Dear R-devel,
Question:
How can I get Sweave to recognize that the \thebibliography section
is already created and generate the vignette pdf with a single pass? Or
is there a way to let R CMD build know that Sweave needs to be run twice?
If (1) is not possible, any suggestions how to auto-generate a
crude generic bibtex .bib file from my existing document?
Background:
I maintain serveral R packages that include package vignettes. The
vignettes include the reference citations inline as\bibitem lines inside
a thebiblilography section. For some reason, this requires running
Sweave twice on the document (the first pass is presumably preformatting
the citation information?) to produce a pdf. This seems to be the source
of problems when included in R's preferred vignette location
(/vignettes/myPackage.Rnw) because the R package builder just runs
Sweave once during the check process, so no pdf is produced and warnings
are generated like
checking package vignettes in ‘inst/doc’ ... WARNING
Package vignette without corresponding PDF/HTML
In the past, it has been possible for me to pre-build the pdf, and
include it in the /inst/doc/ directory. But it seems the upcoming
versions of R may prohibit this.
It appears that it is possible to avoid all this by including a bibtex
.bib file along with the vignette instead of doing the citations inline.
If the .bib files exists, it seems to generate with a single pass. But
reformatting all of the citations for each document into bibtex will be
a huge pain. Including a blank \bibliography{} command above my
\thebibliography environment also allows the document to be build in a
single pass, but generates a warning about duplicate biliography and
writes the section header twice (not surprisingly).
Note: I've cross-posted this question at:
http://stackoverflow.com/questions/22237675/how-to-get-sweave-to-recognize-thebibliography-environment-and-build-r-package
thanks for your help,
best,
-skye
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