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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Hi all,
Making some packages, and having "some" problems with the dependencies,
I was wondering if it possible to increment a sort of R CMD check2 that
do all the steps of the R CMD check except the "* checking package
dependencies".
That would help to process all the check command and avoid the circular
references problem, which is quite common.
This command would obviously be used only if the normal command can not
be used.
What do you think of ?
Is it possible ?
Thanks in advance
~pingou
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