* checking for file 'RamiGO/DESCRIPTION' ... OK
* preparing 'RamiGO':
* checking DESCRIPTION meta-information ... OK
* installing the package to process help pages
* building the PDF package manual
Hmm ... looks like a package
Converting Rd files to LaTeX .
Creating pdf output from LaTeX ...
This is pdfTeX, Version 3.1415926-1.40.11 (TeX Live 2010)
\write18 enabled.
entering extended mode
(/private/tmp/RtmpXp6TIs/Rbuild338f23568ca6/RamiGO/.Rd2dvi13199/Rd2.tex
LaTeX2e <2009/09/24>
Babel <v3.8l> and hyphenation patterns for english, dumylang, nohyphenation, ge
rman-x-2009-06-19, ngerman-x-2009-06-19, ancientgreek, ibycus, arabic, armenian
, basque, bulgarian, catalan, pinyin, coptic, croatian, czech, danish, dutch, u
kenglish, usenglishmax, esperanto, estonian, farsi, finnish, french, galician,
german, ngerman, swissgerman, monogreek, greek, hungarian, icelandic, assamese,
bengali, gujarati, hindi, kannada, malayalam, marathi, oriya, panjabi, tamil,
telugu, indonesian, interlingua, irish, italian, kurmanji, lao, latin, latvian,
lithuanian, mongolian, mongolianlmc, bokmal, nynorsk, polish, portuguese, roma
nian, russian, sanskrit, serbian, slovak, slovenian, spanish, swedish, turkish,
turkmen, ukrainian, uppersorbian, welsh, loaded.
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/book.cls
Document Class: book 2007/10/19 v1.4h Standard LaTeX document class
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/bk10.clo))
(/Library/Frameworks/R.framework/Resources/share/texmf/tex/latex/Rd.sty
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/ifthen.sty)
(/usr/local/texlive/2010/texmf-dist/tex/latex/tools/longtable.sty)
(/usr/local/texlive/2010/texmf-dist/tex/latex/tools/bm.sty)
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/alltt.sty)
(/usr/local/texlive/2010/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/local/texlive/2010/texmf-dist/tex/latex/url/url.sty) NOT loading ae
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/fontenc.sty
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/t1enc.def))
(/usr/local/texlive/2010/texmf-dist/tex/latex/psnfss/times.sty)
NOT loading lmodern
(/usr/local/texlive/2010/texmf-dist/tex/latex/inconsolata/inconsolata.sty
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/textcomp.sty
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/ts1enc.def))
(/usr/local/texlive/2010/texmf-dist/tex/latex/graphics/keyval.sty))
(/usr/local/texlive/2010/texmf-dist/tex/latex/graphics/color.sty
(/usr/local/texlive/2010/texmf-dist/tex/latex/latexconfig/color.cfg)
(/usr/local/texlive/2010/texmf-dist/tex/latex/pdftex-def/pdftex.def))
(/usr/local/texlive/2010/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/local/texlive/2010/texmf-dist/tex/generic/oberdiek/ltxcmds.sty)
(/usr/local/texlive/2010/texmf-dist/tex/generic/oberdiek/kvsetkeys.sty
(/usr/local/texlive/2010/texmf-dist/tex/generic/oberdiek/infwarerr.sty)
(/usr/local/texlive/2010/texmf-dist/tex/generic/oberdiek/etexcmds.sty))
(/usr/local/texlive/2010/texmf-dist/tex/generic/oberdiek/pdfescape.sty
(/usr/local/texlive/2010/texmf-dist/tex/generic/oberdiek/pdftexcmds.sty
(/usr/local/texlive/2010/texmf-dist/tex/generic/oberdiek/ifluatex.sty)))
(/usr/local/texlive/2010/texmf-dist/tex/generic/oberdiek/ifpdf.sty)
(/usr/local/texlive/2010/texmf-dist/tex/generic/oberdiek/ifvtex.sty)
(/usr/local/texlive/2010/texmf-dist/tex/generic/ifxetex/ifxetex.sty)
(/usr/local/texlive/2010/texmf-dist/tex/latex/oberdiek/hycolor.sty
(/usr/local/texlive/2010/texmf-dist/tex/latex/oberdiek/xcolor-patch.sty))
(/usr/local/texlive/2010/texmf-dist/tex/latex/oberdiek/letltxmacro.sty)
(/usr/local/texlive/2010/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/local/texlive/2010/texmf-dist/tex/generic/oberdiek/intcalc.sty)
(/usr/local/texlive/2010/texmf-dist/tex/latex/latexconfig/hyperref.cfg)
(/usr/local/texlive/2010/texmf-dist/tex/latex/oberdiek/kvoptions.sty)
Implicit mode ON; LaTeX internals redefined
(/usr/local/texlive/2010/texmf-dist/tex/generic/oberdiek/bitset.sty
(/usr/local/texlive/2010/texmf-dist/tex/generic/oberdiek/bigintcalc.sty))
(/usr/local/texlive/2010/texmf-dist/tex/generic/oberdiek/atbegshi.sty))
* hyperref using default driver hpdftex *
(/usr/local/texlive/2010/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/local/texlive/2010/texmf-dist/tex/latex/oberdiek/atveryend.sty)
(/usr/local/texlive/2010/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty
(/usr/local/texlive/2010/texmf-dist/tex/generic/oberdiek/uniquecounter.sty)))
Package hyperref Warning: Option `hyperindex' has already been used,
(hyperref) setting the option has no effect on input line 342.
Package hyperref Warning: Option `pagebackref' has already been used,
(hyperref) setting the option has no effect on input line 342.
) (/usr/local/texlive/2010/texmf-dist/tex/latex/base/makeidx.sty)
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/inputenc.sty
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/t1enc.dfu)
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/ot1enc.dfu)
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/omsenc.dfu)
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/ts1enc.dfu))
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/latin1.def))
Writing index file Rd2.idx
No file Rd2.aux.
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/ts1cmr.fd)
(/usr/local/texlive/2010/texmf-dist/tex/latex/psnfss/t1ptm.fd)
(/usr/local/texlive/2010/texmf-dist/tex/context/base/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/local/texlive/2010/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/local/texlive/2010/texmf-dist/tex/latex/oberdiek/refcount.sty)
(/usr/local/texlive/2010/texmf-dist/tex/generic/oberdiek/gettitlestring.sty))
(/usr/local/texlive/2010/texmf-dist/tex/latex/inconsolata/t1fi4.fd)
(/usr/local/texlive/2010/texmf-dist/tex/latex/psnfss/t1phv.fd)
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [1{/usr/local/texl
ive/2010/texmf-var/fonts/map/pdftex/updmap/pdftex.map}]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [2]
Overfull \hbox (4.67784pt too wide) in paragraph at lines 168--170
[]\T1/fi4/m/n/10 leaves(object) <- value\T1/ptm/m/n/10 Sets the the data.frame
con-tain-ing the leaves of the tree with the columns
[3] (/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [4]
Overfull \hbox (29.36072pt too wide) in paragraph at lines 290--293
[]\T1/ptm/m/n/10 See [][]$\T1/fi4/m/n/10 http : / / rcytoscape . systemsbiology
. net / versions / current/$[][] \T1/ptm/m/n/10 and [][]$\T1/fi4/m/n/10 http :
/ / www . bioconductor .
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [5]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [6]
Overfull \hbox (3.19798pt too wide) in paragraph at lines 427--428
[]\T1/ptm/m/n/10 Subramanian A, Tamayo P, Mootha VK, Mukher-jee S, Ebert BL, Gi
llette MA, Paulovich A, Pomeroy
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [7]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [8]
Overfull \hbox (13.60664pt too wide) in paragraph at lines 538--539
[]\T1/ptm/m/n/10 The edge col-ors in the tree rep-re-sent the re-la-tion-ship b
e-tween two nodes. In par-tic-u-lar: green=positively
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [9]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [10]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def)
No file Rd2.ind.
[11] (./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.oldClass.Rdash.class} has been referenced but does not exist, replaced by
a fixed one
pdfTeX warning (dest): name{Rfn.igraph} has been referenced but does not exist,
replaced by a fixed one
{/usr/local/texlive/2010/texmf-dist/fonts/enc/dvips/base/8r.enc}{/usr/local/tex
live/2010/texmf-dist/fonts/enc/dvips/inconsolata/fi4-ec.enc}</usr/local/texlive
/2010/texmf-dist/fonts/type1/public/inconsolata/Inconsolata.pfb></usr/local/tex
live/2010/texmf-dist/fonts/type1/urw/helvetic/uhvr8a.pfb></usr/local/texlive/20
10/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></usr/local/texlive/2010/texmf-d
ist/fonts/type1/urw/times/utmr8a.pfb></usr/local/texlive/2010/texmf-dist/fonts/
type1/urw/times/utmr8a.pfb></usr/local/texlive/2010/texmf-dist/fonts/type1/urw/
times/utmri8a.pfb>
Output written on Rd2.pdf (11 pages, 102550 bytes).
Transcript written on Rd2.log.
This is makeindex, version 2.15 [TeX Live 2010] (kpathsea + Thai support).
Scanning input file ./Rd2.idx....done (57 entries accepted, 0 rejected).
Sorting entries....done (338 comparisons).
Generating output file ./Rd2.ind....done (107 lines written, 0 warnings).
Output written in ./Rd2.ind.
Transcript written in ./Rd2.ilg.
This is pdfTeX, Version 3.1415926-1.40.11 (TeX Live 2010)
\write18 enabled.
entering extended mode
(/private/tmp/RtmpXp6TIs/Rbuild338f23568ca6/RamiGO/.Rd2dvi13199/Rd2.tex
LaTeX2e <2009/09/24>
Babel <v3.8l> and hyphenation patterns for english, dumylang, nohyphenation, ge
rman-x-2009-06-19, ngerman-x-2009-06-19, ancientgreek, ibycus, arabic, armenian
, basque, bulgarian, catalan, pinyin, coptic, croatian, czech, danish, dutch, u
kenglish, usenglishmax, esperanto, estonian, farsi, finnish, french, galician,
german, ngerman, swissgerman, monogreek, greek, hungarian, icelandic, assamese,
bengali, gujarati, hindi, kannada, malayalam, marathi, oriya, panjabi, tamil,
telugu, indonesian, interlingua, irish, italian, kurmanji, lao, latin, latvian,
lithuanian, mongolian, mongolianlmc, bokmal, nynorsk, polish, portuguese, roma
nian, russian, sanskrit, serbian, slovak, slovenian, spanish, swedish, turkish,
turkmen, ukrainian, uppersorbian, welsh, loaded.
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/book.cls
Document Class: book 2007/10/19 v1.4h Standard LaTeX document class
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/bk10.clo))
(/Library/Frameworks/R.framework/Resources/share/texmf/tex/latex/Rd.sty
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/ifthen.sty)
(/usr/local/texlive/2010/texmf-dist/tex/latex/tools/longtable.sty)
(/usr/local/texlive/2010/texmf-dist/tex/latex/tools/bm.sty)
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/alltt.sty)
(/usr/local/texlive/2010/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/local/texlive/2010/texmf-dist/tex/latex/url/url.sty) NOT loading ae
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/fontenc.sty
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/t1enc.def))
(/usr/local/texlive/2010/texmf-dist/tex/latex/psnfss/times.sty)
NOT loading lmodern
(/usr/local/texlive/2010/texmf-dist/tex/latex/inconsolata/inconsolata.sty
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/textcomp.sty
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/ts1enc.def))
(/usr/local/texlive/2010/texmf-dist/tex/latex/graphics/keyval.sty))
(/usr/local/texlive/2010/texmf-dist/tex/latex/graphics/color.sty
(/usr/local/texlive/2010/texmf-dist/tex/latex/latexconfig/color.cfg)
(/usr/local/texlive/2010/texmf-dist/tex/latex/pdftex-def/pdftex.def))
(/usr/local/texlive/2010/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/local/texlive/2010/texmf-dist/tex/generic/oberdiek/ltxcmds.sty)
(/usr/local/texlive/2010/texmf-dist/tex/generic/oberdiek/kvsetkeys.sty
(/usr/local/texlive/2010/texmf-dist/tex/generic/oberdiek/infwarerr.sty)
(/usr/local/texlive/2010/texmf-dist/tex/generic/oberdiek/etexcmds.sty))
(/usr/local/texlive/2010/texmf-dist/tex/generic/oberdiek/pdfescape.sty
(/usr/local/texlive/2010/texmf-dist/tex/generic/oberdiek/pdftexcmds.sty
(/usr/local/texlive/2010/texmf-dist/tex/generic/oberdiek/ifluatex.sty)))
(/usr/local/texlive/2010/texmf-dist/tex/generic/oberdiek/ifpdf.sty)
(/usr/local/texlive/2010/texmf-dist/tex/generic/oberdiek/ifvtex.sty)
(/usr/local/texlive/2010/texmf-dist/tex/generic/ifxetex/ifxetex.sty)
(/usr/local/texlive/2010/texmf-dist/tex/latex/oberdiek/hycolor.sty
(/usr/local/texlive/2010/texmf-dist/tex/latex/oberdiek/xcolor-patch.sty))
(/usr/local/texlive/2010/texmf-dist/tex/latex/oberdiek/letltxmacro.sty)
(/usr/local/texlive/2010/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/local/texlive/2010/texmf-dist/tex/generic/oberdiek/intcalc.sty)
(/usr/local/texlive/2010/texmf-dist/tex/latex/latexconfig/hyperref.cfg)
(/usr/local/texlive/2010/texmf-dist/tex/latex/oberdiek/kvoptions.sty)
Implicit mode ON; LaTeX internals redefined
(/usr/local/texlive/2010/texmf-dist/tex/generic/oberdiek/bitset.sty
(/usr/local/texlive/2010/texmf-dist/tex/generic/oberdiek/bigintcalc.sty))
(/usr/local/texlive/2010/texmf-dist/tex/generic/oberdiek/atbegshi.sty))
* hyperref using default driver hpdftex *
(/usr/local/texlive/2010/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/local/texlive/2010/texmf-dist/tex/latex/oberdiek/atveryend.sty)
(/usr/local/texlive/2010/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty
(/usr/local/texlive/2010/texmf-dist/tex/generic/oberdiek/uniquecounter.sty)))
Package hyperref Warning: Option `hyperindex' has already been used,
(hyperref) setting the option has no effect on input line 342.
Package hyperref Warning: Option `pagebackref' has already been used,
(hyperref) setting the option has no effect on input line 342.
) (/usr/local/texlive/2010/texmf-dist/tex/latex/base/makeidx.sty)
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/inputenc.sty
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/t1enc.dfu)
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/ot1enc.dfu)
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/omsenc.dfu)
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/ts1enc.dfu))
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/latin1.def))
Writing index file Rd2.idx
(./Rd2.aux) (/usr/local/texlive/2010/texmf-dist/tex/latex/base/ts1cmr.fd)
(/usr/local/texlive/2010/texmf-dist/tex/latex/psnfss/t1ptm.fd)
(/usr/local/texlive/2010/texmf-dist/tex/context/base/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/local/texlive/2010/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/local/texlive/2010/texmf-dist/tex/latex/oberdiek/refcount.sty)
(/usr/local/texlive/2010/texmf-dist/tex/generic/oberdiek/gettitlestring.sty))
(./Rd2.out) (./Rd2.out)
(/usr/local/texlive/2010/texmf-dist/tex/latex/inconsolata/t1fi4.fd)
(/usr/local/texlive/2010/texmf-dist/tex/latex/psnfss/t1phv.fd) (./Rd2.toc)
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [1{/usr/local/texl
ive/2010/texmf-var/fonts/map/pdftex/updmap/pdftex.map}]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [2]
Overfull \hbox (4.67784pt too wide) in paragraph at lines 168--170
[]\T1/fi4/m/n/10 leaves(object) <- value\T1/ptm/m/n/10 Sets the the data.frame
con-tain-ing the leaves of the tree with the columns
[3] (/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [4]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (29.36072pt too wide) in paragraph at lines 290--293
[]\T1/ptm/m/n/10 See [][]$\T1/fi4/m/n/10 http : / / rcytoscape . systemsbiology
. net / versions / current/$[][] \T1/ptm/m/n/10 and [][]$\T1/fi4/m/n/10 http :
/ / www . bioconductor .
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [5]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [6]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (3.19798pt too wide) in paragraph at lines 427--428
[]\T1/ptm/m/n/10 Subramanian A, Tamayo P, Mootha VK, Mukher-jee S, Ebert BL, Gi
llette MA, Paulovich A, Pomeroy
[7] (/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [8]
Overfull \hbox (13.60664pt too wide) in paragraph at lines 538--539
[]\T1/ptm/m/n/10 The edge col-ors in the tree rep-re-sent the re-la-tion-ship b
e-tween two nodes. In par-tic-u-lar: green=positively
[9] (/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def)
Underfull \vbox (badness 10000) has occurred while \output is active [10]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [11] (./Rd2.ind
[12]
LaTeX Font Warning: Font shape `T1/fi4/m/it' undefined
(Font) using `T1/fi4/m/n' instead on input line 26.
[13]) (./Rd2.aux)
Package rerunfilecheck Warning: File `Rd2.out' has changed.
(rerunfilecheck) Rerun to get outlines right
(rerunfilecheck) or use package `bookmark'.
LaTeX Font Warning: Some font shapes were not available, defaults substituted.
)
(see the transcript file for additional information)pdfTeX warning (dest): name
{Rfn.oldClass.Rdash.class} has been referenced but does not exist, replaced by
a fixed one
pdfTeX warning (dest): name{Rfn.igraph} has been referenced but does not exist,
replaced by a fixed one
{/usr/local/texlive/2010/texmf-dist/fonts/enc/dvips/base/8r.enc}{/usr/local/tex
live/2010/texmf-dist/fonts/enc/dvips/inconsolata/fi4-ec.enc}</usr/local/texlive
/2010/texmf-dist/fonts/type1/public/inconsolata/Inconsolata.pfb></usr/local/tex
live/2010/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/local/texl
ive/2010/texmf-dist/fonts/type1/urw/helvetic/uhvr8a.pfb></usr/local/texlive/201
0/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></usr/local/texlive/2010/texmf-di
st/fonts/type1/urw/times/utmr8a.pfb></usr/local/texlive/2010/texmf-dist/fonts/t
ype1/urw/times/utmr8a.pfb></usr/local/texlive/2010/texmf-dist/fonts/type1/urw/t
imes/utmri8a.pfb>
Output written on Rd2.pdf (13 pages, 115927 bytes).
Transcript written on Rd2.log.
This is makeindex, version 2.15 [TeX Live 2010] (kpathsea + Thai support).
Scanning input file ./Rd2.idx....done (57 entries accepted, 0 rejected).
Sorting entries....done (338 comparisons).
Generating output file ./Rd2.ind....done (107 lines written, 0 warnings).
Output written in ./Rd2.ind.
Transcript written in ./Rd2.ilg.
This is pdfTeX, Version 3.1415926-1.40.11 (TeX Live 2010)
\write18 enabled.
entering extended mode
(/private/tmp/RtmpXp6TIs/Rbuild338f23568ca6/RamiGO/.Rd2dvi13199/Rd2.tex
LaTeX2e <2009/09/24>
Babel <v3.8l> and hyphenation patterns for english, dumylang, nohyphenation, ge
rman-x-2009-06-19, ngerman-x-2009-06-19, ancientgreek, ibycus, arabic, armenian
, basque, bulgarian, catalan, pinyin, coptic, croatian, czech, danish, dutch, u
kenglish, usenglishmax, esperanto, estonian, farsi, finnish, french, galician,
german, ngerman, swissgerman, monogreek, greek, hungarian, icelandic, assamese,
bengali, gujarati, hindi, kannada, malayalam, marathi, oriya, panjabi, tamil,
telugu, indonesian, interlingua, irish, italian, kurmanji, lao, latin, latvian,
lithuanian, mongolian, mongolianlmc, bokmal, nynorsk, polish, portuguese, roma
nian, russian, sanskrit, serbian, slovak, slovenian, spanish, swedish, turkish,
turkmen, ukrainian, uppersorbian, welsh, loaded.
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/book.cls
Document Class: book 2007/10/19 v1.4h Standard LaTeX document class
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/bk10.clo))
(/Library/Frameworks/R.framework/Resources/share/texmf/tex/latex/Rd.sty
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/ifthen.sty)
(/usr/local/texlive/2010/texmf-dist/tex/latex/tools/longtable.sty)
(/usr/local/texlive/2010/texmf-dist/tex/latex/tools/bm.sty)
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/alltt.sty)
(/usr/local/texlive/2010/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/local/texlive/2010/texmf-dist/tex/latex/url/url.sty) NOT loading ae
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/fontenc.sty
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/t1enc.def))
(/usr/local/texlive/2010/texmf-dist/tex/latex/psnfss/times.sty)
NOT loading lmodern
(/usr/local/texlive/2010/texmf-dist/tex/latex/inconsolata/inconsolata.sty
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/textcomp.sty
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/ts1enc.def))
(/usr/local/texlive/2010/texmf-dist/tex/latex/graphics/keyval.sty))
(/usr/local/texlive/2010/texmf-dist/tex/latex/graphics/color.sty
(/usr/local/texlive/2010/texmf-dist/tex/latex/latexconfig/color.cfg)
(/usr/local/texlive/2010/texmf-dist/tex/latex/pdftex-def/pdftex.def))
(/usr/local/texlive/2010/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/local/texlive/2010/texmf-dist/tex/generic/oberdiek/ltxcmds.sty)
(/usr/local/texlive/2010/texmf-dist/tex/generic/oberdiek/kvsetkeys.sty
(/usr/local/texlive/2010/texmf-dist/tex/generic/oberdiek/infwarerr.sty)
(/usr/local/texlive/2010/texmf-dist/tex/generic/oberdiek/etexcmds.sty))
(/usr/local/texlive/2010/texmf-dist/tex/generic/oberdiek/pdfescape.sty
(/usr/local/texlive/2010/texmf-dist/tex/generic/oberdiek/pdftexcmds.sty
(/usr/local/texlive/2010/texmf-dist/tex/generic/oberdiek/ifluatex.sty)))
(/usr/local/texlive/2010/texmf-dist/tex/generic/oberdiek/ifpdf.sty)
(/usr/local/texlive/2010/texmf-dist/tex/generic/oberdiek/ifvtex.sty)
(/usr/local/texlive/2010/texmf-dist/tex/generic/ifxetex/ifxetex.sty)
(/usr/local/texlive/2010/texmf-dist/tex/latex/oberdiek/hycolor.sty
(/usr/local/texlive/2010/texmf-dist/tex/latex/oberdiek/xcolor-patch.sty))
(/usr/local/texlive/2010/texmf-dist/tex/latex/oberdiek/letltxmacro.sty)
(/usr/local/texlive/2010/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/local/texlive/2010/texmf-dist/tex/generic/oberdiek/intcalc.sty)
(/usr/local/texlive/2010/texmf-dist/tex/latex/latexconfig/hyperref.cfg)
(/usr/local/texlive/2010/texmf-dist/tex/latex/oberdiek/kvoptions.sty)
Implicit mode ON; LaTeX internals redefined
(/usr/local/texlive/2010/texmf-dist/tex/generic/oberdiek/bitset.sty
(/usr/local/texlive/2010/texmf-dist/tex/generic/oberdiek/bigintcalc.sty))
(/usr/local/texlive/2010/texmf-dist/tex/generic/oberdiek/atbegshi.sty))
* hyperref using default driver hpdftex *
(/usr/local/texlive/2010/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/local/texlive/2010/texmf-dist/tex/latex/oberdiek/atveryend.sty)
(/usr/local/texlive/2010/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty
(/usr/local/texlive/2010/texmf-dist/tex/generic/oberdiek/uniquecounter.sty)))
Package hyperref Warning: Option `hyperindex' has already been used,
(hyperref) setting the option has no effect on input line 342.
Package hyperref Warning: Option `pagebackref' has already been used,
(hyperref) setting the option has no effect on input line 342.
) (/usr/local/texlive/2010/texmf-dist/tex/latex/base/makeidx.sty)
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/inputenc.sty
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/t1enc.dfu)
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/ot1enc.dfu)
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/omsenc.dfu)
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/ts1enc.dfu))
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/latin1.def))
Writing index file Rd2.idx
(./Rd2.aux) (/usr/local/texlive/2010/texmf-dist/tex/latex/base/ts1cmr.fd)
(/usr/local/texlive/2010/texmf-dist/tex/latex/psnfss/t1ptm.fd)
(/usr/local/texlive/2010/texmf-dist/tex/context/base/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/local/texlive/2010/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/local/texlive/2010/texmf-dist/tex/latex/oberdiek/refcount.sty)
(/usr/local/texlive/2010/texmf-dist/tex/generic/oberdiek/gettitlestring.sty))
(./Rd2.out) (./Rd2.out)
(/usr/local/texlive/2010/texmf-dist/tex/latex/inconsolata/t1fi4.fd)
(/usr/local/texlive/2010/texmf-dist/tex/latex/psnfss/t1phv.fd) (./Rd2.toc)
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [1{/usr/local/texl
ive/2010/texmf-var/fonts/map/pdftex/updmap/pdftex.map}]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [2]
Overfull \hbox (4.67784pt too wide) in paragraph at lines 168--170
[]\T1/fi4/m/n/10 leaves(object) <- value\T1/ptm/m/n/10 Sets the the data.frame
con-tain-ing the leaves of the tree with the columns
[3] (/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [4]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (29.36072pt too wide) in paragraph at lines 290--293
[]\T1/ptm/m/n/10 See [][]$\T1/fi4/m/n/10 http : / / rcytoscape . systemsbiology
. net / versions / current/$[][] \T1/ptm/m/n/10 and [][]$\T1/fi4/m/n/10 http :
/ / www . bioconductor .
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [5]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [6]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (3.19798pt too wide) in paragraph at lines 427--428
[]\T1/ptm/m/n/10 Subramanian A, Tamayo P, Mootha VK, Mukher-jee S, Ebert BL, Gi
llette MA, Paulovich A, Pomeroy
[7] (/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [8]
Overfull \hbox (13.60664pt too wide) in paragraph at lines 538--539
[]\T1/ptm/m/n/10 The edge col-ors in the tree rep-re-sent the re-la-tion-ship b
e-tween two nodes. In par-tic-u-lar: green=positively
[9] (/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def)
Underfull \vbox (badness 10000) has occurred while \output is active [10]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [11] (./Rd2.ind
[12]
LaTeX Font Warning: Font shape `T1/fi4/m/it' undefined
(Font) using `T1/fi4/m/n' instead on input line 26.
[13]) (./Rd2.aux)
LaTeX Font Warning: Some font shapes were not available, defaults substituted.
)
(see the transcript file for additional information)pdfTeX warning (dest): name
{Rfn.oldClass.Rdash.class} has been referenced but does not exist, replaced by
a fixed one
pdfTeX warning (dest): name{Rfn.igraph} has been referenced but does not exist,
replaced by a fixed one
{/usr/local/texlive/2010/texmf-dist/fonts/enc/dvips/base/8r.enc}{/usr/local/tex
live/2010/texmf-dist/fonts/enc/dvips/inconsolata/fi4-ec.enc}</usr/local/texlive
/2010/texmf-dist/fonts/type1/public/inconsolata/Inconsolata.pfb></usr/local/tex
live/2010/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/local/texl
ive/2010/texmf-dist/fonts/type1/urw/helvetic/uhvr8a.pfb></usr/local/texlive/201
0/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></usr/local/texlive/2010/texmf-di
st/fonts/type1/urw/times/utmr8a.pfb></usr/local/texlive/2010/texmf-dist/fonts/t
ype1/urw/times/utmr8a.pfb></usr/local/texlive/2010/texmf-dist/fonts/type1/urw/t
imes/utmri8a.pfb>
Output written on Rd2.pdf (13 pages, 116243 bytes).
Transcript written on Rd2.log.
Saving output to '/private/tmp/RtmpXp6TIs/Rbuild338f23568ca6/RamiGO/build/RamiGO.pdf' ...
Done
* creating vignettes ... OK
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* looking to see if a 'data/datalist' file should be added
* building 'RamiGO_1.0.0.tar.gz'