[Bioc-devel] developing R package for new release

Nicholas Clark nicholas.clark00 at gmail.com
Fri Mar 17 20:45:24 CET 2017

I’m planning on adding some new features to my package (GRmetrics) before this upcoming release and I have a few development questions.

1) Which version of R should I be using? I looked at this page (http://bioconductor.org/developers/how-to/useDevel/
), but I was still confused as to whether I should use the recently released R 3.3.3 or the R-devel 3.4.0 at http://r.research.att.com/

2) What is the best/easiest way to work with github? Should I fork the repository from the read-only Bioconductor repo and work on that or maintain a separate repo? Or does it not matter?

3) Should I make a “release-3.5” branch and commit changes there, or should it be “devel”, or just the “master” branch? http://bioconductor.org/developers/how-to/git-mirrors/
 talks about this, but again, it’s not clear to me.

4) It looks like my package is failing the Windows build because it requires “SummarizedExperiment”, which is failing the Windows build. Is there anything I can do to fix this? Apologies if this has already been addressed. The error is: ERROR: dependency ‘SummarizedExperiment’ is not available for package ‘GRmetrics' (http://bioconductor.org/checkResults/release/bioc-LATEST/GRmetrics/tokay1-buildsrc.html

Nick Clark

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