On Tue, Mar 20, 2012 at 12:14 PM, Duncan Murdoch <murdoch.dun...@gmail.com> wrote: > This should now be fixed in R-devel, and shortly in the 2.15.0 beta.
Thanks very much. Dan > > Duncan Murdoch > > > On 12-03-20 2:54 PM, Dan Tenenbaum wrote: >> >> On Tue, Mar 20, 2012 at 11:51 AM, Duncan Murdoch >> <murdoch.dun...@gmail.com> wrote: >>> >>> On 12-03-20 1:46 PM, Dan Tenenbaum wrote: >>>> >>>> >>>> On Tue, Mar 20, 2012 at 10:41 AM, Duncan Murdoch >>>> <murdoch.dun...@gmail.com> wrote: >>>>> >>>>> >>>>> On 12-03-20 1:25 PM, Dan Tenenbaum wrote: >>>>>> >>>>>> >>>>>> >>>>>> 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 >>>>> >>>>> >>>>> >>>>> >>>>> Sorry, I didn't see that. >>>>> >>>> >>>> Actually, I goofed, because that file contains the lines: >>>> Version: \tab \Sexpr{packageDescription("genefu")$Version}\cr >>>> Date: \tab \Sexpr{packageDescription("genefu")$Date}\cr >>>> >>>> And those lines require you to have the 'genefu' package installed. >>>> I changed those lines to more innocuous \Sexprs: >>>> >>>> Version: \tab \Sexpr{cat("hello")}\cr >>>> Date: \tab \Sexpr{cat("world")}\cr >>>> >>>> >>>> >>>>> >>>>>> No .tex file is generated. >>>>> >>>>> >>>>> >>>>> >>>>> If you use the --no-clean command line option, then the temporary >>>>> directory >>>>> containing the .tex file will not be deleted. It contains your \Sexpr >>>>> expressions wrapped in verbatim environments. I suspect this is >>>>> happening >>>>> because Rd2pdf isn't running the Sexpr evaluation step. >>>> >>>> >>>> >>>> Yes, that's what I think is happening. >>>> >>>>> I'll try to take a >>>>> look and fix it. >>>> >>>> >>>> >>>> Thanks very much! >>>> >>>> I added the --no-clean flag and still got no .tex file. Here is my new >>>> error output, looks the same as the original error output. >>>> >>>> Thanks, >>>> Dan >>>> >>>> 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. >>>> LaTeX errors: >>>> /Users/dtenenba/tmp/.Rd2pdf4804/Rd2.tex:39: ==> Fatal error >>>> occurred, no >>>> outpu >>>> t PDF file produced! >>>> Output: >>>> This is pdfTeX, Version 3.1415926-2.3-1.40.12 (TeX Live 2011) >>>> restricted \write18 enabled. >>>> entering extended mode >>>> (/Users/dtenenba/tmp/.Rd2pdf4804/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/tmp/.Rd2pdf4804/Rd2.tex:39: Missing \endgroup inserted. >>>> <inserted text> >>>> \endgroup >>>> l.39 } >>>> >>>> ? >>>> /Users/dtenenba/tmp/.Rd2pdf4804/Rd2.tex:39: Emergency stop. >>> >>> >>> >>> That's the file to look at. With --no-clean, it should still be there >>> after >>> the run, but ls won't show the directory because of the dot in the name. >> >> >> Here are the contents of that .tex file: >> >> \documentclass[a4paper]{book} >> \usepackage[times,inconsolata,hyper]{Rd} >> \usepackage{makeidx} >> \usepackage[utf8,latin1]{inputenc} >> % \usepackage{graphicx} % @USE GRAPHICX@ >> \makeindex{} >> \begin{document} >> \chapter*{} >> \begin{center} >> {\textbf{\huge test}} >> \par\bigskip{\large \today} >> \end{center} >> \inputencoding{utf8} >> \HeaderA{genefu-package}{Relevant Functions for Gene Expression >> Analysis, Especially in Breast Cancer.}{genefu.Rdash.package} >> \aliasA{genefu}{genefu-package}{genefu} >> \keyword{clustering}{genefu-package} >> \keyword{models}{genefu-package} >> \keyword{breast cancer}{genefu-package} >> \keyword{prognosis}{genefu-package} >> % >> \begin{Description}\relax >> This package contains functions implementing various tasks usually >> required by gene expression analysis, especially in breast cancer >> studies: gene mapping between different microarray platforms, >> identification of molecular subtypes, implementation of published gene >> signatures, gene selection, survival analysis, ... >> \end{Description} >> % >> \begin{Details}\relax >> >> \Tabular{ll}{ >> Package:& genefu\\{} >> Type:& Package\\{} >> Version:& \begin{verbatim} >> \Sexpr{cat("hello")} >> \end{verbatim} >> \\{} >> Date:& \begin{verbatim} >> \Sexpr{cat("world")} >> \end{verbatim} >> \\{} >> License:& Artistic-2.0\\{} >> } >> \end{Details} >> % >> \begin{Author}\relax >> \bold{Benjamin Haibe-Kains} >> >> - Computational Biology and Functional Genomics, Dana-Farber Cancer >> Institute, Boston, MA, USA >> >> \url{http://compbio.dfci.harvard.edu/} >> >> - Center for Cancer Computational Biology, Dana-Farber Cancer >> Institute, Boston, MA, USA >> >> \url{http://cccb.dfci.harvard.edu/index.html} >> >> Former labs: >> >> - Machine Learning Group (MLG), Universite Libre de Bruxelles, >> Bruxelles, Belgium >> >> \url{http://www.ulb.ac.be/di/mlg/} >> >> - Breast Cancer Translational Laboratory (BCTL), Institut Jules >> Bordet, Bruxelles, Belgium >> >> \url{http://www.bordet.be/en/services/medical/array/practical.htm} >> >> >> \bold{Maintainer}: \bold{Benjamin Haibe-Kains} >> >> \email{bhaib...@jimmy.harvard.edu} >> >> \email{bhaib...@ulb.ac.be} >> >> \bold{Markus Schroeder} >> >> \email{mschr...@jimmy.harvard.edu} >> \end{Author} >> % >> \begin{SeeAlso}\relax >> \code{survcomp} >> \end{SeeAlso} >> \printindex{} >> \end{document} >> >> >> Thanks, >> Dan >> >> >> >>> >>> Duncan Murdoch >>> >>> >>>> <inserted text> >>>> \endgroup >>>> l.39 } >>>> >>>> /Users/dtenenba/tmp/.Rd2pdf4804/Rd2.tex:39: ==> Fatal error >>>> occurred, no >>>> outpu >>>> t PDF file produced! >>>> Transcript written on Rd2.log. >>>> Error in running tools::texi2pdf >>>> You may want to clean up by 'rm -rf .Rd2pdf4804' >>>> >>>> >>>> >>>>> >>>>> Duncan Murdoch >>>>> >>>>> >>>>>> >>>>>> 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 >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>> >>> > 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