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.RdSorry, 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")}\crNo .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.
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 MurdochThanks! DanAlternatively, you could take a look at the .tex files generated, and identify what the problem is. Duncan MurdochBecause 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. 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