[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 16:24:32 CET 2016

Check Jim Hester's thoughts on this issue

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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