From murdoch.duncan at gmail.com  Tue Mar 20 18:21:05 2012
From: murdoch.duncan at gmail.com (Duncan Murdoch)
Date: Tue, 20 Mar 2012 13:21:05 -0400
Subject: [Rd] issue with Rd2pdf and \Sexpr in Rd files
In-Reply-To: <CAF42j20FGqHq67xPwAbYN2K_AmQKZ3PHwW6BVtQTjZVeLEvyTQ@mail.gmail.com>
References: <CAF42j22X+B8aLCEDhY7PzXpPobDcZT80rhNT5DFKFNBa0vkYLg@mail.gmail.com>
	<CAF42j20FGqHq67xPwAbYN2K_AmQKZ3PHwW6BVtQTjZVeLEvyTQ@mail.gmail.com>
Message-ID: <4F68BC81.20506@gmail.com>

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.

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
>
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[Rd] issue with Rd2pdf and \Sexpr in Rd files
Duncan Murdoch