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 Do we want to remain committed to citEntry given that it is superseded by bibentry according to the bibentry man page?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 <st...@channing.harvard.edu <mailto:st...@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.mich...@gene.com <mailto:lawrence.mich...@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 <st...@channing.harvard.edu <mailto:st...@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 <mtmor...@fhcrc.org <mailto:mtmor...@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 <st...@channing.harvard.edu <mailto:st...@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 <whu...@embl.de <mailto:whu...@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 _________________________________________________ Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org> mailing list https://stat.ethz.ch/mailman/__listinfo/bioc-devel <https://stat.ethz.ch/mailman/listinfo/bioc-devel> [[alternative HTML version deleted]] _________________________________________________ Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org> mailing list https://stat.ethz.ch/mailman/__listinfo/bioc-devel <https://stat.ethz.ch/mailman/listinfo/bioc-devel> [[alternative HTML version deleted]] _________________________________________________ Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org> mailing list https://stat.ethz.ch/mailman/__listinfo/bioc-devel <https://stat.ethz.ch/mailman/listinfo/bioc-devel> -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793 <tel:%28206%29%20667-2793>
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