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 208/553HostnameOS / ArchBUILDCHECKBUILD BIN
genefu 1.6.1
Benjamin Haibe-Kains , Markus Schroeder
Snapshot Date: 2012-09-23 17:01:39 -0700 (Sun, 23 Sep 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_10/madman/Rpacks/genefu
Last Changed Rev: 69375 / Revision: 69725
Last Changed Date: 2012-09-12 10:35:46 -0700 (Wed, 12 Sep 2012)
lamb2 Linux (openSUSE 11.4) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Leopard (10.5.8) / i386 [ OK ] OK  OK 

Summary

Package: genefu
Version: 1.6.1
Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data genefu
StartedAt: 2012-09-23 22:25:08 -0700 (Sun, 23 Sep 2012)
EndedAt: 2012-09-23 22:25:56 -0700 (Sun, 23 Sep 2012)
EllapsedTime: 48.6 seconds
RetCode: 0
Status:  OK 
PackageFile: genefu_1.6.1.tar.gz
PackageFileSize: 4.364 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 3.1415926-2.3-1.40.12 (TeX Live 2011)
 \write18 enabled.
entering extended mode
(/private/tmp/RtmpoNdKem/Rbuild78141c3c04a8/genefu/.Rd2pdf30740/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, afrikaans, ancientgreek, ibycus, arabi
c, armenian, basque, bulgarian, catalan, pinyin, coptic, croatian, czech, danis
h, dutch, ukenglish, usenglishmax, esperanto, estonian, ethiopic, farsi, finnis
h, french, galician, german, ngerman, swissgerman, monogreek, greek, hungarian,
 icelandic, assamese, bengali, gujarati, hindi, kannada, malayalam, marathi, or
iya, panjabi, tamil, telugu, indonesian, interlingua, irish, italian, kurmanji,
 lao, latin, latvian, lithuanian, mongolian, mongolianlmc, bokmal, nynorsk, pol
ish, portuguese, romanian, russian, sanskrit, serbian, serbianc, slovak, sloven
ian, spanish, swedish, turkish, turkmen, ukrainian, uppersorbian, welsh, loaded
.
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/book.cls
Document Class: book 2007/10/19 v1.4h Standard LaTeX document class
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/bk10.clo))
(/Library/Frameworks/R.framework/Versions/2.15/Resources/share/texmf/tex/latex/
Rd.sty (/usr/local/texlive/2011/texmf-dist/tex/latex/base/ifthen.sty)
(/usr/local/texlive/2011/texmf-dist/tex/latex/tools/longtable.sty)
(/usr/local/texlive/2011/texmf-dist/tex/latex/tools/bm.sty)
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/alltt.sty)
(/usr/local/texlive/2011/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/local/texlive/2011/texmf-dist/tex/latex/url/url.sty) NOT loading ae
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/fontenc.sty
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/t1enc.def))
(/usr/local/texlive/2011/texmf-dist/tex/latex/psnfss/times.sty)
NOT loading lmodern
(/usr/local/texlive/2011/texmf-dist/tex/latex/inconsolata/inconsolata.sty
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/textcomp.sty
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/ts1enc.def))
(/usr/local/texlive/2011/texmf-dist/tex/latex/graphics/keyval.sty))
(/usr/local/texlive/2011/texmf-dist/tex/latex/graphics/color.sty
(/usr/local/texlive/2011/texmf-dist/tex/latex/latexconfig/color.cfg)
(/usr/local/texlive/2011/texmf-dist/tex/latex/pdftex-def/pdftex.def
(/usr/local/texlive/2011/texmf-dist/tex/generic/oberdiek/infwarerr.sty)
(/usr/local/texlive/2011/texmf-dist/tex/generic/oberdiek/ltxcmds.sty)))
(/usr/local/texlive/2011/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/local/texlive/2011/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
(/usr/local/texlive/2011/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty))
(/usr/local/texlive/2011/texmf-dist/tex/generic/ifxetex/ifxetex.sty)
(/usr/local/texlive/2011/texmf-dist/tex/latex/oberdiek/kvoptions.sty)
(/usr/local/texlive/2011/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/local/texlive/2011/texmf-dist/tex/latex/latexconfig/hyperref.cfg))

Package hyperref Message: Driver (autodetected): hpdftex.

(/usr/local/texlive/2011/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/local/texlive/2011/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty))

Package hyperref Warning: Option `hyperindex' has already been used,
(hyperref)                setting the option has no effect on input line 356.


Package hyperref Warning: Option `pagebackref' has already been used,
(hyperref)                setting the option has no effect on input line 356.

) (/usr/local/texlive/2011/texmf-dist/tex/latex/base/makeidx.sty)
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/inputenc.sty
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/t1enc.dfu)
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/ot1enc.dfu)
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/omsenc.dfu)
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/ts1enc.dfu))
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/latin1.def))
Writing index file Rd2.idx
No file Rd2.aux.
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/ts1cmr.fd)
(/usr/local/texlive/2011/texmf-dist/tex/latex/psnfss/t1ptm.fd)
(/usr/local/texlive/2011/texmf-dist/tex/context/base/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/local/texlive/2011/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/local/texlive/2011/texmf-dist/tex/generic/oberdiek/gettitlestring.sty))
(/usr/local/texlive/2011/texmf-dist/tex/latex/inconsolata/t1fi4.fd)
(/usr/local/texlive/2011/texmf-dist/tex/latex/psnfss/t1phv.fd)
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [1{/usr/local/texl
ive/2011/texmf-var/fonts/map/pdftex/updmap/pdftex.map}]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [2] [3]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [4]
(/usr/local/texlive/2011/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/2011/texmf-dist/tex/latex/base/utf8.def) [6] [7]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [8] [9]
(/usr/local/texlive/2011/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/2011/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/2011/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (104.78088pt 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"), check.w = TRUE, 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"
[12]
Overfull \hbox (137.18091pt too wide) in paragraph at lines 696--698
[][][]$\T1/fi4/m/n/10 http : / / en . wikipedia . org / wiki / T _ test$[][] []
[]$http : / / www . nicebread . de / blog / files / fc02e1635792cb0f2b3cbd1f7e6
c580b-[]10 .

Overfull \hbox (198.78088pt too wide) in paragraph at lines 722--722
 []\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/2011/texmf-dist/tex/latex/base/utf8.def) [13] [14]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [15] [16]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (2.38757pt too wide) in paragraph at lines 982--983
\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/2011/texmf-dist/tex/latex/base/utf8.def) [18]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [19] [20]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [21] [22]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (129.78088pt too wide) in paragraph at lines 1272--1272
 []\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 1279--1280
[]\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 1282--1283
[]\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/2011/texmf-dist/tex/latex/base/utf8.def) [24]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [25]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [26]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [27] [28]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (11.59784pt too wide) in paragraph at lines 1619--1620
[]\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/2011/texmf-dist/tex/latex/base/utf8.def) [30]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [31]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [32]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [33] [34]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [35]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [36]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [37]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (15.78088pt too wide) in paragraph at lines 2087--2088
[][][]$\T1/fi4/m/n/10 http : / / www . thelancet . com / journals / lancet / ar
ticle / PIIS0140-[]6736(05 ) 17947-[]1 / abstract$[][] 
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [38]
Overfull \hbox (2.38757pt too wide) in paragraph at lines 2119--2120
\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/2011/texmf-dist/tex/latex/base/utf8.def) [39]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [40]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [41] [42]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def)
Underfull \hbox (badness 3009) in paragraph at lines 2301--2301
[]\T1/ptm/m/it/10 Tamoxifen Re-sis-tance sig-na-ture com-posed of 13 gene clus-
ters
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [43]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [44] [45]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [46]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [47]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [48] [49]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [50] [51]
Overfull \hbox (10.84094pt too wide) in paragraph at lines 2787--2788
[][][]\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/2011/texmf-dist/tex/latex/base/utf8.def) [53] [54]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [55]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [56]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (11.68091pt too wide) in paragraph at lines 3078--3080
[][][]$\T1/fi4/m/n/10 http : / / www . ncbi . nlm . nih . gov / geo / query / a
cc . cgi ? acc = GSE2034$[][] [][]$http : / / www . ncbi . nlm . nih .
[57] (/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [58]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def)
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/2011/texmf-dist/fonts/enc/dvips/base/8r.enc}{/usr/local/tex
live/2011/texmf-dist/fonts/enc/dvips/inconsolata/fi4-ec.enc}</usr/local/texlive
/2011/texmf-dist/fonts/type1/public/inconsolata/Inconsolata.pfb></usr/local/tex
live/2011/texmf-dist/fonts/type1/urw/helvetic/uhvr8a.pfb></usr/local/texlive/20
11/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></usr/local/texlive/2011/texmf-d
ist/fonts/type1/urw/times/utmr8a.pfb></usr/local/texlive/2011/texmf-dist/fonts/
type1/urw/times/utmr8a.pfb></usr/local/texlive/2011/texmf-dist/fonts/type1/urw/
times/utmri8a.pfb>
Output written on Rd2.pdf (59 pages, 203285 bytes).
Transcript written on Rd2.log.
This is makeindex, version 2.15 [TeX Live 2011] (kpathsea + Thai support).
Scanning input file ./Rd2.idx....done (212 entries accepted, 0 rejected).
Sorting entries.....done (1727 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 3.1415926-2.3-1.40.12 (TeX Live 2011)
 \write18 enabled.
entering extended mode
(/private/tmp/RtmpoNdKem/Rbuild78141c3c04a8/genefu/.Rd2pdf30740/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, afrikaans, ancientgreek, ibycus, arabi
c, armenian, basque, bulgarian, catalan, pinyin, coptic, croatian, czech, danis
h, dutch, ukenglish, usenglishmax, esperanto, estonian, ethiopic, farsi, finnis
h, french, galician, german, ngerman, swissgerman, monogreek, greek, hungarian,
 icelandic, assamese, bengali, gujarati, hindi, kannada, malayalam, marathi, or
iya, panjabi, tamil, telugu, indonesian, interlingua, irish, italian, kurmanji,
 lao, latin, latvian, lithuanian, mongolian, mongolianlmc, bokmal, nynorsk, pol
ish, portuguese, romanian, russian, sanskrit, serbian, serbianc, slovak, sloven
ian, spanish, swedish, turkish, turkmen, ukrainian, uppersorbian, welsh, loaded
.
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/book.cls
Document Class: book 2007/10/19 v1.4h Standard LaTeX document class
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/bk10.clo))
(/Library/Frameworks/R.framework/Versions/2.15/Resources/share/texmf/tex/latex/
Rd.sty (/usr/local/texlive/2011/texmf-dist/tex/latex/base/ifthen.sty)
(/usr/local/texlive/2011/texmf-dist/tex/latex/tools/longtable.sty)
(/usr/local/texlive/2011/texmf-dist/tex/latex/tools/bm.sty)
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/alltt.sty)
(/usr/local/texlive/2011/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/local/texlive/2011/texmf-dist/tex/latex/url/url.sty) NOT loading ae
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/fontenc.sty
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/t1enc.def))
(/usr/local/texlive/2011/texmf-dist/tex/latex/psnfss/times.sty)
NOT loading lmodern
(/usr/local/texlive/2011/texmf-dist/tex/latex/inconsolata/inconsolata.sty
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/textcomp.sty
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/ts1enc.def))
(/usr/local/texlive/2011/texmf-dist/tex/latex/graphics/keyval.sty))
(/usr/local/texlive/2011/texmf-dist/tex/latex/graphics/color.sty
(/usr/local/texlive/2011/texmf-dist/tex/latex/latexconfig/color.cfg)
(/usr/local/texlive/2011/texmf-dist/tex/latex/pdftex-def/pdftex.def
(/usr/local/texlive/2011/texmf-dist/tex/generic/oberdiek/infwarerr.sty)
(/usr/local/texlive/2011/texmf-dist/tex/generic/oberdiek/ltxcmds.sty)))
(/usr/local/texlive/2011/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/local/texlive/2011/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
(/usr/local/texlive/2011/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty))
(/usr/local/texlive/2011/texmf-dist/tex/generic/ifxetex/ifxetex.sty)
(/usr/local/texlive/2011/texmf-dist/tex/latex/oberdiek/kvoptions.sty)
(/usr/local/texlive/2011/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/local/texlive/2011/texmf-dist/tex/latex/latexconfig/hyperref.cfg))

Package hyperref Message: Driver (autodetected): hpdftex.

(/usr/local/texlive/2011/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/local/texlive/2011/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty))

Package hyperref Warning: Option `hyperindex' has already been used,
(hyperref)                setting the option has no effect on input line 356.


Package hyperref Warning: Option `pagebackref' has already been used,
(hyperref)                setting the option has no effect on input line 356.

) (/usr/local/texlive/2011/texmf-dist/tex/latex/base/makeidx.sty)
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/inputenc.sty
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/t1enc.dfu)
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/ot1enc.dfu)
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/omsenc.dfu)
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/ts1enc.dfu))
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/latin1.def))
Writing index file Rd2.idx
(./Rd2.aux) (/usr/local/texlive/2011/texmf-dist/tex/latex/base/ts1cmr.fd)
(/usr/local/texlive/2011/texmf-dist/tex/latex/psnfss/t1ptm.fd)
(/usr/local/texlive/2011/texmf-dist/tex/context/base/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/local/texlive/2011/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/local/texlive/2011/texmf-dist/tex/generic/oberdiek/gettitlestring.sty))
(./Rd2.out) (./Rd2.out)
(/usr/local/texlive/2011/texmf-dist/tex/latex/inconsolata/t1fi4.fd)
(/usr/local/texlive/2011/texmf-dist/tex/latex/psnfss/t1phv.fd) (./Rd2.toc
[1{/usr/local/texlive/2011/texmf-var/fonts/map/pdftex/updmap/pdftex.map}])
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [2]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [3] [4]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [5]
(/usr/local/texlive/2011/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/2011/texmf-dist/tex/latex/base/utf8.def) [7] [8]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [9] [10]
(/usr/local/texlive/2011/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/2011/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/2011/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (104.78088pt 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"), check.w = TRUE, 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"
[13]
Overfull \hbox (137.18091pt too wide) in paragraph at lines 696--698
[][][]$\T1/fi4/m/n/10 http : / / en . wikipedia . org / wiki / T _ test$[][] []
[]$http : / / www . nicebread . de / blog / files / fc02e1635792cb0f2b3cbd1f7e6
c580b-[]10 .

Overfull \hbox (198.78088pt too wide) in paragraph at lines 722--722
 []\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/2011/texmf-dist/tex/latex/base/utf8.def) [14] [15]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [16] [17]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (2.38757pt too wide) in paragraph at lines 982--983
\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/2011/texmf-dist/tex/latex/base/utf8.def) [19]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [20] [21]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [22] [23]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (129.78088pt too wide) in paragraph at lines 1272--1272
 []\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 1279--1280
[]\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 1282--1283
[]\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/2011/texmf-dist/tex/latex/base/utf8.def) [25]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [26]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [27]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [28] [29]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (11.59784pt too wide) in paragraph at lines 1619--1620
[]\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/2011/texmf-dist/tex/latex/base/utf8.def) [31]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [32]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [33]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [34] [35]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [36]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [37]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [38]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (15.78088pt too wide) in paragraph at lines 2087--2088
[][][]$\T1/fi4/m/n/10 http : / / www . thelancet . com / journals / lancet / ar
ticle / PIIS0140-[]6736(05 ) 17947-[]1 / abstract$[][] 
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [39]
Overfull \hbox (2.38757pt too wide) in paragraph at lines 2119--2120
\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/2011/texmf-dist/tex/latex/base/utf8.def) [40]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [41]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [42] [43]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def)
Underfull \hbox (badness 3009) in paragraph at lines 2301--2301
[]\T1/ptm/m/it/10 Tamoxifen Re-sis-tance sig-na-ture com-posed of 13 gene clus-
ters
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [44]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [45] [46]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [47]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [48]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [49] [50]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [51] [52]
Overfull \hbox (10.84094pt too wide) in paragraph at lines 2787--2788
[][][]\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/2011/texmf-dist/tex/latex/base/utf8.def) [54] [55]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [56]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [57]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (11.68091pt too wide) in paragraph at lines 3078--3080
[][][]$\T1/fi4/m/n/10 http : / / www . ncbi . nlm . nih . gov / geo / query / a
cc . cgi ? acc = GSE2034$[][] [][]$http : / / www . ncbi . nlm . nih .
[58] (/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [59]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) (./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/2011/texmf-dist/fonts/enc/dvips/base/8r.enc}{/usr/local/tex
live/2011/texmf-dist/fonts/enc/dvips/inconsolata/fi4-ec.enc}</usr/local/texlive
/2011/texmf-dist/fonts/type1/public/inconsolata/Inconsolata.pfb></usr/local/tex
live/2011/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/local/texl
ive/2011/texmf-dist/fonts/type1/urw/helvetic/uhvr8a.pfb></usr/local/texlive/201
1/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></usr/local/texlive/2011/texmf-di
st/fonts/type1/urw/times/utmr8a.pfb></usr/local/texlive/2011/texmf-dist/fonts/t
ype1/urw/times/utmr8a.pfb></usr/local/texlive/2011/texmf-dist/fonts/type1/urw/t
imes/utmri8a.pfb>
Output written on Rd2.pdf (62 pages, 226440 bytes).
Transcript written on Rd2.log.
This is makeindex, version 2.15 [TeX Live 2011] (kpathsea + Thai support).
Scanning input file ./Rd2.idx....done (212 entries accepted, 0 rejected).
Sorting entries.....done (1727 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 3.1415926-2.3-1.40.12 (TeX Live 2011)
 \write18 enabled.
entering extended mode
(/private/tmp/RtmpoNdKem/Rbuild78141c3c04a8/genefu/.Rd2pdf30740/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, afrikaans, ancientgreek, ibycus, arabi
c, armenian, basque, bulgarian, catalan, pinyin, coptic, croatian, czech, danis
h, dutch, ukenglish, usenglishmax, esperanto, estonian, ethiopic, farsi, finnis
h, french, galician, german, ngerman, swissgerman, monogreek, greek, hungarian,
 icelandic, assamese, bengali, gujarati, hindi, kannada, malayalam, marathi, or
iya, panjabi, tamil, telugu, indonesian, interlingua, irish, italian, kurmanji,
 lao, latin, latvian, lithuanian, mongolian, mongolianlmc, bokmal, nynorsk, pol
ish, portuguese, romanian, russian, sanskrit, serbian, serbianc, slovak, sloven
ian, spanish, swedish, turkish, turkmen, ukrainian, uppersorbian, welsh, loaded
.
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/book.cls
Document Class: book 2007/10/19 v1.4h Standard LaTeX document class
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/bk10.clo))
(/Library/Frameworks/R.framework/Versions/2.15/Resources/share/texmf/tex/latex/
Rd.sty (/usr/local/texlive/2011/texmf-dist/tex/latex/base/ifthen.sty)
(/usr/local/texlive/2011/texmf-dist/tex/latex/tools/longtable.sty)
(/usr/local/texlive/2011/texmf-dist/tex/latex/tools/bm.sty)
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/alltt.sty)
(/usr/local/texlive/2011/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/local/texlive/2011/texmf-dist/tex/latex/url/url.sty) NOT loading ae
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/fontenc.sty
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/t1enc.def))
(/usr/local/texlive/2011/texmf-dist/tex/latex/psnfss/times.sty)
NOT loading lmodern
(/usr/local/texlive/2011/texmf-dist/tex/latex/inconsolata/inconsolata.sty
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/textcomp.sty
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/ts1enc.def))
(/usr/local/texlive/2011/texmf-dist/tex/latex/graphics/keyval.sty))
(/usr/local/texlive/2011/texmf-dist/tex/latex/graphics/color.sty
(/usr/local/texlive/2011/texmf-dist/tex/latex/latexconfig/color.cfg)
(/usr/local/texlive/2011/texmf-dist/tex/latex/pdftex-def/pdftex.def
(/usr/local/texlive/2011/texmf-dist/tex/generic/oberdiek/infwarerr.sty)
(/usr/local/texlive/2011/texmf-dist/tex/generic/oberdiek/ltxcmds.sty)))
(/usr/local/texlive/2011/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/local/texlive/2011/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
(/usr/local/texlive/2011/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty))
(/usr/local/texlive/2011/texmf-dist/tex/generic/ifxetex/ifxetex.sty)
(/usr/local/texlive/2011/texmf-dist/tex/latex/oberdiek/kvoptions.sty)
(/usr/local/texlive/2011/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/local/texlive/2011/texmf-dist/tex/latex/latexconfig/hyperref.cfg))

Package hyperref Message: Driver (autodetected): hpdftex.

(/usr/local/texlive/2011/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/local/texlive/2011/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty))

Package hyperref Warning: Option `hyperindex' has already been used,
(hyperref)                setting the option has no effect on input line 356.


Package hyperref Warning: Option `pagebackref' has already been used,
(hyperref)                setting the option has no effect on input line 356.

) (/usr/local/texlive/2011/texmf-dist/tex/latex/base/makeidx.sty)
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/inputenc.sty
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/t1enc.dfu)
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/ot1enc.dfu)
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/omsenc.dfu)
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/ts1enc.dfu))
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/latin1.def))
Writing index file Rd2.idx
(./Rd2.aux) (/usr/local/texlive/2011/texmf-dist/tex/latex/base/ts1cmr.fd)
(/usr/local/texlive/2011/texmf-dist/tex/latex/psnfss/t1ptm.fd)
(/usr/local/texlive/2011/texmf-dist/tex/context/base/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/local/texlive/2011/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/local/texlive/2011/texmf-dist/tex/generic/oberdiek/gettitlestring.sty))
(./Rd2.out) (./Rd2.out)
(/usr/local/texlive/2011/texmf-dist/tex/latex/inconsolata/t1fi4.fd)
(/usr/local/texlive/2011/texmf-dist/tex/latex/psnfss/t1phv.fd) (./Rd2.toc
[1{/usr/local/texlive/2011/texmf-var/fonts/map/pdftex/updmap/pdftex.map}])
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [2]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [3] [4]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [5]
(/usr/local/texlive/2011/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/2011/texmf-dist/tex/latex/base/utf8.def) [7] [8]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [9] [10]
(/usr/local/texlive/2011/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/2011/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/2011/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (104.78088pt 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"), check.w = TRUE, 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"
[13]
Overfull \hbox (137.18091pt too wide) in paragraph at lines 696--698
[][][]$\T1/fi4/m/n/10 http : / / en . wikipedia . org / wiki / T _ test$[][] []
[]$http : / / www . nicebread . de / blog / files / fc02e1635792cb0f2b3cbd1f7e6
c580b-[]10 .

Overfull \hbox (198.78088pt too wide) in paragraph at lines 722--722
 []\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/2011/texmf-dist/tex/latex/base/utf8.def) [14] [15]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [16] [17]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (2.38757pt too wide) in paragraph at lines 982--983
\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/2011/texmf-dist/tex/latex/base/utf8.def) [19]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [20] [21]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [22] [23]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (129.78088pt too wide) in paragraph at lines 1272--1272
 []\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 1279--1280
[]\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 1282--1283
[]\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/2011/texmf-dist/tex/latex/base/utf8.def) [25]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [26]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [27]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [28] [29]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (11.59784pt too wide) in paragraph at lines 1619--1620
[]\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/2011/texmf-dist/tex/latex/base/utf8.def) [31]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [32]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [33]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [34] [35]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [36]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [37]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [38]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (15.78088pt too wide) in paragraph at lines 2087--2088
[][][]$\T1/fi4/m/n/10 http : / / www . thelancet . com / journals / lancet / ar
ticle / PIIS0140-[]6736(05 ) 17947-[]1 / abstract$[][] 
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [39]
Overfull \hbox (2.38757pt too wide) in paragraph at lines 2119--2120
\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/2011/texmf-dist/tex/latex/base/utf8.def) [40]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [41]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [42] [43]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def)
Underfull \hbox (badness 3009) in paragraph at lines 2301--2301
[]\T1/ptm/m/it/10 Tamoxifen Re-sis-tance sig-na-ture com-posed of 13 gene clus-
ters
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [44]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [45] [46]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [47]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [48]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [49] [50]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [51] [52]
Overfull \hbox (10.84094pt too wide) in paragraph at lines 2787--2788
[][][]\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/2011/texmf-dist/tex/latex/base/utf8.def) [54] [55]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [56]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [57]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (11.68091pt too wide) in paragraph at lines 3078--3080
[][][]$\T1/fi4/m/n/10 http : / / www . ncbi . nlm . nih . gov / geo / query / a
cc . cgi ? acc = GSE2034$[][] [][]$http : / / www . ncbi . nlm . nih .
[58] (/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) [59]
(/usr/local/texlive/2011/texmf-dist/tex/latex/base/utf8.def) (./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/2011/texmf-dist/fonts/enc/dvips/base/8r.enc}{/usr/local/tex
live/2011/texmf-dist/fonts/enc/dvips/inconsolata/fi4-ec.enc}</usr/local/texlive
/2011/texmf-dist/fonts/type1/public/inconsolata/Inconsolata.pfb></usr/local/tex
live/2011/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/local/texl
ive/2011/texmf-dist/fonts/type1/urw/helvetic/uhvr8a.pfb></usr/local/texlive/201
1/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></usr/local/texlive/2011/texmf-di
st/fonts/type1/urw/times/utmr8a.pfb></usr/local/texlive/2011/texmf-dist/fonts/t
ype1/urw/times/utmr8a.pfb></usr/local/texlive/2011/texmf-dist/fonts/type1/urw/t
imes/utmri8a.pfb>
Output written on Rd2.pdf (62 pages, 226461 bytes).
Transcript written on Rd2.log.
Saving output to '/private/tmp/RtmpoNdKem/Rbuild78141c3c04a8/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_1.6.1.tar.gz'