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

[Ramon Diaz-Uriarte]

Dear Martin,

Thanks for your detailed reply.

Best,


R.


mtmorgan at 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)
>>
>>
>> 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
>>
>>


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

http://ligarto.org/rdiaz