From dtenenba at fhcrc.org  Tue Mar 20 03:27:07 2012
From: dtenenba at fhcrc.org (Dan Tenenbaum)
Date: Mon, 19 Mar 2012 19:27:07 -0700
Subject: [Rd] issue with Rd2pdf and \Sexpr in Rd files
In-Reply-To: <CAF42j22X+B8aLCEDhY7PzXpPobDcZT80rhNT5DFKFNBa0vkYLg@mail.gmail.com>
References: <CAF42j22X+B8aLCEDhY7PzXpPobDcZT80rhNT5DFKFNBa0vkYLg@mail.gmail.com>
Message-ID: <CAF42j20FGqHq67xPwAbYN2K_AmQKZ3PHwW6BVtQTjZVeLEvyTQ@mail.gmail.com>

Hello,

Sorry to repeat myself, but I was wondering if anyone had taken a look at this.

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



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