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

Martin Morgan mtmorgan at fhcrc.org
Wed Jun 4 19:33:50 CEST 2014


On 06/04/2014 10:08 AM, Vincent Carey wrote:
> I gather that there is no utility for transforming bibtex text to citEntry.  Do
> we want to remain committed to
> citEntry given that it is superseded by bibentry according to the bibentry man page?

I believe the citations on the landing pages are generated by R from the 
CITATION file (or otherwise) by using citation() or  readCitationFile(), so 
whatever is legal in the CITATION file. This includes (possible multiple, as in 
deepSNV) bibentry.

Martin

>
>
> On Fri, May 30, 2014 at 10:08 AM, Vincent Carey <stvjc at channing.harvard.edu
> <mailto:stvjc at channing.harvard.edu>> wrote:
>
>     yes.  now i have hunted around a little bit but do not find the following
>     utility: convert a BibTex text
>     file to a citEntry structure suitable for including in CITATION.  we can
>     import bibtex using the
>     bibtex package, coerce to bibentry, but not clear how to convert to
>     citEntry.  utils::bibentry is supposedly
>     the current interface, citEntry is "older".  This is not a showstopper, and
>     it is clear that bibtex data may
>     not always be susceptible to the intended conversion, but I want to avoid
>     needless manual data entry.
>     pointers would be appreciated.
>
>
>     On Fri, May 30, 2014 at 9:55 AM, Michael Lawrence <lawrence.michael at gene.com
>     <mailto:lawrence.michael at gene.com>> wrote:
>
>         I was just about to say that this should be a nice carrot for authors to
>         start improving their citations...
>
>
>         On Fri, May 30, 2014 at 6:27 AM, Vincent Carey
>         <stvjc at channing.harvard.edu <mailto:stvjc at channing.harvard.edu>> wrote:
>
>             Very nice.  We'll give it a couple of weeks and then announce more
>             broadly?  I'll start improving
>             my package citations shortly.
>
>
>             On Fri, May 30, 2014 at 9:11 AM, Martin Morgan <mtmorgan at fhcrc.org
>             <mailto:mtmorgan at fhcrc.org>> wrote:
>
>                 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
>                 <http://bioconductor.org/packages/release/bioc/html/GenomicRanges.html>
>                    2.
>                 http://bioconductor.org/__packages/release/bioc/html/__limma.html <http://bioconductor.org/packages/release/bioc/html/limma.html>
>                    3.
>                 http://bioconductor.org/__packages/release/bioc/html/__GenomeInfoDb.html
>                 <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
>                         <mailto: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 <mailto: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
>                                 <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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PO Box 19024 Seattle, WA 98109

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