[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?

Martin Morgan martin.morgan at roswellpark.org
Tue Mar 22 20:49:17 CET 2016

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 

Thanks for the request, Leo.


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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