issue with Rd2pdf and \Sexpr in Rd files

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

No .tex file is generated.

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