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

[Martin Morgan]

On 09/17/2013 01:39 AM, Ramon Diaz-Uriarte wrote:
>
> 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
>
> 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
>
>


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