##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data genefu
###
##############################################################################
##############################################################################
* 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 .Warning: /private/tmp/RtmpNAYt2B/Rbuilda3bf46df0dba/genefu/man/ihc4.Rd:71: All text must be in a section
......
Creating pdf output from LaTeX ...
This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013)
\write18 enabled.
entering extended mode
LaTeX2e <2011/06/27>
Babel <3.9f> and hyphenation patterns for 78 languages loaded.
(./Rd2.tex (/usr/local/texlive/2013/texmf-dist/tex/latex/base/book.cls
Document Class: book 2007/10/19 v1.4h Standard LaTeX document class
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/bk10.clo))
(/Library/Frameworks/R.framework/Resources/share/texmf/tex/latex/Rd.sty
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/ifthen.sty)
(/usr/local/texlive/2013/texmf-dist/tex/latex/tools/longtable.sty)
(/usr/local/texlive/2013/texmf-dist/tex/latex/tools/bm.sty)
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/alltt.sty)
(/usr/local/texlive/2013/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/local/texlive/2013/texmf-dist/tex/latex/url/url.sty)
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/textcomp.sty
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/ts1enc.def))
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/fontenc.sty
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/t1enc.def))
(/usr/local/texlive/2013/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/local/texlive/2013/texmf-dist/tex/latex/inconsolata/inconsolata.sty
(/usr/local/texlive/2013/texmf-dist/tex/latex/graphics/keyval.sty))
(/usr/local/texlive/2013/texmf-dist/tex/latex/graphics/color.sty
(/usr/local/texlive/2013/texmf-dist/tex/latex/latexconfig/color.cfg)
(/usr/local/texlive/2013/texmf-dist/tex/latex/pdftex-def/pdftex.def
(/usr/local/texlive/2013/texmf-dist/tex/generic/oberdiek/infwarerr.sty)
(/usr/local/texlive/2013/texmf-dist/tex/generic/oberdiek/ltxcmds.sty)))
(/usr/local/texlive/2013/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/local/texlive/2013/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
(/usr/local/texlive/2013/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty))
(/usr/local/texlive/2013/texmf-dist/tex/generic/ifxetex/ifxetex.sty)
(/usr/local/texlive/2013/texmf-dist/tex/latex/oberdiek/auxhook.sty)
(/usr/local/texlive/2013/texmf-dist/tex/latex/oberdiek/kvoptions.sty)
(/usr/local/texlive/2013/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/local/texlive/2013/texmf-dist/tex/latex/latexconfig/hyperref.cfg))
Package hyperref Message: Driver (autodetected): hpdftex.
(/usr/local/texlive/2013/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/local/texlive/2013/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 366.
Package hyperref Warning: Option `pagebackref' has already been used,
(hyperref) setting the option has no effect on input line 366.
) (/usr/local/texlive/2013/texmf-dist/tex/latex/base/makeidx.sty)
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/inputenc.sty
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/t1enc.dfu)
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/ot1enc.dfu)
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/omsenc.dfu)
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/ts1enc.dfu))
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/latin1.def))
Writing index file Rd2.idx
No file Rd2.aux.
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/ts1cmr.fd)
(/usr/local/texlive/2013/texmf-dist/tex/latex/psnfss/t1ptm.fd)
(/usr/local/texlive/2013/texmf-dist/tex/context/base/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/local/texlive/2013/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/local/texlive/2013/texmf-dist/tex/generic/oberdiek/gettitlestring.sty))
(/usr/local/texlive/2013/texmf-dist/tex/latex/inconsolata/t1fi4.fd)
Overfull \hbox (46.23257pt too wide) in paragraph at lines 21--22
\T1/ptm/m/n/10 Kains \T1/fi4/m/n/10 <benjamin.haibe.kains@utoronto.ca>\T1/ptm/m
/n/10 , Markus Schroeder \T1/fi4/m/n/10 <markus.schroeder@ucdconnect.ie>
(/usr/local/texlive/2013/texmf-dist/tex/latex/psnfss/t1phv.fd)
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [1{/usr/local/texl
ive/2013/texmf-var/fonts/map/pdftex/updmap/pdftex.map}] [2]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [3] [4]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [5]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (39.78088pt too wide) in paragraph at lines 271--271
[]\T1/fi4/m/n/10 claudinLow(x,classes="",y,nGenes="",priors="equal",std=F,dist
m="euclidean",centroids=F)[]
[6] (/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (44.78088pt too wide) in paragraph at lines 349--349
[] \T1/fi4/m/n/10 p.adjust.m = c("none", "holm", "hochberg", "hommel", "bonfe
rroni", "BH", "BY", "fdr"))[]
[7] [8] (/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [9]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [10]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [11]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (8.95699pt too wide) in paragraph at lines 632--633
[]\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] (/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [13]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [14]
Overfull \hbox (23.38692pt too wide) in paragraph at lines 772--773
[]\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
Overfull \hbox (62.97923pt too wide) in paragraph at lines 780--781
[]\T1/ptm/m/n/10 International Ge-nomics Con-sor-tium, [][]$\T1/fi4/m/n/10 http
: / / www . intgen . org / research-[]services / biobanking-[]experience /
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [15]
Overfull \hbox (6.17755pt too wide) in paragraph at lines 817--818
[]\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"
[16] (/usr/local/texlive/2013/texmf-dist/tex/latex/inconsolata/ts1fi4.fd)
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [17]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [18]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [19] [20]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (2.38757pt too wide) in paragraph at lines 1129--1130
\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
[21] (/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [22]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (44.78088pt too wide) in paragraph at lines 1231--1231
[]\T1/fi4/m/n/10 ihc4(ER, PGR, HER2, Ki67,age,size,grade,node,ana,scoreWithCli
nical=FALSE, na.rm = FALSE)[]
[23]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 1269--1269
[]\T1/fi4/m/n/9 ihc4(ER=sample(x=1:10, size=count,replace=TRUE),PGR=sample(x=1
:10, size=count,replace=TRUE),[]
Overfull \hbox (5.28088pt too wide) in paragraph at lines 1270--1270
[]\T1/fi4/m/n/9 HER2=sample(x=0:1,size=count,replace=TRUE),Ki67=sample(x=1:100
, size=count,replace=TRUE),[]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 1274--1274
[]\T1/fi4/m/n/9 ihc4(ER=sample(x=1:10, size=count,replace=TRUE),PGR=sample(x=1
:10, size=count,replace=TRUE),[]
Overfull \hbox (5.28088pt too wide) in paragraph at lines 1275--1275
[]\T1/fi4/m/n/9 HER2=sample(x=0:1,size=count,replace=TRUE),Ki67=sample(x=1:100
, size=count,replace=TRUE),[]
Overfull \hbox (50.28088pt too wide) in paragraph at lines 1276--1276
[]\T1/fi4/m/n/9 age=demo.nkis[,"age"],size=demo.nkis[ ,"size"],grade=demo.nkis
[ ,"grade"],node=demo.nkis[ ,"node"],[]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [24] [25]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [26] [27]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (0.47766pt too wide) in paragraph at lines 1489--1490
[]\T1/ptm/m/n/10 List of ma-tri-ces of gene ex-pres-sions with sam-ples in rows
and probes in columns,
[28]
Overfull \hbox (0.49751pt too wide) in paragraph at lines 1492--1493
[]\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",
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [29]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [30]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [31]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (24.78088pt too wide) in paragraph at lines 1681--1681
[]\T1/fi4/m/n/10 "pam50", "ssp2006", "ssp2003", "intClust", "AIMS"), data, ann
ot, do.mapping = FALSE)[]
[32] [33] (/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [34]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [35]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [36]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [37]
Overfull \hbox (33.81834pt too wide) in paragraph at lines 1974--1975
[]\T1/ptm/m/n/10 character string con-tain-ing the \T1/fi4/m/n/10 biomaRt \T1/p
tm/m/n/10 at-tribute to use for map-ping if \T1/fi4/m/n/10 do.mapping=TRUE
[38] (/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (33.81834pt too wide) in paragraph at lines 2050--2051
[]\T1/ptm/m/n/10 character string con-tain-ing the \T1/fi4/m/n/10 biomaRt \T1/p
tm/m/n/10 at-tribute to use for map-ping if \T1/fi4/m/n/10 do.mapping=TRUE
[39]
Overfull \hbox (41.28088pt too wide) in paragraph at lines 2096--2096
[]\T1/fi4/m/n/9 ovcCrijns.nkis <- ovcCrijns(data=data.nkis, annot=annot.nkis,
gmap="entrezgene", do.mapping=TRUE)[]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [40]
Overfull \hbox (33.81834pt too wide) in paragraph at lines 2125--2126
[]\T1/ptm/m/n/10 character string con-tain-ing the \T1/fi4/m/n/10 biomaRt \T1/p
tm/m/n/10 at-tribute to use for map-ping if \T1/fi4/m/n/10 do.mapping=TRUE
Overfull \hbox (23.28088pt too wide) in paragraph at lines 2167--2167
[]\T1/fi4/m/n/9 ovcTCGA.nkis <- ovcTCGA(data=data.nkis, annot=annot.nkis, gmap
="entrezgene", do.mapping=TRUE)[]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [41]
Overfull \hbox (19.78088pt too wide) in paragraph at lines 2183--2183
[]\T1/fi4/m/n/10 gmap = c("entrezgene", "ensembl_gene_id", "hgnc_symbol", "uni
gene", "refseq_mrna"),[]
Overfull \hbox (33.81834pt too wide) in paragraph at lines 2200--2201
[]\T1/ptm/m/n/10 character string con-tain-ing the \T1/fi4/m/n/10 biomaRt \T1/p
tm/m/n/10 at-tribute to use for map-ping if \T1/fi4/m/n/10 do.mapping=TRUE
[42] (/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [43]
Overfull \hbox (11.59784pt too wide) in paragraph at lines 2319--2320
[]\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 ).
[44] (/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [45]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [46] [47]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [48]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [49]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [50]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [51]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [52]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [53]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [54]
Overfull \hbox (32.28088pt too wide) in paragraph at lines 2909--2909
[]\T1/fi4/m/n/9 tt <- data.frame(matrix(NA, nrow=3, ncol=3, dimnames=list(1:3,
paste("column", 1:3, sep="."))),[]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [55]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [56]
Overfull \hbox (15.78088pt too wide) in paragraph at lines 2994--2995
[][][]$\T1/fi4/m/n/10 http : / / www . thelancet . com / journals / lancet / ar
ticle / PIIS0140-[]6736(05 ) 17947-[]1 / abstract$[][]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (2.38757pt too wide) in paragraph at lines 3026--3027
\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
[57] (/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [58]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [59]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [60]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def)
Underfull \hbox (badness 3009) in paragraph at lines 3208--3208
[]\T1/ptm/m/it/10 Tamoxifen Re-sis-tance sig-na-ture com-posed of 13 gene clus-
ters
[61] (/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [62]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [63]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [64]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [65]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [66] [67]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [68]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [69]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [70] [71]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [72] [73]
Overfull \hbox (10.84094pt too wide) in paragraph at lines 3875--3876
[][][]\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 ,
[74] (/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [75] [76]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [77]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [78]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (11.68091pt too wide) in paragraph at lines 4166--4168
[][][]$\T1/fi4/m/n/10 http : / / www . ncbi . nlm . nih . gov / geo / query / a
cc . cgi ? acc = GSE2034$[][] [][]$http : / / www . ncbi . nlm . nih .
[79] (/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [80]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def)
No file Rd2.ind.
[81] (./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/2013/texmf-dist/fonts/enc/dvips/base/8r.enc}{/usr/local/tex
live/2013/texmf-dist/fonts/enc/dvips/inconsolata/fi4-ec.enc}</usr/local/texlive
/2013/texmf-dist/fonts/type1/public/inconsolata/Inconsolata.pfb></usr/local/tex
live/2013/texmf-dist/fonts/type1/urw/helvetic/uhvr8a.pfb></usr/local/texlive/20
13/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></usr/local/texlive/2013/texmf-d
ist/fonts/type1/urw/times/utmr8a.pfb></usr/local/texlive/2013/texmf-dist/fonts/
type1/urw/times/utmr8a.pfb></usr/local/texlive/2013/texmf-dist/fonts/type1/urw/
times/utmri8a.pfb>
Output written on Rd2.pdf (81 pages, 244445 bytes).
Transcript written on Rd2.log.
This is makeindex, version 2.15 [TeX Live 2013] (kpathsea + Thai support).
Scanning input file Rd2.idx....done (271 entries accepted, 0 rejected).
Sorting entries.....done (2385 comparisons).
Generating output file Rd2.ind....done (317 lines written, 19 warnings).
Output written in Rd2.ind.
Transcript written in Rd2.ilg.
This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013)
\write18 enabled.
entering extended mode
LaTeX2e <2011/06/27>
Babel <3.9f> and hyphenation patterns for 78 languages loaded.
(./Rd2.tex (/usr/local/texlive/2013/texmf-dist/tex/latex/base/book.cls
Document Class: book 2007/10/19 v1.4h Standard LaTeX document class
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/bk10.clo))
(/Library/Frameworks/R.framework/Resources/share/texmf/tex/latex/Rd.sty
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/ifthen.sty)
(/usr/local/texlive/2013/texmf-dist/tex/latex/tools/longtable.sty)
(/usr/local/texlive/2013/texmf-dist/tex/latex/tools/bm.sty)
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/alltt.sty)
(/usr/local/texlive/2013/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/local/texlive/2013/texmf-dist/tex/latex/url/url.sty)
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/textcomp.sty
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/ts1enc.def))
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/fontenc.sty
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/t1enc.def))
(/usr/local/texlive/2013/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/local/texlive/2013/texmf-dist/tex/latex/inconsolata/inconsolata.sty
(/usr/local/texlive/2013/texmf-dist/tex/latex/graphics/keyval.sty))
(/usr/local/texlive/2013/texmf-dist/tex/latex/graphics/color.sty
(/usr/local/texlive/2013/texmf-dist/tex/latex/latexconfig/color.cfg)
(/usr/local/texlive/2013/texmf-dist/tex/latex/pdftex-def/pdftex.def
(/usr/local/texlive/2013/texmf-dist/tex/generic/oberdiek/infwarerr.sty)
(/usr/local/texlive/2013/texmf-dist/tex/generic/oberdiek/ltxcmds.sty)))
(/usr/local/texlive/2013/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/local/texlive/2013/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
(/usr/local/texlive/2013/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty))
(/usr/local/texlive/2013/texmf-dist/tex/generic/ifxetex/ifxetex.sty)
(/usr/local/texlive/2013/texmf-dist/tex/latex/oberdiek/auxhook.sty)
(/usr/local/texlive/2013/texmf-dist/tex/latex/oberdiek/kvoptions.sty)
(/usr/local/texlive/2013/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/local/texlive/2013/texmf-dist/tex/latex/latexconfig/hyperref.cfg))
Package hyperref Message: Driver (autodetected): hpdftex.
(/usr/local/texlive/2013/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/local/texlive/2013/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 366.
Package hyperref Warning: Option `pagebackref' has already been used,
(hyperref) setting the option has no effect on input line 366.
) (/usr/local/texlive/2013/texmf-dist/tex/latex/base/makeidx.sty)
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/inputenc.sty
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/t1enc.dfu)
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/ot1enc.dfu)
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/omsenc.dfu)
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/ts1enc.dfu))
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/latin1.def))
Writing index file Rd2.idx
(./Rd2.aux) (/usr/local/texlive/2013/texmf-dist/tex/latex/base/ts1cmr.fd)
(/usr/local/texlive/2013/texmf-dist/tex/latex/psnfss/t1ptm.fd)
(/usr/local/texlive/2013/texmf-dist/tex/context/base/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/local/texlive/2013/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/local/texlive/2013/texmf-dist/tex/generic/oberdiek/gettitlestring.sty))
(./Rd2.out) (./Rd2.out)
(/usr/local/texlive/2013/texmf-dist/tex/latex/inconsolata/t1fi4.fd)
Overfull \hbox (46.23257pt too wide) in paragraph at lines 21--22
\T1/ptm/m/n/10 Kains \T1/fi4/m/n/10 <benjamin.haibe.kains@utoronto.ca>\T1/ptm/m
/n/10 , Markus Schroeder \T1/fi4/m/n/10 <markus.schroeder@ucdconnect.ie>
(/usr/local/texlive/2013/texmf-dist/tex/latex/psnfss/t1phv.fd) (./Rd2.toc
[1{/usr/local/texlive/2013/texmf-var/fonts/map/pdftex/updmap/pdftex.map}]
[2]) (/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [3]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [4]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [5]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [6]
Overfull \hbox (39.78088pt too wide) in paragraph at lines 271--271
[]\T1/fi4/m/n/10 claudinLow(x,classes="",y,nGenes="",priors="equal",std=F,dist
m="euclidean",centroids=F)[]
[7] (/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (44.78088pt too wide) in paragraph at lines 349--349
[] \T1/fi4/m/n/10 p.adjust.m = c("none", "holm", "hochberg", "hommel", "bonfe
rroni", "BH", "BY", "fdr"))[]
[8] (/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [9]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [10]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [11]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [12]
Overfull \hbox (8.95699pt too wide) in paragraph at lines 632--633
[]\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] (/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [14]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (23.38692pt too wide) in paragraph at lines 772--773
[]\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
[15]
Overfull \hbox (62.97923pt too wide) in paragraph at lines 780--781
[]\T1/ptm/m/n/10 International Ge-nomics Con-sor-tium, [][]$\T1/fi4/m/n/10 http
: / / www . intgen . org / research-[]services / biobanking-[]experience /
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (6.17755pt too wide) in paragraph at lines 817--818
[]\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"
[16] (/usr/local/texlive/2013/texmf-dist/tex/latex/inconsolata/ts1fi4.fd)
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [17] [18]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [19]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [20]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [21]
Overfull \hbox (2.38757pt too wide) in paragraph at lines 1129--1130
\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/2013/texmf-dist/tex/latex/base/utf8.def) [22] [23]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (44.78088pt too wide) in paragraph at lines 1231--1231
[]\T1/fi4/m/n/10 ihc4(ER, PGR, HER2, Ki67,age,size,grade,node,ana,scoreWithCli
nical=FALSE, na.rm = FALSE)[]
[24]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 1269--1269
[]\T1/fi4/m/n/9 ihc4(ER=sample(x=1:10, size=count,replace=TRUE),PGR=sample(x=1
:10, size=count,replace=TRUE),[]
Overfull \hbox (5.28088pt too wide) in paragraph at lines 1270--1270
[]\T1/fi4/m/n/9 HER2=sample(x=0:1,size=count,replace=TRUE),Ki67=sample(x=1:100
, size=count,replace=TRUE),[]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 1274--1274
[]\T1/fi4/m/n/9 ihc4(ER=sample(x=1:10, size=count,replace=TRUE),PGR=sample(x=1
:10, size=count,replace=TRUE),[]
Overfull \hbox (5.28088pt too wide) in paragraph at lines 1275--1275
[]\T1/fi4/m/n/9 HER2=sample(x=0:1,size=count,replace=TRUE),Ki67=sample(x=1:100
, size=count,replace=TRUE),[]
Overfull \hbox (50.28088pt too wide) in paragraph at lines 1276--1276
[]\T1/fi4/m/n/9 age=demo.nkis[,"age"],size=demo.nkis[ ,"size"],grade=demo.nkis
[ ,"grade"],node=demo.nkis[ ,"node"],[]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [25] [26]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [27] [28]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (0.47766pt too wide) in paragraph at lines 1489--1490
[]\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 1492--1493
[]\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",
[29] (/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [30]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [31]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [32]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 1681--1681
[]\T1/fi4/m/n/10 "pam50", "ssp2006", "ssp2003", "intClust", "AIMS"), data, ann
ot, do.mapping = FALSE)[]
[33] [34] (/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [35]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [36] [37]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (33.81834pt too wide) in paragraph at lines 1974--1975
[]\T1/ptm/m/n/10 character string con-tain-ing the \T1/fi4/m/n/10 biomaRt \T1/p
tm/m/n/10 at-tribute to use for map-ping if \T1/fi4/m/n/10 do.mapping=TRUE
[38] (/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (33.81834pt too wide) in paragraph at lines 2050--2051
[]\T1/ptm/m/n/10 character string con-tain-ing the \T1/fi4/m/n/10 biomaRt \T1/p
tm/m/n/10 at-tribute to use for map-ping if \T1/fi4/m/n/10 do.mapping=TRUE
[39]
Overfull \hbox (41.28088pt too wide) in paragraph at lines 2096--2096
[]\T1/fi4/m/n/9 ovcCrijns.nkis <- ovcCrijns(data=data.nkis, annot=annot.nkis,
gmap="entrezgene", do.mapping=TRUE)[]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [40]
Overfull \hbox (33.81834pt too wide) in paragraph at lines 2125--2126
[]\T1/ptm/m/n/10 character string con-tain-ing the \T1/fi4/m/n/10 biomaRt \T1/p
tm/m/n/10 at-tribute to use for map-ping if \T1/fi4/m/n/10 do.mapping=TRUE
[41]
Overfull \hbox (23.28088pt too wide) in paragraph at lines 2167--2167
[]\T1/fi4/m/n/9 ovcTCGA.nkis <- ovcTCGA(data=data.nkis, annot=annot.nkis, gmap
="entrezgene", do.mapping=TRUE)[]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (19.78088pt too wide) in paragraph at lines 2183--2183
[]\T1/fi4/m/n/10 gmap = c("entrezgene", "ensembl_gene_id", "hgnc_symbol", "uni
gene", "refseq_mrna"),[]
Overfull \hbox (33.81834pt too wide) in paragraph at lines 2200--2201
[]\T1/ptm/m/n/10 character string con-tain-ing the \T1/fi4/m/n/10 biomaRt \T1/p
tm/m/n/10 at-tribute to use for map-ping if \T1/fi4/m/n/10 do.mapping=TRUE
[42] (/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [43]
Overfull \hbox (11.59784pt too wide) in paragraph at lines 2319--2320
[]\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 ).
[44] (/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [45]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [46] [47]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [48]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [49]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [50]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [51]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [52]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [53]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [54]
Overfull \hbox (32.28088pt too wide) in paragraph at lines 2909--2909
[]\T1/fi4/m/n/9 tt <- data.frame(matrix(NA, nrow=3, ncol=3, dimnames=list(1:3,
paste("column", 1:3, sep="."))),[]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [55]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [56]
Overfull \hbox (15.78088pt too wide) in paragraph at lines 2994--2995
[][][]$\T1/fi4/m/n/10 http : / / www . thelancet . com / journals / lancet / ar
ticle / PIIS0140-[]6736(05 ) 17947-[]1 / abstract$[][]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (2.38757pt too wide) in paragraph at lines 3026--3027
\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
[57] (/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [58]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [59]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [60]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def)
Underfull \hbox (badness 3009) in paragraph at lines 3208--3208
[]\T1/ptm/m/it/10 Tamoxifen Re-sis-tance sig-na-ture com-posed of 13 gene clus-
ters
[61] (/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [62]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [63]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [64]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [65]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [66] [67]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [68]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [69]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [70] [71]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [72] [73]
Overfull \hbox (10.84094pt too wide) in paragraph at lines 3875--3876
[][][]\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 ,
[74] (/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [75] [76]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [77]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [78]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (11.68091pt too wide) in paragraph at lines 4166--4168
[][][]$\T1/fi4/m/n/10 http : / / www . ncbi . nlm . nih . gov / geo / query / a
cc . cgi ? acc = GSE2034$[][] [][]$http : / / www . ncbi . nlm . nih .
[79] (/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [80]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) (./Rd2.ind
[81]
LaTeX Font Warning: Font shape `T1/fi4/m/it' undefined
(Font) using `T1/fi4/m/n' instead on input line 90.
[82] [83] [84]) (./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/2013/texmf-dist/fonts/enc/dvips/base/8r.enc}{/usr/local/tex
live/2013/texmf-dist/fonts/enc/dvips/inconsolata/fi4-ec.enc}</usr/local/texlive
/2013/texmf-dist/fonts/type1/public/inconsolata/Inconsolata.pfb></usr/local/tex
live/2013/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/local/texl
ive/2013/texmf-dist/fonts/type1/urw/helvetic/uhvr8a.pfb></usr/local/texlive/201
3/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></usr/local/texlive/2013/texmf-di
st/fonts/type1/urw/times/utmr8a.pfb></usr/local/texlive/2013/texmf-dist/fonts/t
ype1/urw/times/utmr8a.pfb></usr/local/texlive/2013/texmf-dist/fonts/type1/urw/t
imes/utmri8a.pfb>
Output written on Rd2.pdf (84 pages, 272779 bytes).
Transcript written on Rd2.log.
This is makeindex, version 2.15 [TeX Live 2013] (kpathsea + Thai support).
Scanning input file Rd2.idx....done (271 entries accepted, 0 rejected).
Sorting entries.....done (2388 comparisons).
Generating output file Rd2.ind....done (316 lines written, 23 warnings).
Output written in Rd2.ind.
Transcript written in Rd2.ilg.
This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013)
\write18 enabled.
entering extended mode
LaTeX2e <2011/06/27>
Babel <3.9f> and hyphenation patterns for 78 languages loaded.
(./Rd2.tex (/usr/local/texlive/2013/texmf-dist/tex/latex/base/book.cls
Document Class: book 2007/10/19 v1.4h Standard LaTeX document class
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/bk10.clo))
(/Library/Frameworks/R.framework/Resources/share/texmf/tex/latex/Rd.sty
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/ifthen.sty)
(/usr/local/texlive/2013/texmf-dist/tex/latex/tools/longtable.sty)
(/usr/local/texlive/2013/texmf-dist/tex/latex/tools/bm.sty)
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/alltt.sty)
(/usr/local/texlive/2013/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/local/texlive/2013/texmf-dist/tex/latex/url/url.sty)
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/textcomp.sty
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/ts1enc.def))
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/fontenc.sty
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/t1enc.def))
(/usr/local/texlive/2013/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/local/texlive/2013/texmf-dist/tex/latex/inconsolata/inconsolata.sty
(/usr/local/texlive/2013/texmf-dist/tex/latex/graphics/keyval.sty))
(/usr/local/texlive/2013/texmf-dist/tex/latex/graphics/color.sty
(/usr/local/texlive/2013/texmf-dist/tex/latex/latexconfig/color.cfg)
(/usr/local/texlive/2013/texmf-dist/tex/latex/pdftex-def/pdftex.def
(/usr/local/texlive/2013/texmf-dist/tex/generic/oberdiek/infwarerr.sty)
(/usr/local/texlive/2013/texmf-dist/tex/generic/oberdiek/ltxcmds.sty)))
(/usr/local/texlive/2013/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/local/texlive/2013/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
(/usr/local/texlive/2013/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty))
(/usr/local/texlive/2013/texmf-dist/tex/generic/ifxetex/ifxetex.sty)
(/usr/local/texlive/2013/texmf-dist/tex/latex/oberdiek/auxhook.sty)
(/usr/local/texlive/2013/texmf-dist/tex/latex/oberdiek/kvoptions.sty)
(/usr/local/texlive/2013/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/local/texlive/2013/texmf-dist/tex/latex/latexconfig/hyperref.cfg))
Package hyperref Message: Driver (autodetected): hpdftex.
(/usr/local/texlive/2013/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/local/texlive/2013/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 366.
Package hyperref Warning: Option `pagebackref' has already been used,
(hyperref) setting the option has no effect on input line 366.
) (/usr/local/texlive/2013/texmf-dist/tex/latex/base/makeidx.sty)
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/inputenc.sty
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/t1enc.dfu)
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/ot1enc.dfu)
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/omsenc.dfu)
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/ts1enc.dfu))
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/latin1.def))
Writing index file Rd2.idx
(./Rd2.aux) (/usr/local/texlive/2013/texmf-dist/tex/latex/base/ts1cmr.fd)
(/usr/local/texlive/2013/texmf-dist/tex/latex/psnfss/t1ptm.fd)
(/usr/local/texlive/2013/texmf-dist/tex/context/base/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/local/texlive/2013/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/local/texlive/2013/texmf-dist/tex/generic/oberdiek/gettitlestring.sty))
(./Rd2.out) (./Rd2.out)
(/usr/local/texlive/2013/texmf-dist/tex/latex/inconsolata/t1fi4.fd)
Overfull \hbox (46.23257pt too wide) in paragraph at lines 21--22
\T1/ptm/m/n/10 Kains \T1/fi4/m/n/10 <benjamin.haibe.kains@utoronto.ca>\T1/ptm/m
/n/10 , Markus Schroeder \T1/fi4/m/n/10 <markus.schroeder@ucdconnect.ie>
(/usr/local/texlive/2013/texmf-dist/tex/latex/psnfss/t1phv.fd) (./Rd2.toc
[1{/usr/local/texlive/2013/texmf-var/fonts/map/pdftex/updmap/pdftex.map}]
[2]) (/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [3]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [4]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [5]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [6]
Overfull \hbox (39.78088pt too wide) in paragraph at lines 271--271
[]\T1/fi4/m/n/10 claudinLow(x,classes="",y,nGenes="",priors="equal",std=F,dist
m="euclidean",centroids=F)[]
[7] (/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (44.78088pt too wide) in paragraph at lines 349--349
[] \T1/fi4/m/n/10 p.adjust.m = c("none", "holm", "hochberg", "hommel", "bonfe
rroni", "BH", "BY", "fdr"))[]
[8] (/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [9]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [10]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [11]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [12]
Overfull \hbox (8.95699pt too wide) in paragraph at lines 632--633
[]\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] (/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [14]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (23.38692pt too wide) in paragraph at lines 772--773
[]\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
[15]
Overfull \hbox (62.97923pt too wide) in paragraph at lines 780--781
[]\T1/ptm/m/n/10 International Ge-nomics Con-sor-tium, [][]$\T1/fi4/m/n/10 http
: / / www . intgen . org / research-[]services / biobanking-[]experience /
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (6.17755pt too wide) in paragraph at lines 817--818
[]\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"
[16] (/usr/local/texlive/2013/texmf-dist/tex/latex/inconsolata/ts1fi4.fd)
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [17] [18]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [19]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [20]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [21]
Overfull \hbox (2.38757pt too wide) in paragraph at lines 1129--1130
\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/2013/texmf-dist/tex/latex/base/utf8.def) [22] [23]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (44.78088pt too wide) in paragraph at lines 1231--1231
[]\T1/fi4/m/n/10 ihc4(ER, PGR, HER2, Ki67,age,size,grade,node,ana,scoreWithCli
nical=FALSE, na.rm = FALSE)[]
[24]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 1269--1269
[]\T1/fi4/m/n/9 ihc4(ER=sample(x=1:10, size=count,replace=TRUE),PGR=sample(x=1
:10, size=count,replace=TRUE),[]
Overfull \hbox (5.28088pt too wide) in paragraph at lines 1270--1270
[]\T1/fi4/m/n/9 HER2=sample(x=0:1,size=count,replace=TRUE),Ki67=sample(x=1:100
, size=count,replace=TRUE),[]
Overfull \hbox (18.78088pt too wide) in paragraph at lines 1274--1274
[]\T1/fi4/m/n/9 ihc4(ER=sample(x=1:10, size=count,replace=TRUE),PGR=sample(x=1
:10, size=count,replace=TRUE),[]
Overfull \hbox (5.28088pt too wide) in paragraph at lines 1275--1275
[]\T1/fi4/m/n/9 HER2=sample(x=0:1,size=count,replace=TRUE),Ki67=sample(x=1:100
, size=count,replace=TRUE),[]
Overfull \hbox (50.28088pt too wide) in paragraph at lines 1276--1276
[]\T1/fi4/m/n/9 age=demo.nkis[,"age"],size=demo.nkis[ ,"size"],grade=demo.nkis
[ ,"grade"],node=demo.nkis[ ,"node"],[]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [25] [26]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [27] [28]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (0.47766pt too wide) in paragraph at lines 1489--1490
[]\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 1492--1493
[]\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",
[29] (/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [30]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [31]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [32]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 1681--1681
[]\T1/fi4/m/n/10 "pam50", "ssp2006", "ssp2003", "intClust", "AIMS"), data, ann
ot, do.mapping = FALSE)[]
[33] [34] (/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [35]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [36] [37]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (33.81834pt too wide) in paragraph at lines 1974--1975
[]\T1/ptm/m/n/10 character string con-tain-ing the \T1/fi4/m/n/10 biomaRt \T1/p
tm/m/n/10 at-tribute to use for map-ping if \T1/fi4/m/n/10 do.mapping=TRUE
[38] (/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (33.81834pt too wide) in paragraph at lines 2050--2051
[]\T1/ptm/m/n/10 character string con-tain-ing the \T1/fi4/m/n/10 biomaRt \T1/p
tm/m/n/10 at-tribute to use for map-ping if \T1/fi4/m/n/10 do.mapping=TRUE
[39]
Overfull \hbox (41.28088pt too wide) in paragraph at lines 2096--2096
[]\T1/fi4/m/n/9 ovcCrijns.nkis <- ovcCrijns(data=data.nkis, annot=annot.nkis,
gmap="entrezgene", do.mapping=TRUE)[]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [40]
Overfull \hbox (33.81834pt too wide) in paragraph at lines 2125--2126
[]\T1/ptm/m/n/10 character string con-tain-ing the \T1/fi4/m/n/10 biomaRt \T1/p
tm/m/n/10 at-tribute to use for map-ping if \T1/fi4/m/n/10 do.mapping=TRUE
[41]
Overfull \hbox (23.28088pt too wide) in paragraph at lines 2167--2167
[]\T1/fi4/m/n/9 ovcTCGA.nkis <- ovcTCGA(data=data.nkis, annot=annot.nkis, gmap
="entrezgene", do.mapping=TRUE)[]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (19.78088pt too wide) in paragraph at lines 2183--2183
[]\T1/fi4/m/n/10 gmap = c("entrezgene", "ensembl_gene_id", "hgnc_symbol", "uni
gene", "refseq_mrna"),[]
Overfull \hbox (33.81834pt too wide) in paragraph at lines 2200--2201
[]\T1/ptm/m/n/10 character string con-tain-ing the \T1/fi4/m/n/10 biomaRt \T1/p
tm/m/n/10 at-tribute to use for map-ping if \T1/fi4/m/n/10 do.mapping=TRUE
[42] (/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [43]
Overfull \hbox (11.59784pt too wide) in paragraph at lines 2319--2320
[]\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 ).
[44] (/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [45]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [46] [47]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [48]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [49]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [50]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [51]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [52]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [53]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [54]
Overfull \hbox (32.28088pt too wide) in paragraph at lines 2909--2909
[]\T1/fi4/m/n/9 tt <- data.frame(matrix(NA, nrow=3, ncol=3, dimnames=list(1:3,
paste("column", 1:3, sep="."))),[]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [55]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [56]
Overfull \hbox (15.78088pt too wide) in paragraph at lines 2994--2995
[][][]$\T1/fi4/m/n/10 http : / / www . thelancet . com / journals / lancet / ar
ticle / PIIS0140-[]6736(05 ) 17947-[]1 / abstract$[][]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (2.38757pt too wide) in paragraph at lines 3026--3027
\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
[57] (/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [58]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [59]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [60]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def)
Underfull \hbox (badness 3009) in paragraph at lines 3208--3208
[]\T1/ptm/m/it/10 Tamoxifen Re-sis-tance sig-na-ture com-posed of 13 gene clus-
ters
[61] (/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [62]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [63]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [64]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [65]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [66] [67]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [68]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [69]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [70] [71]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [72] [73]
Overfull \hbox (10.84094pt too wide) in paragraph at lines 3875--3876
[][][]\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 ,
[74] (/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [75] [76]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [77]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [78]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (11.68091pt too wide) in paragraph at lines 4166--4168
[][][]$\T1/fi4/m/n/10 http : / / www . ncbi . nlm . nih . gov / geo / query / a
cc . cgi ? acc = GSE2034$[][] [][]$http : / / www . ncbi . nlm . nih .
[79] (/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) [80]
(/usr/local/texlive/2013/texmf-dist/tex/latex/base/utf8.def) (./Rd2.ind
[81]
LaTeX Font Warning: Font shape `T1/fi4/m/it' undefined
(Font) using `T1/fi4/m/n' instead on input line 90.
[82] [83] [84]) (./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/2013/texmf-dist/fonts/enc/dvips/base/8r.enc}{/usr/local/tex
live/2013/texmf-dist/fonts/enc/dvips/inconsolata/fi4-ec.enc}</usr/local/texlive
/2013/texmf-dist/fonts/type1/public/inconsolata/Inconsolata.pfb></usr/local/tex
live/2013/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/local/texl
ive/2013/texmf-dist/fonts/type1/urw/helvetic/uhvr8a.pfb></usr/local/texlive/201
3/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></usr/local/texlive/2013/texmf-di
st/fonts/type1/urw/times/utmr8a.pfb></usr/local/texlive/2013/texmf-dist/fonts/t
ype1/urw/times/utmr8a.pfb></usr/local/texlive/2013/texmf-dist/fonts/type1/urw/t
imes/utmri8a.pfb>
Output written on Rd2.pdf (84 pages, 272705 bytes).
Transcript written on Rd2.log.
Saving output to ‘/private/tmp/RtmpNAYt2B/Rbuilda3bf46df0dba/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_2.3.1.tar.gz’
