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

[Dan Tenenbaum]

Hi Wolfgang, Martin,

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

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


> Martin
>
>
>
>>         Best wishes
>>         Wolfgang
>>
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>>
>
>
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