Travis CI/AppVeyor CI verified on Linux and Windows with various R versions - as soon as macOS binaries are rolled out, I'd expect it to also work there too. This means that aroma.light should build and pass all checks on Bioc release & devel at the next round of Bioc builds.