Hi Wolfgang, Martin, On Sun, Feb 3, 2013 at 8:01 AM, Martin Morgan <mtmor...@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 >> >> _______________________________________________ >> Bioc-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> > > > -- > Computational Biology / Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. > PO Box 19024 Seattle, WA 98109 > > Location: Arnold Building M1 B861 > Phone: (206) 667-2793 > > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel