From mtmorgan at fhcrc.org  Fri May 23 00:52:57 2014
From: mtmorgan at fhcrc.org (Martin Morgan)
Date: Thu, 22 May 2014 15:52:57 -0700
Subject: [Rd] citEntry handling of encoded URLs
Message-ID: <537E7FC9.7030408@fhcrc.org>

The following citEntry includes a url with %3A and other encodings

citEntry(entry="article",
          title = "Software for Computing and Annotating Genomic Ranges",
          author = personList( as.person("Michael Lawrence" )),
          year = 2013,
          journal = "{PLoS} Computational Biology",
          volume = "9",
          issue = "8",
          doi = "10.1371/journal.pcbi.1003118",
          url = 
"http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003118",
          textVersion = "Lawrence M..." )

Evaluating this as R code doesn't parse correctly and generates a warning

Lawrence M (2013). ?Software for Computing and Annotating Genomic
Ranges.? _PLoS Computational Biology_, *9*. <URL:
http://dx.doi.org/10.1371/journal.pcbi.1003118>, <URL:
http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003118}.>
Warning message:
In parse_Rd(Rd, encoding = encoding, fragment = fragment, ...) :
   <connection>:5: unexpected END_OF_INPUT '
'

A work-around is, apparently, to quote the %, \\%3A etc., but is this the 
intention?

Also, citEntry points to bibentry points to *Entry Fields*, but the 'url' tag is 
not mentioned there, even though url appears in the examples; if the list of 
supported tags is not easy to enumerate, perhaps some insight can be provided at 
this point as to how the supported tags are determined?

Thanks

Martin Morgan
-- 
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



[Rd] citEntry handling of encoded URLs
Martin Morgan