From dtenenba at fhcrc.org  Tue Mar 20 20:19:49 2012
From: dtenenba at fhcrc.org (Dan Tenenbaum)
Date: Tue, 20 Mar 2012 12:19:49 -0700
Subject: [Rd] issue with Rd2pdf and \Sexpr in Rd files
In-Reply-To: <4F68D70E.7080906@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>
	<4F68D70E.7080906@gmail.com>
Message-ID: <CAF42j21ebRvARj77XYBffiy-FNYOXzNZAXhFsB50RwZsQVGsqA@mail.gmail.com>

On Tue, Mar 20, 2012 at 12:14 PM, Duncan Murdoch
<murdoch.duncan at gmail.com> wrote:
> This should now be fixed in R-devel, and shortly in the 2.15.0 beta.

Thanks very much.
Dan

>
> 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
Dan Tenenbaum