[Bioc-devel] BiocInstaller not supporting R 3.4.0 -- yes, it's early, but shouldn't it default to using Bioc-devel instead of Bioc-release in this scenario?

Leonardo Collado Torres lcollado at jhu.edu
Tue Mar 22 21:33:50 CET 2016

Thanks for the new feature Martin! I also have to thank Jim Hester for
adding support for R version 3.3.0 on Travis.

I know that we'll use R-3-3-branch for Bioc 3.4, but it's good to
mention it on the thread for reference.


On Tue, Mar 22, 2016 at 3:49 PM, Martin Morgan
<martin.morgan at roswellpark.org> wrote:
> the biocLite.R script has been changed to use bioc-devel when the R version
> is 'too new'.
> Worth pointing out perhaps that Bioconductor will not use R-devel again for
> another six months -- after our next release, both release and devel
> versions of Bioconductor will use the R-3-3-branch, because that will be the
> 'user' version of R available for both the 3.3 and 3.4 releases of
> Bioconductor.
> Thanks for the request, Leo.
> Martin
> On 03/22/2016 11:24 AM, Leonardo Collado Torres wrote:
>> Check Jim Hester's thoughts on this issue
>> https://github.com/travis-ci/travis-ci/issues/5809#issuecomment-199858950
>> One way of solving it is by having BiocInstaller allow using
>> Bioc-devel with R 3.4.0.
>> On Tue, Mar 22, 2016 at 10:43 AM, Leonardo Collado Torres
>> <lcollado at jhu.edu> wrote:
>>> Hi,
>>> This is definitely 4 weeks early and things are working as intended.
>>> Due to https://github.com/travis-ci/travis-ci/issues/5809 I noticed
>>> that BiocInstaller does not yet support R 3.4.0. The main issue was my
>>> assumption that R-travis using `r: devel` would install R 3.3.0 as I
>>> describe in the issue I linked above.
>>> I was failing to see this because builds for `regionReport` were
>>> completing successfully. However, builds for `derfinderPlot` failed
>>> and that's because `derfinderPlot` has Bioc-devel dependencies
>>> (S4Vectors >= 0.9.38). Thanks to Jim Hester I realized that both
>>> packages were being tested on R 3.4.0, and that BiocInstaller after
>>> failing would then default on Bioc-release. See
>>> https://travis-ci.org/leekgroup/derfinderPlot/builds/117500745#L419-L420
>>> and
>>> https://travis-ci.org/leekgroup/regionReport/builds/117499393#L418-L419
>>> Bioconductor version 3.2 (BiocInstaller 1.20.1), ?biocLite for help
>>> Bioconductor does not yet support R version 3.4.0
>>> As for BiocInstaller, I'm a bit curious why it falls back to
>>> Bioc-release instead of Bioc-devel when trying to use it in a future R
>>> version that is not yet supported.
>>> In any case, I can fix my R-travis builds by specifying that I want
>>> them to be run on R 3.3.0 for now.
>>> I'm guessing that other developers who use R-travis might run into
>>> this issue in these 4 weeks before R 3.3.0 is released.
>>> Best,
>>> Leo
>>> Leonardo Collado Torres, PhD Candidate
>>> Department of Biostatistics
>>> Johns Hopkins University
>>> Bloomberg School of Public Health
>>> Website: http://lcolladotor.github.io/about.html
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