From dtenenba at fhcrc.org  Tue Mar 20 18:25:13 2012
From: dtenenba at fhcrc.org (Dan Tenenbaum)
Date: Tue, 20 Mar 2012 10:25:13 -0700
Subject: [Rd] issue with Rd2pdf and \Sexpr in Rd files
In-Reply-To: <4F68BC81.20506@gmail.com>
References: <CAF42j22X+B8aLCEDhY7PzXpPobDcZT80rhNT5DFKFNBa0vkYLg@mail.gmail.com>
	<CAF42j20FGqHq67xPwAbYN2K_AmQKZ3PHwW6BVtQTjZVeLEvyTQ@mail.gmail.com>
	<4F68BC81.20506@gmail.com>
Message-ID: <CAF42j22icfTTsN6=2ocJw2pVWh4QxoYyFNaZ9BkdNuotLnu6Ng@mail.gmail.com>

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
No .tex file is generated.

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