Dear Martin, I am not sure to fully understand (or understand the consequences)
mtmor...@fhcrc.org writes: > Bioconductor developers: > > The Bioc release schedule is available > > http://bioconductor.org/developers/release-schedule/ > > A reminder that version 2.13 of Bioconductor will be released on October 15, > and > will work with R-3.0.2. Package authors should be testing the Bioc 'devel' > version of their package with R-3.0.2 pre-release. > > R-3.0.2 is scheduled for release on September 25. The lack of synchrony > between > R and Bioc releases introduces a wrinkle. Users of R-3.0.2 (including the > pre-release, which became available earlier today) using install.packages() > (rather than the recommended biocLite()) will be directed toward Bioconductor > 2.13 packages, so will be getting a preview of the Bioconductor release > scheduled for October 15. So the recommended way (for now) to test our packages is to get any possible BioC dependencies using install.packages (after setting the repository with, say, biocinstallRepos() )? So the mechanism in http://www.bioconductor.org/developers/useDevel/ followed by biocLite() is not recommended? > > Unfortunately, the scheduling requirements of our own release cycle > (including > building annotation packages and providing fair warning for new package > contributors) did not allow us to move the Bioconductor release forward. The > chosen solution seemed least disruptive of the available options. Let me make sure I fully understand. a) The tests in http://www.bioconductor.org/checkResults/2.13/bioc-LATEST/ use R-3.0.1. And it will continue to do so up to October 15? b) Suppose package A depends on package B. Package B (with version as available in BioC devel, and with tests as shown in http://www.bioconductor.org/checkResults/2.13/bioc-LATEST/) is working OK with R-3.0.1. However, package B now breaks under R-3.0.2, or generates new warning (which would mean it is not acceptable for BioC). What will the developer of A get when she or he tries to install the dependencies of A? And what should the developer of A do? c) What will be the policy of BioC regarding the new notes that R-3.0.2 might generate (and that have been the source of several threads in the R-devel list in the last few weeks)? I've re-read http://www.bioconductor.org/developers/package-guidelines/ and I can only find "Authors should also try to address all notes that arise during build or check." Best, R. > > R-3.0.2 allows for an environment variable to influence the version of > Bioconductor in use, from the R NEWS file: > > • The default ‘version’ of Bioconductor for its packages has been > changed to the upcoming 2.13, but this can be set by the > environment variable R_BIOC_VERSION, e.g. in file Renviron.site. > > Martin Morgan, > Bioconductor -- Ramon Diaz-Uriarte Department of Biochemistry, Lab B-25 Facultad de Medicina Universidad Autónoma de Madrid Arzobispo Morcillo, 4 28029 Madrid Spain Phone: +34-91-497-2412 Email: rdia...@gmail.com ramon.d...@iib.uam.es http://ligarto.org/rdiaz _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
