From murdoch.duncan at gmail.com  Tue Mar 20 19:51:54 2012
From: murdoch.duncan at gmail.com (Duncan Murdoch)
Date: Tue, 20 Mar 2012 14:51:54 -0400
Subject: [Rd] issue with Rd2pdf and \Sexpr in Rd files
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Message-ID: <4F68D1CA.6050900@gmail.com>

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.

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