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] 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?
4 messages · Martin Morgan, Leonardo Collado Torres
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
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 <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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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.morgan at 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 <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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