Dear Martin,
Thanks for your detailed reply. Best, R. mtmor...@fhcrc.org writes: > On 09/17/2013 01:39 AM, Ramon Diaz-Uriarte wrote: >> >> 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? > > Use the pre-release version of R 3.0.2. Use biocLite(), after having said > useDevel() as outlined here: > > http://bioconductor.org/developers/how-to/useDevel/ > >> >> >> >>> >>> 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? > > Actually, R-3.0.1 _Patched_, from 2013-09-03 r63824. > > The R used in bioc-devel tracks approximately the R which users will > eventually > experience when bioc-devel becomes release 2.13. The R used for bioc-LATEST > is > updated periodically and will be updated (to the pre-release version of > R-3.0.2) > 'soon' (perhaps this has already been done, and we'll see when the build > reports > appear at around 10am today). > >> >> >> 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? > > The packages should be passing build and check under the latest version of > R-3.0.2 available. > >> 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." > > Almost always notes point to good programming practice. This applies to more > recent notes as much as it does to previously existing notes and warnings. > The > long threads on R-devel have been interspersed with valuable insights into, > e.g., how to correctly place packages in to Imports:, how to use importFrom > and > export, and when to use :: (and when not to use :::). It is almost always in > the > developer's best interest to pay attention to the notes, warnings, and > errors, > and Bioconductor expects our developers to act accordingly > > Martin > >> >> >> 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
