[Bioc-devel] CITATION on the Bioc package landing page?

[Martin Morgan]

On 04/25/2014 01:46 PM, Martin Morgan wrote:
> On 04/24/2014 01:51 PM, Michael Lawrence wrote:
>> Agreed. Would be nice if the build system could detect changes to CITATION
>> and update the web page accordingly. Must already happen for DESCRIPTION.
>
> This will be implemented (over the next several weeks).

Dan has implemented this, see e.g.,

   1. http://bioconductor.org/packages/release/bioc/html/GenomicRanges.html
   2. http://bioconductor.org/packages/release/bioc/html/limma.html
   3. http://bioconductor.org/packages/release/bioc/html/GenomeInfoDb.html

The citations are derived from a CITATION file if it exists (examples 1 and 2) 
or auto-generated from the DESCRIPTION file (example 3), using the equivalent of 
print(citation("GenomicRanges"), style="html") with some post-processing to work 
around bugs in print.bibentry related to parsing strings with embedded escape 
sequences '%' (example 1). print.bibentry prints the citation, but not for 
instance citHeader (in example 2).

Martin

>
> Martin
>
>>
>>
>> On Thu, Apr 24, 2014 at 1:44 PM, Vincent Carey
>> <stvjc at channing.harvard.edu>wrote:
>>
>>> +1.  this will be a good motivation for maintainers to get the CITATION
>>> entry right.
>>>
>>>
>>> On Thu, Apr 24, 2014 at 3:39 PM, Wolfgang Huber <whuber at embl.de> wrote:
>>>
>>>> I wonder whether the software that makes the package landing pages (e.g.:
>>>> http://bioconductor.org/packages/release/bioc/html/minfi.html ) could be
>>>> tweaked to display the actual citation suggested in a package CITATION
>>> file.
>>>>
>>>> Right now, it says 'To cite this package in a publication, start R and
>>>> enter: citation("minfi")'. Which is already a good start, but requires
>>> the
>>>> reader to have an R session available, install the package, and type
>>> these
>>>> words. Things that could be easily automated, and where there is no
>>> obvious
>>>> benefit from having the user do these computations, as their result is
>>>> anyway predictable.
>>>>
>>>> What do you think?
>>>>
>>>> Kind regards
>>>>          Wolfgang
>>>>
>>>> _______________________________________________
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>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>
>>>
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>>>
>>>
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>>>
>>
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>>
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>
>


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