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
<lcoll...@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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