[Bioc-devel] support the stable version of R

Alexey Sergushichev @l@ergbox @ending from gm@il@com
Tue Jan 15 08:45:14 CET 2019


> Having said that, I'll note that specifying R as a dependency, and a
version of R as a criterion for your package, is really a mis-nomer for a
Bioconductor package -- of course it uses R, and the version of R in use
determines the Bioconductor version(s) that can be used! So a rational
change is to remove R and its version requirement from the DESCRIPTION file
entirely, a strategy taken by I think about 400 of our 1650+ packages.

Oh, it's actually an option not to include an R dependency at all. I find
it non-obvious, given the warning message that suggest to change the
version dependency to R-devel, not mentioning that omitting dependency will
fix the warning too. Should it be put somewhere in BiocCheck message?

Also, given that, I find it even more strange to have such R requirement in
BiocCheck. You are either allowed very strict dependency: R >= R-devel or
very lenient (not specifying any), but nothing in the middle.


On Tue, Jan 15, 2019 at 3:03 AM Martin Morgan <mtmorgan.bioc using gmail.com>

> Maybe a little more helpfully, I think you should create a branch for
> 'before' Bioconductor, where you can specify R version dependency as you
> see fit.
> Indeed, at each release the version of your package at
> git.bioconductor.org will have a branch created for that release, e.g.,
> the RELEASE_3_8 branch, and you will want to sync that branch with your
> github repository as outlined in step 10 of
> https://bioconductor.org/developers/how-to/git/sync-existing-repositories/
> .
> A conscientious developer would take the opportunity to increment the
> version dependency of R in the master branch to the version of R in use in
> the devel builds of Bioconductor.
> Martin
> On 1/14/19, 5:40 PM, "Bioc-devel on behalf of Lulu Chen" <
> bioc-devel-bounces using r-project.org on behalf of luluchen using vt.edu> wrote:
>     Dear all,
>     When submitting package to bioconductor, it is required to change R
> version
>     in "Depends" to be >= the develop version (3.6) . As my package is also
>     available in GitHub, someone asks if it be possible to make it
> available
>     with the stable version of R (R3.5). In fact, my package can work well
> with
>     R3.5 if I change "Depends" back to R(>=3.5) .
>     So I hope to support R3.5 for the moment before next release. Should I
>     create another repository? Can I use a branch to support R3.5?
>     Thanks,
>     Lulu
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