[Bioc-devel] Section~\ref{sec:bla} idiom in vignettes

Martin Morgan mtmorgan at fhcrc.org
Sun Feb 3 17:01:56 CET 2013

On 02/03/2013 03:35 AM, Wolfgang Huber wrote:
> Hi,
> In LaTeX, I like to use the tilde in connection with equation or section references, e.g. "Equation~(\ref{eq:bla})" or "Section~\ref{sec:blo}", to make sure they are not separated by a line break.
> This has worked well for two decades and still does on my system. However, in some vignettes coming from the devel branch of the build server e.g. http://bioconductor.org/packages/devel/bioc/vignettes/DESeq/inst/doc/DESeq.pdf this is now rendered with a visible "~", which looks ugly.
> Interestingly, the release version http://bioconductor.org/packages/2.11/bioc/vignettes/DESeq/inst/doc/DESeq.pdf does not render the tilde.
> This was today 3 Feb, 12:20h CET. I wonder what causes this, and who/what can restore the intended behaviour.

to contribute a few pieces to the puzzle...

I'm not sure about the build system but the root problem is I think here


where texi2dvi --pdf fails to remove the ~; texi2dvi --pdf is used by R to build 
vignettes. The release build system uses openSUSE 12.1, whereas devel has ubuntu 
12.04 and presumably different version sof texi2pdf. I can confirm the bug on my 
ubuntu 12.04 system with

$ cat > x.tex
/tmp$ texi2dvi --pdf x.tex


> 	Best wishes
> 	Wolfgang
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