[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 citEntry given that it is superseded by bibentry according to the bibentry man page?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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