[Rd] citEntry handling of encoded URLs

Martin Morgan mtmorgan at fhcrc.org
Fri May 23 00:52:57 CEST 2014

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

          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 = 
          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:
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 

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?


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

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