Hmm ... looks like a package This is pdfTeX, Version 3.1415926-2.4-1.40.13 (TeX Live 2012) restricted \write18 enabled. entering extended mode (/private/var/folders/dz/dz-rCNOVF5usf8YGr4lR-++++TM/-Tmp-/Rtmp7YOHzj/Rd2pdf3fd 233e3/Rd2.tex LaTeX2e <2011/06/27> Babel and hyphenation patterns for english, dumylang, nohyphenation, ge rman-x-2012-05-30, ngerman-x-2012-05-30, 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, friulan, galician, german, ngerman, swissgerman, monogreek, greek, h ungarian, icelandic, assamese, bengali, gujarati, hindi, kannada, malayalam, ma rathi, oriya, panjabi, tamil, telugu, indonesian, interlingua, irish, italian, kurmanji, latin, latvian, lithuanian, mongolian, mongolianlmc, bokmal, nynorsk, polish, portuguese, romanian, romansh, russian, sanskrit, serbian, serbianc, s lovak, slovenian, spanish, swedish, turkish, turkmen, ukrainian, uppersorbian, welsh, loaded. 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(/usr/local/texlive/2012/texmf-dist/tex/latex/base/ts1cmr.fd) (/usr/local/texlive/2012/texmf-dist/tex/latex/psnfss/t1ptm.fd) (/usr/local/texlive/2012/texmf-dist/tex/context/base/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/local/texlive/2012/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/local/texlive/2012/texmf-dist/tex/generic/oberdiek/gettitlestring.sty)) (/usr/local/texlive/2012/texmf-dist/tex/latex/psnfss/t1pcr.fd) (/usr/local/texlive/2012/texmf-dist/tex/latex/psnfss/t1phv.fd) (/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def) Underfull \vbox (badness 10000) has occurred while \output is active [1{/usr/lo cal/texlive/2012/texmf-var/fonts/map/pdftex/updmap/pdftex.map}] (/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def) No file Rd2.ind. [2] (./Rd2.aux) Package rerunfilecheck Warning: File `Rd2.out' has changed. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. ) (see the transcript file for additional information)pdfTeX warning (dest): name {Rfn.} has been referenced but does not exist, replaced by a fixed one {/usr/local/texlive/2012/texmf-dist/fonts/enc/dvips/base/8r.enc} Output written on Rd2.pdf (2 pages, 62760 bytes). Transcript written on Rd2.log. This is makeindex, version 2.15 [TeX Live 2012] (kpathsea + Thai support). Scanning input file ./Rd2.idx....done (7 entries accepted, 0 rejected). Sorting entries....done (18 comparisons). Generating output file ./Rd2.ind....done (21 lines written, 0 warnings). Output written in ./Rd2.ind. Transcript written in ./Rd2.ilg. This is pdfTeX, Version 3.1415926-2.4-1.40.13 (TeX Live 2012) restricted \write18 enabled. entering extended mode (/private/var/folders/dz/dz-rCNOVF5usf8YGr4lR-++++TM/-Tmp-/Rtmp7YOHzj/Rd2pdf3fd 233e3/Rd2.tex LaTeX2e <2011/06/27> Babel and hyphenation patterns for english, dumylang, nohyphenation, ge rman-x-2012-05-30, ngerman-x-2012-05-30, 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, friulan, galician, german, ngerman, swissgerman, monogreek, greek, h ungarian, icelandic, assamese, bengali, gujarati, hindi, kannada, malayalam, ma rathi, oriya, panjabi, tamil, telugu, indonesian, interlingua, irish, italian, kurmanji, latin, latvian, lithuanian, mongolian, mongolianlmc, bokmal, nynorsk, polish, portuguese, romanian, romansh, russian, sanskrit, serbian, serbianc, s lovak, slovenian, spanish, swedish, turkish, turkmen, ukrainian, uppersorbian, welsh, loaded. 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(rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. ) (see the transcript file for additional information)pdfTeX warning (dest): name {Rfn.} has been referenced but does not exist, replaced by a fixed one {/usr/local/texlive/2012/texmf-dist/fonts/enc/dvips/base/8r.enc} Output written on Rd2.pdf (3 pages, 78072 bytes). Transcript written on Rd2.log. This is makeindex, version 2.15 [TeX Live 2012] (kpathsea + Thai support). Scanning input file ./Rd2.idx....done (7 entries accepted, 0 rejected). Sorting entries....done (18 comparisons). Generating output file ./Rd2.ind....done (21 lines written, 0 warnings). Output written in ./Rd2.ind. Transcript written in ./Rd2.ilg. This is pdfTeX, Version 3.1415926-2.4-1.40.13 (TeX Live 2012) restricted \write18 enabled. entering extended mode (/private/var/folders/dz/dz-rCNOVF5usf8YGr4lR-++++TM/-Tmp-/Rtmp7YOHzj/Rd2pdf3fd 233e3/Rd2.tex LaTeX2e <2011/06/27> Babel and hyphenation patterns for english, dumylang, nohyphenation, ge rman-x-2012-05-30, ngerman-x-2012-05-30, 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, friulan, galician, german, ngerman, swissgerman, monogreek, greek, h ungarian, icelandic, assamese, bengali, gujarati, hindi, kannada, malayalam, ma rathi, oriya, panjabi, tamil, telugu, indonesian, interlingua, irish, italian, kurmanji, latin, latvian, lithuanian, mongolian, mongolianlmc, bokmal, nynorsk, polish, portuguese, romanian, romansh, russian, sanskrit, serbian, serbianc, s lovak, slovenian, spanish, swedish, turkish, turkmen, ukrainian, uppersorbian, welsh, loaded. (/usr/local/texlive/2012/texmf-dist/tex/latex/base/book.cls Document Class: book 2007/10/19 v1.4h Standard LaTeX document class (/usr/local/texlive/2012/texmf-dist/tex/latex/base/bk10.clo)) (/Library/Frameworks/R.framework/Resources/share/texmf/tex/latex/Rd.sty (/usr/local/texlive/2012/texmf-dist/tex/latex/base/ifthen.sty) (/usr/local/texlive/2012/texmf-dist/tex/latex/tools/longtable.sty) (/usr/local/texlive/2012/texmf-dist/tex/latex/tools/bm.sty) (/usr/local/texlive/2012/texmf-dist/tex/latex/base/alltt.sty) (/usr/local/texlive/2012/texmf-dist/tex/latex/tools/verbatim.sty) (/usr/local/texlive/2012/texmf-dist/tex/latex/url/url.sty) (/Library/Frameworks/R.framework/Resources/share/texmf/tex/latex/upquote.sty (/usr/local/texlive/2012/texmf-dist/tex/latex/base/textcomp.sty (/usr/local/texlive/2012/texmf-dist/tex/latex/base/ts1enc.def))) NOT loading ae (/usr/local/texlive/2012/texmf-dist/tex/latex/base/fontenc.sty (/usr/local/texlive/2012/texmf-dist/tex/latex/base/t1enc.def)) (/usr/local/texlive/2012/texmf-dist/tex/latex/psnfss/times.sty) NOT loading lmodern (/usr/local/texlive/2012/texmf-dist/tex/latex/graphics/color.sty (/usr/local/texlive/2012/texmf-dist/tex/latex/latexconfig/color.cfg) (/usr/local/texlive/2012/texmf-dist/tex/latex/pdftex-def/pdftex.def (/usr/local/texlive/2012/texmf-dist/tex/generic/oberdiek/infwarerr.sty) (/usr/local/texlive/2012/texmf-dist/tex/generic/oberdiek/ltxcmds.sty))) (/usr/local/texlive/2012/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/local/texlive/2012/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty (/usr/local/texlive/2012/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty)) (/usr/local/texlive/2012/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/local/texlive/2012/texmf-dist/tex/generic/ifxetex/ifxetex.sty) (/usr/local/texlive/2012/texmf-dist/tex/latex/oberdiek/kvoptions.sty) (/usr/local/texlive/2012/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/local/texlive/2012/texmf-dist/tex/latex/latexconfig/hyperref.cfg)) Package hyperref Message: Driver (autodetected): hpdftex. 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Package hyperref Warning: Option `pagebackref' has already been used, (hyperref) setting the option has no effect on input line 332. ) (/usr/local/texlive/2012/texmf-dist/tex/latex/base/makeidx.sty) (/usr/local/texlive/2012/texmf-dist/tex/latex/base/inputenc.sty (/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def (/usr/local/texlive/2012/texmf-dist/tex/latex/base/t1enc.dfu) (/usr/local/texlive/2012/texmf-dist/tex/latex/base/ot1enc.dfu) (/usr/local/texlive/2012/texmf-dist/tex/latex/base/omsenc.dfu) (/usr/local/texlive/2012/texmf-dist/tex/latex/base/ts1enc.dfu)) (/usr/local/texlive/2012/texmf-dist/tex/latex/base/latin1.def)) Writing index file Rd2.idx (./Rd2.aux) (/usr/local/texlive/2012/texmf-dist/tex/latex/base/ts1cmr.fd) (/usr/local/texlive/2012/texmf-dist/tex/latex/psnfss/t1ptm.fd) (/usr/local/texlive/2012/texmf-dist/tex/context/base/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/local/texlive/2012/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/local/texlive/2012/texmf-dist/tex/generic/oberdiek/gettitlestring.sty)) (./Rd2.out) (./Rd2.out) (/usr/local/texlive/2012/texmf-dist/tex/latex/psnfss/t1pcr.fd) (/usr/local/texlive/2012/texmf-dist/tex/latex/psnfss/t1phv.fd) (./Rd2.toc) (/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def) Overfull \vbox (32.37697pt too high) has occurred while \output is active [1{/usr/local/texlive/2012/texmf-var/fonts/map/pdftex/updmap/pdftex.map}] (/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def) (./Rd2.ind [2] [3]) (./Rd2.aux) ) (see the transcript file for additional information)pdfTeX warning (dest): name {Rfn.} has been referenced but does not exist, replaced by a fixed one {/usr/local/texlive/2012/texmf-dist/fonts/enc/dvips/base/8r.enc} Output written on Rd2.pdf (3 pages, 78732 bytes). Transcript written on Rd2.log. Saving output to 'mypkg-manual.pdf' ... Done You may want to clean up by 'rm -rf /var/folders/dz/dz-rCNOVF5usf8YGr4lR-++++TM/-Tmp-//Rtmp7YOHzj/Rd2pdf3fd233e3'