Back to the "Multiple platform build/check report" A  B  C  D  E  F  G  H  I  J  K  L  M  N  O  P  Q [R] S  T  U  V  W  X  Y  Z 

BioC 2.13: BUILD report for RamiGO on perceval

This page was generated on 2014-04-05 09:52:40 -0700 (Sat, 05 Apr 2014).

Package 570/750HostnameOS / ArchBUILDCHECKBUILD BIN
RamiGO 1.8.1
Markus Schroeder
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/RamiGO
Last Changed Rev: 88423 / Revision: 88450
Last Changed Date: 2014-04-04 09:43:57 -0700 (Fri, 04 Apr 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64 [ OK ] OK  OK 

Summary

Package: RamiGO
Version: 1.8.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data RamiGO
StartedAt: 2014-04-04 21:30:20 -0700 (Fri, 04 Apr 2014)
EndedAt: 2014-04-04 21:30:43 -0700 (Fri, 04 Apr 2014)
EllapsedTime: 22.7 seconds
RetCode: 0
Status:  OK 
PackageFile: RamiGO_1.8.1.tar.gz
PackageFileSize: 419.5 KiB

Command output

* 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 3.1415926-2.4-1.40.13 (TeX Live 2012)
 \write18 enabled.
entering extended mode
(/private/tmp/Rtmp1wwfMq/Rbuild96085c2ca7da/RamiGO/.Rd2pdf38408/Rd2.tex
LaTeX2e <2011/06/27>
Babel <v3.8m> 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)
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/textcomp.sty
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/ts1enc.def))
(/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)
(/usr/local/texlive/2012/texmf-dist/tex/latex/inconsolata/inconsolata.sty
(/usr/local/texlive/2012/texmf-dist/tex/latex/graphics/keyval.sty))
(/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/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.

(/usr/local/texlive/2012/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/local/texlive/2012/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 361.


Package hyperref Warning: Option `pagebackref' has already been used,
(hyperref)                setting the option has no effect on input line 361.

) (/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
No file 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))
(/usr/local/texlive/2012/texmf-dist/tex/latex/inconsolata/t1fi4.fd)
(/usr/local/texlive/2012/texmf-dist/tex/latex/psnfss/t1phv.fd)
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def) [1{/usr/local/texl
ive/2012/texmf-var/fonts/map/pdftex/updmap/pdftex.map}]
(/usr/local/texlive/2012/texmf-dist/tex/latex/inconsolata/ts1fi4.fd)
(/usr/local/texlive/2012/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/2012/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2012/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/2012/texmf-dist/tex/latex/base/utf8.def) [5]
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2012/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/2012/texmf-dist/tex/latex/base/utf8.def) [7]
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def) [8]
Overfull \hbox (13.60664pt too wide) in paragraph at lines 548--549
[]\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

Overfull \hbox (68.28088pt too wide) in paragraph at lines 580--580
 []\T1/fi4/m/n/9 #goIDs <- c("GO:0051130","GO:0050789","GO:0019912","GO:0016301
","GO:0003824","GO:0005783","GO:0043229")[] 
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def) [9]
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def)
Underfull \vbox (badness 10000) has occurred while \output is active [10]
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def) [11]
No file Rd2.ind.
[12] (./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/2012/texmf-dist/fonts/enc/dvips/base/8r.enc}{/usr/local/tex
live/2012/texmf-dist/fonts/enc/dvips/inconsolata/fi4-ec.enc}</usr/local/texlive
/2012/texmf-dist/fonts/type1/public/inconsolata/Inconsolata.pfb></usr/local/tex
live/2012/texmf-dist/fonts/type1/urw/helvetic/uhvr8a.pfb></usr/local/texlive/20
12/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></usr/local/texlive/2012/texmf-d
ist/fonts/type1/urw/times/utmr8a.pfb></usr/local/texlive/2012/texmf-dist/fonts/
type1/urw/times/utmr8a.pfb></usr/local/texlive/2012/texmf-dist/fonts/type1/urw/
times/utmri8a.pfb>
Output written on Rd2.pdf (12 pages, 89381 bytes).
Transcript written on Rd2.log.
This is makeindex, version 2.15 [TeX Live 2012] (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 3.1415926-2.4-1.40.13 (TeX Live 2012)
 \write18 enabled.
entering extended mode
(/private/tmp/Rtmp1wwfMq/Rbuild96085c2ca7da/RamiGO/.Rd2pdf38408/Rd2.tex
LaTeX2e <2011/06/27>
Babel <v3.8m> 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)
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/textcomp.sty
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/ts1enc.def))
(/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)
(/usr/local/texlive/2012/texmf-dist/tex/latex/inconsolata/inconsolata.sty
(/usr/local/texlive/2012/texmf-dist/tex/latex/graphics/keyval.sty))
(/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/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.

(/usr/local/texlive/2012/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/local/texlive/2012/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 361.


Package hyperref Warning: Option `pagebackref' has already been used,
(hyperref)                setting the option has no effect on input line 361.

) (/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/inconsolata/t1fi4.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) [1{/usr/local/texl
ive/2012/texmf-var/fonts/map/pdftex/updmap/pdftex.map}]
(/usr/local/texlive/2012/texmf-dist/tex/latex/inconsolata/ts1fi4.fd)
(/usr/local/texlive/2012/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/2012/texmf-dist/tex/latex/base/utf8.def) [4]
(/usr/local/texlive/2012/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/2012/texmf-dist/tex/latex/base/utf8.def) [5]
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def) [6]
(/usr/local/texlive/2012/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/2012/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def) [8]
Overfull \hbox (13.60664pt too wide) in paragraph at lines 548--549
[]\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]
Overfull \hbox (68.28088pt too wide) in paragraph at lines 580--580
 []\T1/fi4/m/n/9 #goIDs <- c("GO:0051130","GO:0050789","GO:0019912","GO:0016301
","GO:0003824","GO:0005783","GO:0043229")[] 
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def) [10]
(/usr/local/texlive/2012/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/2012/texmf-dist/fonts/enc/dvips/base/8r.enc}{/usr/local/tex
live/2012/texmf-dist/fonts/enc/dvips/inconsolata/fi4-ec.enc}</usr/local/texlive
/2012/texmf-dist/fonts/type1/public/inconsolata/Inconsolata.pfb></usr/local/tex
live/2012/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/local/texl
ive/2012/texmf-dist/fonts/type1/urw/helvetic/uhvr8a.pfb></usr/local/texlive/201
2/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></usr/local/texlive/2012/texmf-di
st/fonts/type1/urw/times/utmr8a.pfb></usr/local/texlive/2012/texmf-dist/fonts/t
ype1/urw/times/utmr8a.pfb></usr/local/texlive/2012/texmf-dist/fonts/type1/urw/t
imes/utmri8a.pfb>
Output written on Rd2.pdf (13 pages, 102248 bytes).
Transcript written on Rd2.log.
This is makeindex, version 2.15 [TeX Live 2012] (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 3.1415926-2.4-1.40.13 (TeX Live 2012)
 \write18 enabled.
entering extended mode
(/private/tmp/Rtmp1wwfMq/Rbuild96085c2ca7da/RamiGO/.Rd2pdf38408/Rd2.tex
LaTeX2e <2011/06/27>
Babel <v3.8m> 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)
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/textcomp.sty
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/ts1enc.def))
(/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)
(/usr/local/texlive/2012/texmf-dist/tex/latex/inconsolata/inconsolata.sty
(/usr/local/texlive/2012/texmf-dist/tex/latex/graphics/keyval.sty))
(/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/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.

(/usr/local/texlive/2012/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/local/texlive/2012/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 361.


Package hyperref Warning: Option `pagebackref' has already been used,
(hyperref)                setting the option has no effect on input line 361.

) (/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/inconsolata/t1fi4.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) [1{/usr/local/texl
ive/2012/texmf-var/fonts/map/pdftex/updmap/pdftex.map}]
(/usr/local/texlive/2012/texmf-dist/tex/latex/inconsolata/ts1fi4.fd)
(/usr/local/texlive/2012/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/2012/texmf-dist/tex/latex/base/utf8.def) [4]
(/usr/local/texlive/2012/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/2012/texmf-dist/tex/latex/base/utf8.def) [5]
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def) [6]
(/usr/local/texlive/2012/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/2012/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def) [8]
Overfull \hbox (13.60664pt too wide) in paragraph at lines 548--549
[]\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]
Overfull \hbox (68.28088pt too wide) in paragraph at lines 580--580
 []\T1/fi4/m/n/9 #goIDs <- c("GO:0051130","GO:0050789","GO:0019912","GO:0016301
","GO:0003824","GO:0005783","GO:0043229")[] 
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def) [10]
(/usr/local/texlive/2012/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/2012/texmf-dist/fonts/enc/dvips/base/8r.enc}{/usr/local/tex
live/2012/texmf-dist/fonts/enc/dvips/inconsolata/fi4-ec.enc}</usr/local/texlive
/2012/texmf-dist/fonts/type1/public/inconsolata/Inconsolata.pfb></usr/local/tex
live/2012/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/local/texl
ive/2012/texmf-dist/fonts/type1/urw/helvetic/uhvr8a.pfb></usr/local/texlive/201
2/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></usr/local/texlive/2012/texmf-di
st/fonts/type1/urw/times/utmr8a.pfb></usr/local/texlive/2012/texmf-dist/fonts/t
ype1/urw/times/utmr8a.pfb></usr/local/texlive/2012/texmf-dist/fonts/type1/urw/t
imes/utmri8a.pfb>
Output written on Rd2.pdf (13 pages, 102610 bytes).
Transcript written on Rd2.log.
Saving output to ‘/private/tmp/Rtmp1wwfMq/Rbuild96085c2ca7da/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_1.8.1.tar.gz’