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 <dtene...@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@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
