From murdoch.duncan at gmail.com  Tue Mar 20 18:41:15 2012
From: murdoch.duncan at gmail.com (Duncan Murdoch)
Date: Tue, 20 Mar 2012 13:41:15 -0400
Subject: [Rd] issue with Rd2pdf and \Sexpr in Rd files
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Message-ID: <4F68C13B.7080806@gmail.com>

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.

> 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.  I'll try to take a look and fix it.

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