[Bioc-devel] Short URLs for packages?

[Tim Triche, Jr.]

.../release/... silently changes every six months or so, as does .../devel/..., so I don't see how this changes anything beyond that.  It does make finding the packages a lot easier in general, and more mnemonic. 

If you want to document the versions of packages used in an analysis, there's always sessionInfo() and/or a dockerfile, rite?

--t

> On Mar 23, 2015, at 8:38 AM, Gabe Becker <becker.gabe at gene.com> wrote:
> 
> On Mon, Mar 23, 2015 at 8:05 AM, Fischer, Bernd <
> b.fischer at dkfz-heidelberg.de> wrote:
> 
>> 
>> During the production process of the paper we want to link to the
>> accompanying
>> BioC package that is in devel, but not yet in release. Before the first
>> release, the
>> link (e.g. www.bioconductor.org/<packagename>) should go to the devel
>> version
>> (maybe with an additional warning that it is only available in devel),
>> before the
>> first release of the package and should go to release afterwards.
> 
> I understand the appeal of this, but decoupling publications from the
> actual, exact versions they discuss or use seems like a relatively large
> step backwards in terms of reproducibility. At the very least, I think
> there is some nuance here that warrants careful consideration before we
> adopt a single-silently-changing-link-per-package paradigm.
> 
> ~G
> 
> 
> 
> 
>> 
>> Bernd
>> 
>> 
>>> On 23.03.2015, at 11:45, Sean Davis <seandavi at gmail.com> wrote:
>>> 
>>> Just so we don't lose the thoughts that have come before, here is a link
>> to
>>> a similar proposal from last year.
>>> 
>>> https://stat.ethz.ch/pipermail/bioc-devel/2014-February/005292.html
>>> 
>>> Sean
>>> 
>>> 
>>> 
>>>> On Mon, Mar 23, 2015 at 6:17 AM, Wolfgang Huber <whuber at embl.de> wrote:
>>>> 
>>>> I wonder whether it’d possible to have the website understand URLs like
>>>>       http://www.bioconductor.org/<pkgname>
>>>> 
>>>> This could resolve to
>>>> http://www.bioconductor.org/packages/release/bioc/html/<pkgname>.html
>>>> or
>>>> http://www.bioconductor.org/packages/devel/bioc/html/<pkgname>.html
>>>> depending on whether the package was yet released.
>>>> 
>>>> This could be handy in papers or grants that mention packages.
>>>> 
>>>> Wolfgang
>>>> 
>>>> 
>>>> ----
>>>> Wolfgang Huber
>>>> Principal Investigator, EMBL Senior Scientist
>>>> Genome Biology Unit
>>>> European Molecular Biology Laboratory (EMBL)
>>>> Heidelberg, Germany
>>>> 
>>>> T +49-6221-3878823
>>>> wolfgang.huber at embl.de
>>>> http://www.huber.embl.de
>>>> 
>>>> _______________________________________________
>>>> Bioc-devel at r-project.org mailing list
>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>> 
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>> 
>> _______________________________________________
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> 
> 
> 
> -- 
> Gabriel Becker, Ph.D
> Computational Biologist
> Genentech Research
> 
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> 
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