From murdoch.duncan at gmail.com  Tue Mar 20 20:14:22 2012
From: murdoch.duncan at gmail.com (Duncan Murdoch)
Date: Tue, 20 Mar 2012 15:14:22 -0400
Subject: [Rd] issue with Rd2pdf and \Sexpr in Rd files
In-Reply-To: <CAF42j23qhzGMuhUp5qiEf2oSY+mOf38aTbTtB=zM_kDupno7eg@mail.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>
	<CAF42j23qhzGMuhUp5qiEf2oSY+mOf38aTbTtB=zM_kDupno7eg@mail.gmail.com>
Message-ID: <4F68D70E.7080906@gmail.com>

This should now be fixed in R-devel, and shortly in the 2.15.0 beta.

Duncan Murdoch

On 12-03-20 2:54 PM, Dan Tenenbaum wrote:
> 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
Duncan Murdoch