[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 15:43:56 CET 2016


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
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.


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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