On Tue, Mar 20, 2012 at 10:21 AM, Duncan Murdoch <murdoch.dun...@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<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 > > ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
