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

3 messages · Wolfgang Huber, Martin Morgan, Dan Tenenbaum

Original
Wolfgang Huber
# 
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.

	Best wishes
	Wolfgang
Martin Morgan
#
On 02/03/2013 03:35 AM, Wolfgang Huber wrote:
to contribute a few pieces to the puzzle...

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

   http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=534458

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
\documentclass{article}
\begin{document}
Foo~bar.
\end{document}
/tmp$ texi2dvi --pdf x.tex


Martin

  
    

      
      
    

  


  


      

    

    
18 days later

    

      
      

        


  

        

      Dan Tenenbaum
    

    

      
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Hi Wolfgang, Martin,

        
On Sun, Feb 3, 2013 at 8:01 AM, Martin Morgan <mtmorgan at fhcrc.org> wrote:

            

      
      
      
    

        
We've worked around this issue.
http://bioconductor.org/packages/devel/bioc/vignettes/DESeq/inst/doc/DESeq.pdf
should look OK now, as well as the vignette inside
http://www.bioconductor.org/packages/devel/bioc/src/contrib/DESeq_1.11.5.tar.gz.
If you see any further problems with this, let us know.
Dan