[Bioc-devel] R and Bioconductor versions for the forthcoming release

Ramon Diaz-Uriarte rdiaz02 at gmail.com
Tue Sep 17 10:39:54 CEST 2013

Dear Martin,

I am not sure to fully understand (or understand the consequences)

mtmorgan at 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


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 


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 


and I can only find "Authors should also try to address all notes that arise
during build or check."



> 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

Phone: +34-91-497-2412

Email: rdiaz02 at gmail.com
       ramon.diaz at iib.uam.es


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