From dtenenba at fhcrc.org  Tue Mar 20 19:54:40 2012
From: dtenenba at fhcrc.org (Dan Tenenbaum)
Date: Tue, 20 Mar 2012 11:54:40 -0700
Subject: [Rd] issue with Rd2pdf and \Sexpr in Rd files
In-Reply-To: <4F68D1CA.6050900@gmail.com>
References: <CAF42j22X+B8aLCEDhY7PzXpPobDcZT80rhNT5DFKFNBa0vkYLg@mail.gmail.com>
	<CAF42j20FGqHq67xPwAbYN2K_AmQKZ3PHwW6BVtQTjZVeLEvyTQ@mail.gmail.com>
	<4F68BC81.20506@gmail.com>
	<CAF42j22icfTTsN6=2ocJw2pVWh4QxoYyFNaZ9BkdNuotLnu6Ng@mail.gmail.com>
	<4F68C13B.7080806@gmail.com>
	<CAF42j223UuHwMwQ+tNVt3rEwUA4FB+mR8uQX4yEZjd3bn0C4=Q@mail.gmail.com>
	<4F68D1CA.6050900@gmail.com>
Message-ID: <CAF42j23qhzGMuhUp5qiEf2oSY+mOf38aTbTtB=zM_kDupno7eg@mail.gmail.com>

On Tue, Mar 20, 2012 at 11:51 AM, Duncan Murdoch
<murdoch.duncan at gmail.com> wrote:
> On 12-03-20 1:46 PM, Dan Tenenbaum wrote:
>>
>> On Tue, Mar 20, 2012 at 10:41 AM, Duncan Murdoch
>> <murdoch.duncan at gmail.com> ?wrote:
>>>
>>> On 12-03-20 1:25 PM, Dan Tenenbaum wrote:
>>>>
>>>>
>>>> On Tue, Mar 20, 2012 at 10:21 AM, Duncan Murdoch
>>>> <murdoch.duncan at gmail.com> ? ?wrote:
>>>>>
>>>>>
>>>>> On 12-03-19 10:27 PM, Dan Tenenbaum wrote:
>>>>>>
>>>>>>
>>>>>>
>>>>>> Hello,
>>>>>>
>>>>>> Sorry to repeat myself, but I was wondering if anyone had taken a look
>>>>>> at
>>>>>> this.
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> No. ?Could you put together a simple self contained example? ?I don't
>>>>> have
>>>>> any BioC packages installed.
>>>>>
>>>>
>>>> I did supply a self-contained example.
>>>> You do not need any BioC packages installed.
>>>> All you need is this file:
>>>>
>>>>
>>>>
>>>> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/genefu/man/genefu-package.Rd
>>>> (username: readonly, password: readonly)
>>>> And this command:
>>>> R CMD Rd2pdf --no-preview --output=./tmp.pdf --title=test
>>>> genefu-package.Rd
>>>
>>>
>>>
>>> Sorry, I didn't see that.
>>>
>>
>> Actually, ?I goofed, because that file contains the lines:
>> Version: \tab \Sexpr{packageDescription("genefu")$Version}\cr
>> Date: \tab \Sexpr{packageDescription("genefu")$Date}\cr
>>
>> And those lines require you to have the 'genefu' package installed.
>> ?I changed those lines to more innocuous \Sexprs:
>>
>> Version: \tab \Sexpr{cat("hello")}\cr
>> Date: \tab \Sexpr{cat("world")}\cr
>>
>>
>>
>>>
>>>> No .tex file is generated.
>>>
>>>
>>>
>>> If you use the --no-clean command line option, then the temporary
>>> directory
>>> containing the .tex file will not be deleted. ?It contains your \Sexpr
>>> expressions wrapped in verbatim environments. ?I suspect this is
>>> happening
>>> because Rd2pdf isn't running the Sexpr evaluation step.
>>
>>
>> Yes, that's what I think is happening.
>>
>>> ?I'll try to take a
>>> look and fix it.
>>
>>
>> Thanks very much!
>>
>> I added the --no-clean flag and still got no .tex file. Here is my new
>> error output, looks the same as the original error output.
>>
>> Thanks,
>> Dan
>>
>> Converting Rd files to LaTeX ...
>> ? genefu-package.Rd
>> Creating pdf output from LaTeX ...
>> Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,
>> ?:
>> ? Running 'texi2dvi' on 'Rd2.tex' failed.
>> LaTeX errors:
>> /Users/dtenenba/tmp/.Rd2pdf4804/Rd2.tex:39: ?==> ?Fatal error occurred, no
>> outpu
>> t PDF file produced!
>> Output:
>> This is pdfTeX, Version 3.1415926-2.3-1.40.12 (TeX Live 2011)
>> ?restricted \write18 enabled.
>> entering extended mode
>> (/Users/dtenenba/tmp/.Rd2pdf4804/Rd2.tex
>> LaTeX2e<2011/06/27>
>> Babel<v3.8m> ?and hyphenation patterns for english, dumylang,
>> nohyphenation, ge
>> rman-x-2011-07-01, ngerman-x-2011-07-01, afrikaans, ancientgreek, ibycus,
>> arabi
>> c, armenian, basque, bulgarian, catalan, pinyin, coptic, croatian, czech,
>> danis
>> h, dutch, ukenglish, usenglishmax, esperanto, estonian, ethiopic, farsi,
>> finnis
>> h, french, galician, german, ngerman, swissgerman, monogreek, greek,
>> hungarian,
>> ?icelandic, assamese, bengali, gujarati, hindi, kannada, malayalam,
>> marathi, or
>> iya, panjabi, tamil, telugu, indonesian, interlingua, irish, italian,
>> kurmanji,
>> ?lao, latin, latvian, lithuanian, mongolian, mongolianlmc, bokmal,
>> nynorsk, pol
>> ish, portuguese, romanian, russian, sanskrit, serbian, serbianc, slovak,
>> sloven
>> ian, spanish, swedish, turkish, turkmen, ukrainian, uppersorbian, welsh,
>> loaded
>> .
>> (/usr/local/texlive/2011/texmf-dist/tex/latex/base/book.cls
>> Document Class: book 2007/10/19 v1.4h Standard LaTeX document class
>> (/usr/local/texlive/2011/texmf-dist/tex/latex/base/bk10.clo))
>> (/Library/Frameworks/R.framework/Resources/share/texmf/tex/latex/Rd.sty
>> (/usr/local/texlive/2011/texmf-dist/tex/latex/base/ifthen.sty)
>> (/usr/local/texlive/2011/texmf-dist/tex/latex/tools/longtable.sty)
>> (/usr/local/texlive/2011/texmf-dist/tex/latex/tools/bm.sty)
>> (/usr/local/texlive/2011/texmf-dist/tex/latex/base/alltt.sty)
>> (/usr/local/texlive/2011/texmf-dist/tex/latex/tools/verbatim.sty)
>> (/usr/local/texlive/2011/texmf-dist/tex/latex/url/url.sty) NOT loading ae
>> (/usr/local/texlive/2011/texmf-dist/tex/latex/base/fontenc.sty
>> (/usr/local/texlive/2011/texmf-dist/tex/latex/base/t1enc.def))
>> (/usr/local/texlive/2011/texmf-dist/tex/latex/psnfss/times.sty)
>> NOT loading lmodern
>> (/usr/local/texlive/2011/texmf-dist/tex/latex/inconsolata/inconsolata.sty
>> (/usr/local/texlive/2011/texmf-dist/tex/latex/base/textcomp.sty
>> (/usr/local/texlive/2011/texmf-dist/tex/latex/base/ts1enc.def))
>> (/usr/local/texlive/2011/texmf-dist/tex/latex/graphics/keyval.sty))
>> (/usr/local/texlive/2011/texmf-dist/tex/latex/graphics/color.sty
>> (/usr/local/texlive/2011/texmf-dist/tex/latex/latexconfig/color.cfg)
>> (/usr/local/texlive/2011/texmf-dist/tex/latex/pdftex-def/pdftex.def
>> (/usr/local/texlive/2011/texmf-dist/tex/generic/oberdiek/infwarerr.sty)
>> (/usr/local/texlive/2011/texmf-dist/tex/generic/oberdiek/ltxcmds.sty)))
>> (/usr/local/texlive/2011/texmf-dist/tex/latex/hyperref/hyperref.sty
>>
>> (/usr/local/texlive/2011/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
>>
>> (/usr/local/texlive/2011/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty))
>> (/usr/local/texlive/2011/texmf-dist/tex/generic/ifxetex/ifxetex.sty)
>> (/usr/local/texlive/2011/texmf-dist/tex/latex/oberdiek/kvoptions.sty)
>> (/usr/local/texlive/2011/texmf-dist/tex/latex/hyperref/pd1enc.def)
>> (/usr/local/texlive/2011/texmf-dist/tex/latex/latexconfig/hyperref.cfg))
>>
>> Package hyperref Message: Driver (autodetected): hpdftex.
>>
>> (/usr/local/texlive/2011/texmf-dist/tex/latex/hyperref/hpdftex.def
>>
>> (/usr/local/texlive/2011/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty))
>>
>> Package hyperref Warning: Option `hyperindex' has already been used,
>> (hyperref) ? ? ? ? ? ? ? ?setting the option has no effect on input line
>> 356.
>>
>>
>> Package hyperref Warning: Option `pagebackref' has already been used,
>> (hyperref) ? ? ? ? ? ? ? ?setting the option has no effect on input line
>> 356.
>>
>> ) (/usr/local/texlive/2011/texmf-dist/tex/latex/base/makeidx.sty)
>> (/usr/local/texlive/2011/texmf-dist/tex/latex/base/inputenc.sty
>> (/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def
>> (/usr/local/texlive/2011/texmf-dist/tex/latex/base/t1enc.dfu)
>> (/usr/local/texlive/2011/texmf-dist/tex/latex/base/ot1enc.dfu)
>> (/usr/local/texlive/2011/texmf-dist/tex/latex/base/omsenc.dfu)
>> (/usr/local/texlive/2011/texmf-dist/tex/latex/base/ts1enc.dfu))
>> (/usr/local/texlive/2011/texmf-dist/tex/latex/base/latin1.def))
>> Writing index file Rd2.idx
>> No file Rd2.aux.
>> (/usr/local/texlive/2011/texmf-dist/tex/latex/base/ts1cmr.fd)
>> (/usr/local/texlive/2011/texmf-dist/tex/latex/psnfss/t1ptm.fd)
>> (/usr/local/texlive/2011/texmf-dist/tex/context/base/supp-pdf.mkii
>> [Loading MPS to PDF converter (version 2006.09.02).]
>> ) (/usr/local/texlive/2011/texmf-dist/tex/latex/hyperref/nameref.sty
>>
>> (/usr/local/texlive/2011/texmf-dist/tex/generic/oberdiek/gettitlestring.sty))
>> (/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def)
>> (/usr/local/texlive/2011/texmf-dist/tex/latex/inconsolata/t1fi4.fd)
>> /Users/dtenenba/tmp/.Rd2pdf4804/Rd2.tex:39: Missing \endgroup inserted.
>> <inserted text>
>> ? ? ? ? ? ? ? ? \endgroup
>> l.39 }
>>
>> ?
>> /Users/dtenenba/tmp/.Rd2pdf4804/Rd2.tex:39: Emergency stop.
>
>
> That's the file to look at. ?With --no-clean, it should still be there after
> the run, but ls won't show the directory because of the dot in the name.

Here are the contents of that .tex file:

\documentclass[a4paper]{book}
\usepackage[times,inconsolata,hyper]{Rd}
\usepackage{makeidx}
\usepackage[utf8,latin1]{inputenc}
% \usepackage{graphicx} % @USE GRAPHICX@
\makeindex{}
\begin{document}
\chapter*{}
\begin{center}
{\textbf{\huge test}}
\par\bigskip{\large \today}
\end{center}
\inputencoding{utf8}
\HeaderA{genefu-package}{Relevant Functions for Gene Expression
Analysis, Especially in Breast Cancer.}{genefu.Rdash.package}
\aliasA{genefu}{genefu-package}{genefu}
\keyword{clustering}{genefu-package}
\keyword{models}{genefu-package}
\keyword{breast cancer}{genefu-package}
\keyword{prognosis}{genefu-package}
%
\begin{Description}\relax
This package contains functions implementing various tasks usually
required by gene expression analysis, especially in breast cancer
studies: gene mapping between different microarray platforms,
identification of molecular subtypes, implementation of published gene
signatures, gene selection, survival analysis, ...
\end{Description}
%
\begin{Details}\relax

\Tabular{ll}{
Package: & genefu\\{}
Type: & Package\\{}
Version: & \begin{verbatim}
\Sexpr{cat("hello")}
\end{verbatim}
\\{}
Date: & \begin{verbatim}
\Sexpr{cat("world")}
\end{verbatim}
\\{}
License: & Artistic-2.0\\{}
}
\end{Details}
%
\begin{Author}\relax
\bold{Benjamin Haibe-Kains}

- Computational Biology and Functional Genomics, Dana-Farber Cancer
Institute, Boston, MA, USA

\url{http://compbio.dfci.harvard.edu/}

- Center for Cancer Computational Biology, Dana-Farber Cancer
Institute, Boston, MA, USA

\url{http://cccb.dfci.harvard.edu/index.html}

Former labs:

- Machine Learning Group (MLG), Universite Libre de Bruxelles,
Bruxelles, Belgium

\url{http://www.ulb.ac.be/di/mlg/}

- Breast Cancer Translational Laboratory (BCTL), Institut Jules
Bordet, Bruxelles, Belgium

\url{http://www.bordet.be/en/services/medical/array/practical.htm}


\bold{Maintainer}: \bold{Benjamin Haibe-Kains}

\email{bhaibeka at jimmy.harvard.edu}

\email{bhaibeka at ulb.ac.be}

\bold{Markus Schroeder}

\email{mschroed at jimmy.harvard.edu}
\end{Author}
%
\begin{SeeAlso}\relax
\code{survcomp}
\end{SeeAlso}
\printindex{}
\end{document}


Thanks,
Dan



>
> Duncan Murdoch
>
>
>> <inserted text>
>> ? ? ? ? ? ? ? ? \endgroup
>> l.39 }
>>
>> /Users/dtenenba/tmp/.Rd2pdf4804/Rd2.tex:39: ?==> ?Fatal error occurred, no
>> outpu
>> t PDF file produced!
>> Transcript written on Rd2.log.
>> Error in running tools::texi2pdf
>> You may want to clean up by 'rm -rf .Rd2pdf4804'
>>
>>
>>
>>>
>>> Duncan Murdoch
>>>
>>>
>>>>
>>>> Thanks!
>>>> Dan
>>>>
>>>>
>>>>> Alternatively, you could take a look at the .tex files generated, and
>>>>> identify what the problem is.
>>>>>
>>>>> Duncan Murdoch
>>>>>
>>>>>>
>>>>>> Because of this problem, reference manuals are not being created for
>>>>>> many Bioconductor packages (any package where there is a \Sexpr in an
>>>>>> .Rd file).
>>>>>>
>>>>>> Thanks in advance--we appreciate your help very much.
>>>>>> Dan
>>>>>>
>>>>>>
>>>>>> On Wed, Mar 14, 2012 at 1:13 PM, Dan Tenenbaum<dtenenba at fhcrc.org>
>>>>>> ?wrote:
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Hi,
>>>>>>>
>>>>>>> The following command:
>>>>>>> R CMD Rd2pdf --no-preview --output=./tmp.pdf --title=test
>>>>>>> genefu-package.Rd
>>>>>>> run against this file:
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/genefu/man/genefu-package.Rd
>>>>>>> (username: readonly; password: readonly)
>>>>>>>
>>>>>>> produces a very verbose error (see below)
>>>>>>> with R version 2.15.0 alpha (2012-03-07 r58622).
>>>>>>>
>>>>>>> The .Rd file has these lines in it:
>>>>>>>
>>>>>>> Version: \tab \Sexpr{packageDescription("genefu")$Version}\cr
>>>>>>> Date: \tab \Sexpr{packageDescription("genefu")$Date}\cr
>>>>>>>
>>>>>>> If I take these lines out, or take out the \Sexpr part, the Rd2pdf
>>>>>>> command will complete successfully.
>>>>>>>
>>>>>>> Is there some other step I need to run to evaluate the \Sexpr tags
>>>>>>> before running Rd2pdf, or is there an issue that needs to be fixed?
>>>>>>>
>>>>>>> Thanks,
>>>>>>> Dan
>>>>>>>
>>>>>>> Error output:
>>>>>>>
>>>>>>> Converting Rd files to LaTeX ...
>>>>>>> ?genefu-package.Rd
>>>>>>> Creating pdf output from LaTeX ...
>>>>>>> Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet =
>>>>>>> quiet,
>>>>>>> ?:
>>>>>>> ?Running 'texi2dvi' on 'Rd2.tex' failed.
>>>>>>> Messages:
>>>>>>> /usr/bin/texi2dvi: pdflatex exited with bad status, quitting.
>>>>>>> /usr/bin/texi2dvi: see Rd2.log for errors.
>>>>>>> Output:
>>>>>>> This is pdfTeX, Version 3.1415926-2.3-1.40.12 (TeX Live 2011)
>>>>>>> ?restricted \write18 enabled.
>>>>>>> entering extended mode
>>>>>>> (/Users/dtenenba/dev/bioc_devel/genefu/man/.Rd2pdf62869/Rd2.tex
>>>>>>> LaTeX2e<2011/06/27>
>>>>>>> Babel<v3.8m> ? ? ?and hyphenation patterns for english, dumylang,
>>>>>>> nohyphenation, ge
>>>>>>> rman-x-2011-07-01, ngerman-x-2011-07-01, afrikaans, ancientgreek,
>>>>>>> ibycus,
>>>>>>> arabi
>>>>>>> c, armenian, basque, bulgarian, catalan, pinyin, coptic, croatian,
>>>>>>> czech,
>>>>>>> danis
>>>>>>> h, dutch, ukenglish, usenglishmax, esperanto, estonian, ethiopic,
>>>>>>> farsi,
>>>>>>> finnis
>>>>>>> h, french, galician, german, ngerman, swissgerman, monogreek, greek,
>>>>>>> hungarian,
>>>>>>> ?icelandic, assamese, bengali, gujarati, hindi, kannada, malayalam,
>>>>>>> marathi, or
>>>>>>> iya, panjabi, tamil, telugu, indonesian, interlingua, irish, italian,
>>>>>>> kurmanji,
>>>>>>> ?lao, latin, latvian, lithuanian, mongolian, mongolianlmc, bokmal,
>>>>>>> nynorsk, pol
>>>>>>> ish, portuguese, romanian, russian, sanskrit, serbian, serbianc,
>>>>>>> slovak,
>>>>>>> sloven
>>>>>>> ian, spanish, swedish, turkish, turkmen, ukrainian, uppersorbian,
>>>>>>> welsh,
>>>>>>> loaded
>>>>>>> .
>>>>>>> (/usr/local/texlive/2011/texmf-dist/tex/latex/base/book.cls
>>>>>>> Document Class: book 2007/10/19 v1.4h Standard LaTeX document class
>>>>>>> (/usr/local/texlive/2011/texmf-dist/tex/latex/base/bk10.clo))
>>>>>>>
>>>>>>> (/Library/Frameworks/R.framework/Resources/share/texmf/tex/latex/Rd.sty
>>>>>>> (/usr/local/texlive/2011/texmf-dist/tex/latex/base/ifthen.sty)
>>>>>>> (/usr/local/texlive/2011/texmf-dist/tex/latex/tools/longtable.sty)
>>>>>>> (/usr/local/texlive/2011/texmf-dist/tex/latex/tools/bm.sty)
>>>>>>> (/usr/local/texlive/2011/texmf-dist/tex/latex/base/alltt.sty)
>>>>>>> (/usr/local/texlive/2011/texmf-dist/tex/latex/tools/verbatim.sty)
>>>>>>> (/usr/local/texlive/2011/texmf-dist/tex/latex/url/url.sty) NOT
>>>>>>> loading
>>>>>>> ae
>>>>>>> (/usr/local/texlive/2011/texmf-dist/tex/latex/base/fontenc.sty
>>>>>>> (/usr/local/texlive/2011/texmf-dist/tex/latex/base/t1enc.def))
>>>>>>> (/usr/local/texlive/2011/texmf-dist/tex/latex/psnfss/times.sty)
>>>>>>> NOT loading lmodern
>>>>>>>
>>>>>>>
>>>>>>> (/usr/local/texlive/2011/texmf-dist/tex/latex/inconsolata/inconsolata.sty
>>>>>>> (/usr/local/texlive/2011/texmf-dist/tex/latex/base/textcomp.sty
>>>>>>> (/usr/local/texlive/2011/texmf-dist/tex/latex/base/ts1enc.def))
>>>>>>> (/usr/local/texlive/2011/texmf-dist/tex/latex/graphics/keyval.sty))
>>>>>>> (/usr/local/texlive/2011/texmf-dist/tex/latex/graphics/color.sty
>>>>>>> (/usr/local/texlive/2011/texmf-dist/tex/latex/latexconfig/color.cfg)
>>>>>>> (/usr/local/texlive/2011/texmf-dist/tex/latex/pdftex-def/pdftex.def
>>>>>>>
>>>>>>> (/usr/local/texlive/2011/texmf-dist/tex/generic/oberdiek/infwarerr.sty)
>>>>>>>
>>>>>>> (/usr/local/texlive/2011/texmf-dist/tex/generic/oberdiek/ltxcmds.sty)))
>>>>>>> (/usr/local/texlive/2011/texmf-dist/tex/latex/hyperref/hyperref.sty
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> (/usr/local/texlive/2011/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> (/usr/local/texlive/2011/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty))
>>>>>>> (/usr/local/texlive/2011/texmf-dist/tex/generic/ifxetex/ifxetex.sty)
>>>>>>> (/usr/local/texlive/2011/texmf-dist/tex/latex/oberdiek/kvoptions.sty)
>>>>>>> (/usr/local/texlive/2011/texmf-dist/tex/latex/hyperref/pd1enc.def)
>>>>>>>
>>>>>>>
>>>>>>> (/usr/local/texlive/2011/texmf-dist/tex/latex/latexconfig/hyperref.cfg))
>>>>>>>
>>>>>>> Package hyperref Message: Driver (autodetected): hpdftex.
>>>>>>>
>>>>>>> (/usr/local/texlive/2011/texmf-dist/tex/latex/hyperref/hpdftex.def
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> (/usr/local/texlive/2011/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty))
>>>>>>>
>>>>>>> Package hyperref Warning: Option `hyperindex' has already been used,
>>>>>>> (hyperref) ? ? ? ? ? ? ? ?setting the option has no effect on input
>>>>>>> line
>>>>>>> 356.
>>>>>>>
>>>>>>>
>>>>>>> Package hyperref Warning: Option `pagebackref' has already been used,
>>>>>>> (hyperref) ? ? ? ? ? ? ? ?setting the option has no effect on input
>>>>>>> line
>>>>>>> 356.
>>>>>>>
>>>>>>> ) (/usr/local/texlive/2011/texmf-dist/tex/latex/base/makeidx.sty)
>>>>>>> (/usr/local/texlive/2011/texmf-dist/tex/latex/base/inputenc.sty
>>>>>>> (/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def
>>>>>>> (/usr/local/texlive/2011/texmf-dist/tex/latex/base/t1enc.dfu)
>>>>>>> (/usr/local/texlive/2011/texmf-dist/tex/latex/base/ot1enc.dfu)
>>>>>>> (/usr/local/texlive/2011/texmf-dist/tex/latex/base/omsenc.dfu)
>>>>>>> (/usr/local/texlive/2011/texmf-dist/tex/latex/base/ts1enc.dfu))
>>>>>>> (/usr/local/texlive/2011/texmf-dist/tex/latex/base/latin1.def))
>>>>>>> Writing index file Rd2.idx
>>>>>>> No file Rd2.aux.
>>>>>>> (/usr/local/texlive/2011/texmf-dist/tex/latex/base/ts1cmr.fd)
>>>>>>> (/usr/local/texlive/2011/texmf-dist/tex/latex/psnfss/t1ptm.fd)
>>>>>>> (/usr/local/texlive/2011/texmf-dist/tex/context/base/supp-pdf.mkii
>>>>>>> [Loading MPS to PDF converter (version 2006.09.02).]
>>>>>>> ) (/usr/local/texlive/2011/texmf-dist/tex/latex/hyperref/nameref.sty
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> (/usr/local/texlive/2011/texmf-dist/tex/generic/oberdiek/gettitlestring.sty))
>>>>>>> (/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def)
>>>>>>> (/usr/local/texlive/2011/texmf-dist/tex/latex/inconsolata/t1fi4.fd)
>>>>>>> /Users/dtenenba/dev/bioc_devel/genefu/man/.Rd2pdf62869/Rd2.tex:39:
>>>>>>> Missing \end
>>>>>>> group inserted.
>>>>>>> <inserted text>
>>>>>>> ? ? ? ? ? ? ? ?\endgroup
>>>>>>> l.39 }
>>>>>>>
>>>>>>> ?
>>>>>>> /Users/dtenenba/dev/bioc_devel/genefu/man/.Rd2pdf62869/Rd2.tex:39:
>>>>>>> Emergency st
>>>>>>> op.
>>>>>>> <inserted text>
>>>>>>> ? ? ? ? ? ? ? ?\endgroup
>>>>>>> l.39 }
>>>>>>>
>>>>>>> /Users/dtenenba/dev/bioc_devel/genefu/man/.Rd2pdf62869/Rd2.tex:39:
>>>>>>> ?==>
>>>>>>> ?Fatal e
>>>>>>> rror occurred, no output PDF file produced!
>>>>>>> Transcript written on Rd2.log.
>>>>>>> Error in running tools::texi2pdf
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> ______________________________________________
>>>>>> R-devel at r-project.org mailing list
>>>>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>>>>
>>>>>
>>>>>
>>>>>
>>>
>



[Rd] issue with Rd2pdf and \Sexpr in Rd files
Dan Tenenbaum