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 

Package 192/514HostnameOS / ArchBUILDCHECKBUILD BIN
genefu 1.4.0
Benjamin Haibe-Kains , Markus Schroeder
Snapshot Date: 2012-03-23 18:21:46 -0700 (Fri, 23 Mar 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_9/madman/Rpacks/genefu
Last Changed Rev: 59920 / Revision: 64395
Last Changed Date: 2011-10-31 15:59:03 -0700 (Mon, 31 Oct 2011)
wilson2 Linux (openSUSE 11.4) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
pitt Mac OS X Leopard (10.5.8) / i386 [ OK ] OK  OK 

Summary

Package: genefu
Version: 1.4.0
Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data genefu
StartedAt: 2012-03-23 22:17:48 -0700 (Fri, 23 Mar 2012)
EndedAt: 2012-03-23 22:19:00 -0700 (Fri, 23 Mar 2012)
EllapsedTime: 71.9 seconds
RetCode: 0
Status:  OK 
PackageFile: genefu_1.4.0.tar.gz
PackageFileSize: 5.503 MiB

Command output

* checking for file 'genefu/DESCRIPTION' ... OK
* preparing 'genefu':
* 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/RtmpB1FMr2/Rbuild17193f5385bf/genefu/.Rd2dvi5913/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] [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 (44.78088pt too wide) in paragraph at lines 269--269
 []  \T1/fi4/m/n/10 p.adjust.m = c("none", "holm", "hochberg", "hommel", "bonfe
rroni", "BH", "BY", "fdr"))[] 
[5] (/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [6] [7]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [8] [9]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (8.95699pt too wide) in paragraph at lines 552--553
[]\T1/ptm/m/n/10 A char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of "two.sided"
[10] (/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (23.38692pt too wide) in paragraph at lines 626--627
[]\T1/ptm/m/n/10 This dataset has been gen-er-ated by the In-ter-na-tional Ge-n
omics Con-sor-tium us-ing Affymetrix hgu133plus2
[11] (/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (24.78088pt too wide) in paragraph at lines 654--654
 []\T1/fi4/m/n/10 fuzzy.ttest(x, w1, w2, alternative=c("two.sided", "less", "gr
eater"), na.rm = FALSE)[] 

Overfull \hbox (6.17755pt too wide) in paragraph at lines 670--671
[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of "two.sided"

Overfull \hbox (137.18091pt too wide) in paragraph at lines 693--695
[][][]$\T1/fi4/m/n/10 http : / / en . wikipedia . org / wiki / T _ test$[][] []
[]$http : / / www . nicebread . de / blog / files / fc02e1635792cb0f2b3cbd1f7e6
c580b-[]10 .
[12]
Overfull \hbox (198.78088pt too wide) in paragraph at lines 719--719
 []\T1/fi4/m/n/9 randst <- apply(rands, 1, function(x, xx, ww1, ww2) { return(f
uzzy.ttest(x=xx, w1=ww1[x], w2=ww2[x])[2]) }, xx=xx, ww1=ww1, ww2=ww2)[] 
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [13]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [14]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [15] [16]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (2.38757pt too wide) in paragraph at lines 979--980
\T1/ptm/m/n/10 based com-pu-ta-tional ap-proach im-proves breast can-cer prog-n
os-ti-ca-tion", \T1/ptm/m/it/10 Genome Bi-ol-ogy\T1/ptm/m/n/10 , \T1/ptm/b/n/10
 11\T1/ptm/m/n/10 (2):R18 
[17] (/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [18]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [19] [20]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [21] [22]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (129.78088pt too wide) in paragraph at lines 1269--1269
 []\T1/fi4/m/n/10 map.datasets(datas, annots, do.mapping = FALSE, mapping.coln 
= "EntrezGene.ID", mapping, verbose = FALSE)[] 

Overfull \hbox (0.47766pt too wide) in paragraph at lines 1276--1277
[]\T1/ptm/m/n/10 List of ma-tri-ces of gene ex-pres-sions with sam-ples in rows
 and probes in columns,

Overfull \hbox (0.49751pt too wide) in paragraph at lines 1279--1280
[]\T1/ptm/m/n/10 List of ma-tri-ces of an-no-ta-tions with at least one col-umn
 named "En-trez-Gene.ID",
[23] (/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [24]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [25]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [26]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [27] [28]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (11.59784pt too wide) in paragraph at lines 1616--1617
[]\T1/ptm/m/n/10 Use of the of-fi-cial cen-troids with ro-bust scal-ing of the 
gene ex-pres-sions (see [][]\T1/fi4/m/n/10 rescale[][][]\T1/ptm/m/n/10 ). 
[29] (/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [30]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [31]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [32]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [33] [34]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [35]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [36]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [37]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (15.78088pt too wide) in paragraph at lines 2084--2085
[][][]$\T1/fi4/m/n/10 http : / / www . thelancet . com / journals / lancet / ar
ticle / PIIS0140-[]6736(05 ) 17947-[]1 / abstract$[][] 
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [38]
Overfull \hbox (2.38757pt too wide) in paragraph at lines 2116--2117
\T1/ptm/m/n/10 based com-pu-ta-tional ap-proach im-proves breast can-cer prog-n
os-ti-ca-tion", \T1/ptm/m/it/10 Genome Bi-ol-ogy\T1/ptm/m/n/10 , \T1/ptm/b/n/10
 11\T1/ptm/m/n/10 (2):R18 
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [39]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [40]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [41] [42]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def)
Underfull \hbox (badness 3009) in paragraph at lines 2298--2298
[]\T1/ptm/m/it/10 Tamoxifen Re-sis-tance sig-na-ture com-posed of 13 gene clus-
ters
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [43]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [44] [45]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [46]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [47]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [48] [49]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [50] [51]
Overfull \hbox (10.84094pt too wide) in paragraph at lines 2784--2785
[][][]\T1/fi4/m/n/10 subtype.cluster.predict[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/
m/n/10 intrinsic.cluster[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/n/10 intrinsic.clu
ster.predict[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/n/10 scmod1.robust[][][]\T1/pt
m/m/n/10 ,
[52] (/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [53] [54]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [55]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [56]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (11.68091pt too wide) in paragraph at lines 3065--3067
[][][]$\T1/fi4/m/n/10 http : / / www . ncbi . nlm . nih . gov / geo / query / a
cc . cgi ? acc = GSE2034$[][] [][]$http : / / www . ncbi . nlm . nih .
[57] (/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [58]
No file Rd2.ind.
[59] (./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.chron} has been referenced but does not exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.stresc} has been referenced but does not exist,
 replaced by a fixed one

pdfTeX warning (dest): name{Rfn.read.csv} has been referenced but does not exis
t, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.scale} has been referenced but does not exist, 
replaced by a fixed one

pdfTeX warning (dest): name{Rfn.weighted.mean} has been referenced but does not
 exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.t.test} has been referenced but does not exist,
 replaced by a fixed one

pdfTeX warning (dest): name{Rfn.cor} has been referenced but does not exist, re
placed by a fixed one

pdfTeX warning (dest): name{Rfn.cordif.dep} has been referenced but does not ex
ist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.p.adjust} has been referenced but does not exis
t, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.jitter} has been referenced but does not exist,
 replaced by a fixed one

pdfTeX warning (dest): name{Rfn.boxplot} has been referenced but does not exist
, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.points} has been referenced but does not exist,
 replaced by a fixed one

pdfTeX warning (dest): name{Rfn.Mclust} 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 (59 pages, 217876 bytes).
Transcript written on Rd2.log.
This is makeindex, version 2.15 [TeX Live 2010] (kpathsea + Thai support).
Scanning input file ./Rd2.idx....done (212 entries accepted, 0 rejected).
Sorting entries.....done (1726 comparisons).
Generating output file ./Rd2.ind....done (262 lines written, 14 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/RtmpB1FMr2/Rbuild17193f5385bf/genefu/.Rd2dvi5913/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
[1{/usr/local/texlive/2010/texmf-var/fonts/map/pdftex/updmap/pdftex.map}])
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [2]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [3] [4]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [5]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (44.78088pt too wide) in paragraph at lines 269--269
 []  \T1/fi4/m/n/10 p.adjust.m = c("none", "holm", "hochberg", "hommel", "bonfe
rroni", "BH", "BY", "fdr"))[] 
[6] (/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [7] [8]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [9] [10]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (8.95699pt too wide) in paragraph at lines 552--553
[]\T1/ptm/m/n/10 A char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of "two.sided"
[11] (/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (23.38692pt too wide) in paragraph at lines 626--627
[]\T1/ptm/m/n/10 This dataset has been gen-er-ated by the In-ter-na-tional Ge-n
omics Con-sor-tium us-ing Affymetrix hgu133plus2
[12] (/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (24.78088pt too wide) in paragraph at lines 654--654
 []\T1/fi4/m/n/10 fuzzy.ttest(x, w1, w2, alternative=c("two.sided", "less", "gr
eater"), na.rm = FALSE)[] 

Overfull \hbox (6.17755pt too wide) in paragraph at lines 670--671
[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of "two.sided"

Overfull \hbox (137.18091pt too wide) in paragraph at lines 693--695
[][][]$\T1/fi4/m/n/10 http : / / en . wikipedia . org / wiki / T _ test$[][] []
[]$http : / / www . nicebread . de / blog / files / fc02e1635792cb0f2b3cbd1f7e6
c580b-[]10 .
[13]
Overfull \hbox (198.78088pt too wide) in paragraph at lines 719--719
 []\T1/fi4/m/n/9 randst <- apply(rands, 1, function(x, xx, ww1, ww2) { return(f
uzzy.ttest(x=xx, w1=ww1[x], w2=ww2[x])[2]) }, xx=xx, ww1=ww1, ww2=ww2)[] 
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [14]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [15]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [16] [17]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (2.38757pt too wide) in paragraph at lines 979--980
\T1/ptm/m/n/10 based com-pu-ta-tional ap-proach im-proves breast can-cer prog-n
os-ti-ca-tion", \T1/ptm/m/it/10 Genome Bi-ol-ogy\T1/ptm/m/n/10 , \T1/ptm/b/n/10
 11\T1/ptm/m/n/10 (2):R18 
[18] (/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [19]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [20] [21]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [22] [23]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (129.78088pt too wide) in paragraph at lines 1269--1269
 []\T1/fi4/m/n/10 map.datasets(datas, annots, do.mapping = FALSE, mapping.coln 
= "EntrezGene.ID", mapping, verbose = FALSE)[] 

Overfull \hbox (0.47766pt too wide) in paragraph at lines 1276--1277
[]\T1/ptm/m/n/10 List of ma-tri-ces of gene ex-pres-sions with sam-ples in rows
 and probes in columns,

Overfull \hbox (0.49751pt too wide) in paragraph at lines 1279--1280
[]\T1/ptm/m/n/10 List of ma-tri-ces of an-no-ta-tions with at least one col-umn
 named "En-trez-Gene.ID",
[24] (/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [25]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [26]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [27]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [28] [29]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (11.59784pt too wide) in paragraph at lines 1616--1617
[]\T1/ptm/m/n/10 Use of the of-fi-cial cen-troids with ro-bust scal-ing of the 
gene ex-pres-sions (see [][]\T1/fi4/m/n/10 rescale[][][]\T1/ptm/m/n/10 ). 
[30] (/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [31]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [32]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [33]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [34] [35]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [36]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [37]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [38]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (15.78088pt too wide) in paragraph at lines 2084--2085
[][][]$\T1/fi4/m/n/10 http : / / www . thelancet . com / journals / lancet / ar
ticle / PIIS0140-[]6736(05 ) 17947-[]1 / abstract$[][] 
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [39]
Overfull \hbox (2.38757pt too wide) in paragraph at lines 2116--2117
\T1/ptm/m/n/10 based com-pu-ta-tional ap-proach im-proves breast can-cer prog-n
os-ti-ca-tion", \T1/ptm/m/it/10 Genome Bi-ol-ogy\T1/ptm/m/n/10 , \T1/ptm/b/n/10
 11\T1/ptm/m/n/10 (2):R18 
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [40]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [41]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [42] [43]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def)
Underfull \hbox (badness 3009) in paragraph at lines 2298--2298
[]\T1/ptm/m/it/10 Tamoxifen Re-sis-tance sig-na-ture com-posed of 13 gene clus-
ters
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [44]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [45] [46]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [47]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [48]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [49] [50]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [51] [52]
Overfull \hbox (10.84094pt too wide) in paragraph at lines 2784--2785
[][][]\T1/fi4/m/n/10 subtype.cluster.predict[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/
m/n/10 intrinsic.cluster[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/n/10 intrinsic.clu
ster.predict[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/n/10 scmod1.robust[][][]\T1/pt
m/m/n/10 ,
[53] (/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [54] [55]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [56]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [57]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (11.68091pt too wide) in paragraph at lines 3065--3067
[][][]$\T1/fi4/m/n/10 http : / / www . ncbi . nlm . nih . gov / geo / query / a
cc . cgi ? acc = GSE2034$[][] [][]$http : / / www . ncbi . nlm . nih .
[58] (/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [59] (./Rd2.ind
[60]

LaTeX Font Warning: Font shape `T1/fi4/m/it' undefined
(Font)              using `T1/fi4/m/n' instead on input line 73.

[61] [62]) (./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.chron} has been referenced but does not exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.stresc} has been referenced but does not exist,
 replaced by a fixed one

pdfTeX warning (dest): name{Rfn.read.csv} has been referenced but does not exis
t, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.scale} has been referenced but does not exist, 
replaced by a fixed one

pdfTeX warning (dest): name{Rfn.weighted.mean} has been referenced but does not
 exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.t.test} has been referenced but does not exist,
 replaced by a fixed one

pdfTeX warning (dest): name{Rfn.cor} has been referenced but does not exist, re
placed by a fixed one

pdfTeX warning (dest): name{Rfn.cordif.dep} has been referenced but does not ex
ist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.p.adjust} has been referenced but does not exis
t, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.jitter} has been referenced but does not exist,
 replaced by a fixed one

pdfTeX warning (dest): name{Rfn.boxplot} has been referenced but does not exist
, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.points} has been referenced but does not exist,
 replaced by a fixed one

pdfTeX warning (dest): name{Rfn.Mclust} 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 (62 pages, 240934 bytes).
Transcript written on Rd2.log.
This is makeindex, version 2.15 [TeX Live 2010] (kpathsea + Thai support).
Scanning input file ./Rd2.idx....done (212 entries accepted, 0 rejected).
Sorting entries.....done (1726 comparisons).
Generating output file ./Rd2.ind....done (262 lines written, 14 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/RtmpB1FMr2/Rbuild17193f5385bf/genefu/.Rd2dvi5913/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
[1{/usr/local/texlive/2010/texmf-var/fonts/map/pdftex/updmap/pdftex.map}])
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [2]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [3] [4]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [5]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (44.78088pt too wide) in paragraph at lines 269--269
 []  \T1/fi4/m/n/10 p.adjust.m = c("none", "holm", "hochberg", "hommel", "bonfe
rroni", "BH", "BY", "fdr"))[] 
[6] (/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [7] [8]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [9] [10]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (8.95699pt too wide) in paragraph at lines 552--553
[]\T1/ptm/m/n/10 A char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of "two.sided"
[11] (/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (23.38692pt too wide) in paragraph at lines 626--627
[]\T1/ptm/m/n/10 This dataset has been gen-er-ated by the In-ter-na-tional Ge-n
omics Con-sor-tium us-ing Affymetrix hgu133plus2
[12] (/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (24.78088pt too wide) in paragraph at lines 654--654
 []\T1/fi4/m/n/10 fuzzy.ttest(x, w1, w2, alternative=c("two.sided", "less", "gr
eater"), na.rm = FALSE)[] 

Overfull \hbox (6.17755pt too wide) in paragraph at lines 670--671
[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of "two.sided"

Overfull \hbox (137.18091pt too wide) in paragraph at lines 693--695
[][][]$\T1/fi4/m/n/10 http : / / en . wikipedia . org / wiki / T _ test$[][] []
[]$http : / / www . nicebread . de / blog / files / fc02e1635792cb0f2b3cbd1f7e6
c580b-[]10 .
[13]
Overfull \hbox (198.78088pt too wide) in paragraph at lines 719--719
 []\T1/fi4/m/n/9 randst <- apply(rands, 1, function(x, xx, ww1, ww2) { return(f
uzzy.ttest(x=xx, w1=ww1[x], w2=ww2[x])[2]) }, xx=xx, ww1=ww1, ww2=ww2)[] 
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [14]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [15]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [16] [17]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (2.38757pt too wide) in paragraph at lines 979--980
\T1/ptm/m/n/10 based com-pu-ta-tional ap-proach im-proves breast can-cer prog-n
os-ti-ca-tion", \T1/ptm/m/it/10 Genome Bi-ol-ogy\T1/ptm/m/n/10 , \T1/ptm/b/n/10
 11\T1/ptm/m/n/10 (2):R18 
[18] (/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [19]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [20] [21]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [22] [23]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (129.78088pt too wide) in paragraph at lines 1269--1269
 []\T1/fi4/m/n/10 map.datasets(datas, annots, do.mapping = FALSE, mapping.coln 
= "EntrezGene.ID", mapping, verbose = FALSE)[] 

Overfull \hbox (0.47766pt too wide) in paragraph at lines 1276--1277
[]\T1/ptm/m/n/10 List of ma-tri-ces of gene ex-pres-sions with sam-ples in rows
 and probes in columns,

Overfull \hbox (0.49751pt too wide) in paragraph at lines 1279--1280
[]\T1/ptm/m/n/10 List of ma-tri-ces of an-no-ta-tions with at least one col-umn
 named "En-trez-Gene.ID",
[24] (/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [25]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [26]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [27]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [28] [29]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (11.59784pt too wide) in paragraph at lines 1616--1617
[]\T1/ptm/m/n/10 Use of the of-fi-cial cen-troids with ro-bust scal-ing of the 
gene ex-pres-sions (see [][]\T1/fi4/m/n/10 rescale[][][]\T1/ptm/m/n/10 ). 
[30] (/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [31]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [32]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [33]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [34] [35]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [36]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [37]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [38]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (15.78088pt too wide) in paragraph at lines 2084--2085
[][][]$\T1/fi4/m/n/10 http : / / www . thelancet . com / journals / lancet / ar
ticle / PIIS0140-[]6736(05 ) 17947-[]1 / abstract$[][] 
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [39]
Overfull \hbox (2.38757pt too wide) in paragraph at lines 2116--2117
\T1/ptm/m/n/10 based com-pu-ta-tional ap-proach im-proves breast can-cer prog-n
os-ti-ca-tion", \T1/ptm/m/it/10 Genome Bi-ol-ogy\T1/ptm/m/n/10 , \T1/ptm/b/n/10
 11\T1/ptm/m/n/10 (2):R18 
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [40]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [41]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [42] [43]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def)
Underfull \hbox (badness 3009) in paragraph at lines 2298--2298
[]\T1/ptm/m/it/10 Tamoxifen Re-sis-tance sig-na-ture com-posed of 13 gene clus-
ters
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [44]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [45] [46]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [47]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [48]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [49] [50]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [51] [52]
Overfull \hbox (10.84094pt too wide) in paragraph at lines 2784--2785
[][][]\T1/fi4/m/n/10 subtype.cluster.predict[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/
m/n/10 intrinsic.cluster[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/n/10 intrinsic.clu
ster.predict[][][]\T1/ptm/m/n/10 , [][]\T1/fi4/m/n/10 scmod1.robust[][][]\T1/pt
m/m/n/10 ,
[53] (/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [54] [55]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [56]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [57]
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (11.68091pt too wide) in paragraph at lines 3065--3067
[][][]$\T1/fi4/m/n/10 http : / / www . ncbi . nlm . nih . gov / geo / query / a
cc . cgi ? acc = GSE2034$[][] [][]$http : / / www . ncbi . nlm . nih .
[58] (/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2010/texmf-dist/tex/latex/base/utf8.def) [59] (./Rd2.ind
[60]

LaTeX Font Warning: Font shape `T1/fi4/m/it' undefined
(Font)              using `T1/fi4/m/n' instead on input line 73.

[61] [62]) (./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.chron} has been referenced but does not exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.stresc} has been referenced but does not exist,
 replaced by a fixed one

pdfTeX warning (dest): name{Rfn.read.csv} has been referenced but does not exis
t, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.scale} has been referenced but does not exist, 
replaced by a fixed one

pdfTeX warning (dest): name{Rfn.weighted.mean} has been referenced but does not
 exist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.t.test} has been referenced but does not exist,
 replaced by a fixed one

pdfTeX warning (dest): name{Rfn.cor} has been referenced but does not exist, re
placed by a fixed one

pdfTeX warning (dest): name{Rfn.cordif.dep} has been referenced but does not ex
ist, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.p.adjust} has been referenced but does not exis
t, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.jitter} has been referenced but does not exist,
 replaced by a fixed one

pdfTeX warning (dest): name{Rfn.boxplot} has been referenced but does not exist
, replaced by a fixed one

pdfTeX warning (dest): name{Rfn.points} has been referenced but does not exist,
 replaced by a fixed one

pdfTeX warning (dest): name{Rfn.Mclust} 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 (62 pages, 241176 bytes).
Transcript written on Rd2.log.
Saving output to '/private/tmp/RtmpB1FMr2/Rbuild17193f5385bf/genefu/build/genefu.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 'genefu_1.4.0.tar.gz'