[Bioc-devel] R version check in BiocChech

Alexey Sergushichev alsergbox at gmail.com
Mon Feb 19 13:19:11 CET 2018

Hello Kevin,

Well, bioc-devel packages are tested against bioc-devel (and R-3.5) in any
case. What I'm saying is that aside from testing the package against
bioc-devel, I can as well test against bioc-release too on my own. If the
package doesn't work with bioc-devel it shouldn't pass bioc-devel checks,
if the package is properly developed and has a good test coverage. So I see
no problem in allowing developers to test against other versions, on top of
developing against bioc-devel. And as it's only possible to install the
package from github and not from Bioconductor, the developer alone is
responsible for the package to work properly.

I can't really see a scenario, where requiring R >= 3.5 helps to improve
the package quality.

> A short-term workaround can be to create a git branch (e.g. "3.4").

That's the way I'm doing too, but supporting two branches different only in
R version looks ridiculous and unnecessary.


On Mon, Feb 19, 2018 at 12:48 PM, Kevin RUE <kevinrue67 at gmail.com> wrote:

> Dear Alexey,
> The reason is somewhat implicitly given at https://www.bioconductor.or
> g/developers/how-to/useDevel/ :
> "Package authors should develop against the version of *R* that will be
> available to users when the *Bioconductor* devel branch becomes the
> *Bioconductor* release branch."
> In other words, developing against the _next_ version of R ensures that
> all packages in development are tested in the environment where they will
> be released to the general community. In particular, that environment
> includes the latest devel version of all Bioconductor packages, that will
> become their next release version.
> If developers were allowed to develop and test their package in the
> _current_ version of R, there is no guarantee that those packages would
> still work when they are made available with the _next_ version of R (e.g.
> if one of their dependencies is about to introduce some breaking changes).
> That could cause all sorts of trouble in the first builds on the next
> Bioconductor release, which is meant to be a place storing stable working
> code.
> Overall, you will do yourself and your users a favor developing with the
> _next_ version of R, as this is a forward-looking strategy, as explained
> above. In contrast, the short-term benefit of developing with the _current_
> version of R is largely outweighed by the risk of wasting time looking at
> code that is about to be deprecated.
> A short-term workaround can be to create a git branch (e.g. "3.4"), where
> the R version requirement is downgraded. Then, you can always keep
> developing against R-devel on your master branch and back-port the more
> recent commit to the "3.4" branch by typing "git rebase master 3.4" in your
> shell.
> A recent example of this situation can be found in the discussion here as
> a branch to the original repository https://github.com/csoneson/iS
> EE/pull/124 and here as a fork https://github.com/mdshw5
> /iSEE/commit/6fb98192a635a6222491b66fb0474dc38f922495
> I hope this helps.
> Best wishes,
> Kevin
> On Mon, Feb 19, 2018 at 8:02 AM, Alexey Sergushichev <alsergbox at gmail.com>
> wrote:
>> Dear Bioconducotr community,
>> I wonder, what is the reason behind requirement for dependency R >= 3.5
>> (currently) for new packages?
>> As a developer I really want an installation of my package to be as easy
>> as
>> possible and want my package to be easily installed from github. So
>> currently, when I develop a package I put a R >= 3.4 in my DESCRIPTION and
>> test it using Travis against bioc-release. Then, before submission
>> to Bioconductor, I have to change R >= 3.4 dependency to R >= 3.5, so that
>> the package passes BiocCheck. However, most users don't have R-devel
>> installed, so they have R 3.4 in the best case, and for these users I
>> create another repository branch with R >= 3.4 dependency.
>> Overall, it is quite bothersome and it doesn't really make sense to me to
>> to restrict potential users in this way. Am I the only one who have issues
>> with this? Am I missing something? Or may be this check could be removed?
>> Best,
>> Alexey Sergushichev
>>         [[alternative HTML version deleted]]
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel

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