CRAN checks: Packages required but not available: 'biocViews', 'BiocPkgTools'

[bschilder]

CRAN checks are failing when using R devel:
https://cran.r-project.org/web/checks/check_results_rworkflows.html

All errors are due to the following:

Packages required but not available: 'biocViews', 'BiocPkgTools'

biocViews is actually fine on Bioc devel. So not sure why CRAN is reporting a problem.
https://bioconductor.org/packages/devel/bioc/html/biocViews.html

But BiocPkgTools is indeed failing on devel. I've notified the maintainers and hopefully they'll fix this soon.
https://bioconductor.org/packages/devel/bioc/html/BiocPkgTools.html

[bschilder]

Fix was made, just waiting for updates to propagate to Bioc devel --> CRAN.
seandavi/BiocPkgTools#70 (comment)

[bschilder]

Fixes have propagated to Bioc, but CRAN is still showing the errors.

I reached out to the CRAN team, was told to find the guy who handles Mac problems. Found him, but he's on leave for an unknown period of time. Asked for a secondary contact to address this.

[bschilder]

Since I still haven't heard back form the CRAN maintainer, and there appears to be no secondary personnel who can handle this, I've decided to go the route of removing these pkgs as hard deps. Will push to dev and if all goes well, will merge with master.

[bschilder]

Merged dev --> master and submitted rworkflows v0.99.13 to CRAN. Just waiting for checks to finish.

[bschilder]

So despite the CRAN reviewer's suggestion, changing 'biocViews'/'BiocPkgTools' from Imports to Suggests did not remove the Note.

What's more, there are new errors regarding pandoc missing (a very standard system dep for most R packages). It seems the CRAN servers are a bit of a mess lately, and the only option is for me to wait until someone fixes it on their end.

https://cran.r-project.org/web/checks/check_results_rworkflows.html

[bschilder]

So despite the CRAN reviewer's suggestion, changing 'biocViews'/'BiocPkgTools' from Imports to Suggests did not remove the Note.

I've asked the Mac VM maintainer at CRAN to install these. Waiting for a reply.

What's more, there are new errors regarding pandoc missing (a very standard system dep for most R packages). It seems the CRAN servers are a bit of a mess lately, and the only option is for me to wait until someone fixes it on their end.

https://cran.r-project.org/web/checks/check_results_rworkflows.html

I flagged with the Mac VM maintainer at CRAN, and he has fixed it.

There are also some new errors on CRAN, which I've logged here: #77

[bschilder]

I believe it was @aedin that recently suggested to me to try adding the Bioc repos to the .Rprofile. You can even control installation repo priority this way. Will give this a go and see if it helps!

[bschilder]

I've added an .Rprofile to try and resolve this. Everything passes locally, will push to CRAN and see if it helps there.

This assumes BiocManager is already installed, which is only the case when using the bioc docker on Linux (the other OS fail):

rworkflows/.Rprofile

Line 1 in 7ea95b0

options(repos = BiocManager::repositories())

Instead, I've copied the output and hard-coded it:

rworkflows/.Rprofile

Line 1 in 9bf2a17

options(repos = c(BioCsoft = "https://bioconductor.org/packages/3.18/bioc",

[bschilder]

Just submitted rworkflows 1.0.0 to CRAN 🤞

[bschilder]

Had to make some final edits to the Roxygen notes to comply with some new CRAN standards:

• Change \itemize --> describe to avoid CRAN check errors.

But after that, all checks passed and rworkflows 1.0.0 was approved autoamtically! Should be on CRAN within the next day or so:

[bschilder]

Only about half of the runners on CRAN seem to be using rworkflow 1.0.0. Hopefully this is just due to a lag in when those machines are rerun and it resolves itself in time.
https://cran.r-project.org/web/checks/check_results_rworkflows.html

Also just came across the CRAN MacOS Builder. Still not really clear on what it is, but might be a way to get rid of some of the NOTES about biocViews and BiocPkgTools:
https://mac.r-project.org/macbuilder/submit.html