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

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citEntry given that it is superseded by bibentry according to the bibentry man page?

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