R devel - Mar 2014 - Problems building package vignette: Sweave requires multiple passes to build document.

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

On 14/03/2014 12:28 PM, Skye Bender-deMoll wrote:
> 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?
I think the problem isn't Sweave:  it ignores LaTeX code.  The problem 
is the following step that converts the .tex output into a .pdf, which 
is handled by tools::texi2pdf (which runs tools::texi2dvi).  That 
function makes an effort to determine how many LaTeX passes are 
required, but it appears you are fooling it somehow.

Take a look at the source to tools::texi2dvi, and see if you can spot 
what's going wrong in your case.  There are a number of different paths 
through that code that depend on your particular setup, so we can't do 
that.  If you don't succeed in this, then post a simplified sample 
package and someone else will be able to see if they have the same 
problem as you, and perhaps fix it.

Duncan Murdoch
>
>       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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