Dear all

Please find here the answer that I had from somebody from the bioconductor-devel mailing list.

The subject was (originally) more or less related to the R CMD check that we use by default on the spec :

A lot of packages also use a Suggest field (e.g. Biobase suggests ALL, Biostrings suggests BSgenome.Celegans.UCSC.ce2). Most of the times, people don't need the suggested stuff. It could be that this stuff is only used in the vignette or in some of the man pages (in the example section). That's the case for Biostrings. Forcing people to install all the stuff suggested by Biostrings (by putting it in the Depends field) would be a bad idea. First it would introduce circular dependencies. Second it >would force them to download gigabytes of data that they don't need!

All this to say that I don't think that people using the RPM version of Bioconductor should be forced to install the suggested stuff.

Packaging quite some libraries from that repository, I would say that the resolution of the dependences is quite an important issue for that repository. I addition, I believe that he is true when he stands that most of the suggest dependences are only of interest for examples or so...

My question is then, should we stick to the present packaging guidelines or should we take this into account ?

I agree that the r cmd check make sure that all the dependencies are present, but make sure that they are is (to my opinion) also a packager and reviewer job, and is also quite easy with the DESCRIPTION file.

What is your opinion on that point ?

Thanks for your help, Best regards ~pingou

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