From dtenenba at fhcrc.org  Wed Mar 14 21:13:20 2012
From: dtenenba at fhcrc.org (Dan Tenenbaum)
Date: Wed, 14 Mar 2012 13:13:20 -0700
Subject: [Rd] issue with Rd2pdf and \Sexpr in Rd files
Message-ID: <CAF42j22X+B8aLCEDhY7PzXpPobDcZT80rhNT5DFKFNBa0vkYLg@mail.gmail.com>

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



[Rd] issue with Rd2pdf and \Sexpr in Rd files
Dan Tenenbaum