[Bioc-devel] support the stable version of R

Martin Morgan mtmorg@n@bioc @ending from gm@il@com
Tue Jan 15 13:01:28 CET 2019

Probably my rant yesterday was a bit confused.

BiocCheck tries to encourage better practice. If you've chosen to specify version (maybe there are reasons for this, e.g., because in the past you have distributed your package through non-Bioconductor channels), then specify it correctly.

On the other hand, the Bioconductor release model doesn't require a version specification and in practice maintainers do a poor job updating this information. If the maintainer hasn't specified version, then no need to suggest that they do so.

I guess it's analogous to many other tests where guidance is provided on mis-use, rather than on non-use -- 'we notice that you didn't test for class, but if you had a better approach is to use `is()` rather than `class() == `'. Or perhaps suggesting straight-forward solutions rather than nuanced solutions of uncertain merit  'instead of testing for class incorrectly with `class() == `, use method dispatch to avoid conditional code'.

Again, a best practice for github and other repositories outside Bioconductor is likely to maintain distinct release branches. If one is choosing to specify version, then each branch should closely specify relevant version.


On 1/15/19, 2:45 AM, "Alexey Sergushichev" <alsergbox using gmail.com> wrote:

    > 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> wrote:
    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 <http://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/ <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.
    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?
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