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. Best, Leo On Tue, Mar 22, 2016 at 3:49 PM, Martin Morgan <martin.mor...@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 >> <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 >> >> >> _______________________________________________ >> Bioc-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> > > > This email message may contain legally privileged and/or confidential > information. If you are not the intended recipient(s), or the employee or > agent responsible for the delivery of this message to the intended > recipient(s), you are hereby notified that any disclosure, copying, > distribution, or use of this email message is prohibited. If you have > received this message in error, please notify the sender immediately by > e-mail and delete this email message from your computer. Thank you. _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
