Document best way to handle BioConductor package dependencies for CRAN packages.

[noamross]

Packages on CRAN can have BioConductor dependencies but they need the empty field biocViews: in their DESCRIPTION for installation to work properly. This is under-documented around the web so it will be useful to put it in the packaging guide as another way to find it.

https://bioinformatics.stackexchange.com/questions/3365/r-package-development-how-does-one-automatically-install-bioconductor-packages

The above is wrong but we should note the best way for packages to rely on BioConductor pacakges.

[maelle]

would you like to make a PR for that @noamross? :-)

[maelle]

@noamross how does this work?! I can't find the related code via https://github.com/wch/r-source/search?utf8=%E2%9C%93&q=biocViews&type= and I only know of the remotes support

[maelle]

For https://cran.r-project.org/web/packages/aroma.core/ (where Bioconductor packages have correct links), the DESCRIPTION file as a DependsNote.

[noamross]

Oh wow I have no idea and now I am very curious.

[maelle]

https://stat.ethz.ch/pipermail/bioc-devel/2015-March/007064.html

[maelle]

Relevant tools:::.get_standard_repository_URLs()

[maelle]

wch/r-source@94c4f33

[maelle]

https://stat.ethz.ch/pipermail/r-package-devel/2016q3/000909.html

[maelle]

https://support.bioconductor.org/p/124812/

[maelle]

It seems to be that there's no need to add anything to DESCRIPTION, i.e. one can handle Bioc dependencies like CRAN dependencies.

[maelle]

The user needs getOptions("repos") to return the necessary Bioc repo(s). See https://github.com/bioimaginggroup/nucim#installation (tested but I got a compilation error)

[maelle]

Now I'm not sure installing Bioc packages like that is recommended?! (e.g. now I can do install.packages("IRanges")).