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 487/658HostnameOS / ArchBUILDCHECKBUILD BIN
predictionet 1.5.0
Benjamin Haibe-Kains , Catharina Olsen
Snapshot Date: 2013-03-23 17:02:20 -0700 (Sat, 23 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/predictionet
Last Changed Rev: 70052 / Revision: 74756
Last Changed Date: 2012-10-01 15:43:56 -0700 (Mon, 01 Oct 2012)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 N O T   S U P P O R T E D
petty Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 
pelham Mac OS X Snow Leopard (10.6.8) / x86_64 [ OK ] OK  OK 

Summary

Package: predictionet
Version: 1.5.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data predictionet
StartedAt: 2013-03-23 23:58:11 -0700 (Sat, 23 Mar 2013)
EndedAt: 2013-03-23 23:59:56 -0700 (Sat, 23 Mar 2013)
EllapsedTime: 105.0 seconds
RetCode: 0
Status:  OK 
PackageFile: predictionet_1.5.0.tar.gz
PackageFileSize: 2.703 MiB

Command output

* checking for file 'predictionet/DESCRIPTION' ... OK
* preparing 'predictionet':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to process help pages
* building the PDF package manual
Hmm ... looks like a package
Converting Rd files to LaTeX .
Creating pdf output from LaTeX ...

This is pdfTeX, Version 3.1415926-2.4-1.40.13 (TeX Live 2012)
 \write18 enabled.
entering extended mode
(/private/tmp/RtmpjS8fF5/Rbuild2393318dd8c7/predictionet/.Rd2pdf9107/Rd2.tex
LaTeX2e <2011/06/27>
Babel <v3.8m> and hyphenation patterns for english, dumylang, nohyphenation, ge
rman-x-2012-05-30, ngerman-x-2012-05-30, afrikaans, ancientgreek, ibycus, arabi
c, armenian, basque, bulgarian, catalan, pinyin, coptic, croatian, czech, danis
h, dutch, ukenglish, usenglishmax, esperanto, estonian, ethiopic, farsi, finnis
h, french, friulan, galician, german, ngerman, swissgerman, monogreek, greek, h
ungarian, icelandic, assamese, bengali, gujarati, hindi, kannada, malayalam, ma
rathi, oriya, panjabi, tamil, telugu, indonesian, interlingua, irish, italian, 
kurmanji, latin, latvian, lithuanian, mongolian, mongolianlmc, bokmal, nynorsk,
 polish, portuguese, romanian, romansh, russian, sanskrit, serbian, serbianc, s
lovak, slovenian, spanish, swedish, turkish, turkmen, ukrainian, uppersorbian, 
welsh, loaded.
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/book.cls
Document Class: book 2007/10/19 v1.4h Standard LaTeX document class
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/bk10.clo))
(/Library/Frameworks/R.framework/Resources/share/texmf/tex/latex/Rd.sty
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/ifthen.sty)
(/usr/local/texlive/2012/texmf-dist/tex/latex/tools/longtable.sty)
(/usr/local/texlive/2012/texmf-dist/tex/latex/tools/bm.sty)
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/alltt.sty)
(/usr/local/texlive/2012/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/local/texlive/2012/texmf-dist/tex/latex/url/url.sty) NOT loading ae
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/fontenc.sty
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/t1enc.def))
(/usr/local/texlive/2012/texmf-dist/tex/latex/psnfss/times.sty)
NOT loading lmodern
(/usr/local/texlive/2012/texmf-dist/tex/latex/inconsolata/inconsolata.sty
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/textcomp.sty
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/ts1enc.def))
(/usr/local/texlive/2012/texmf-dist/tex/latex/graphics/keyval.sty))
(/usr/local/texlive/2012/texmf-dist/tex/latex/graphics/color.sty
(/usr/local/texlive/2012/texmf-dist/tex/latex/latexconfig/color.cfg)
(/usr/local/texlive/2012/texmf-dist/tex/latex/pdftex-def/pdftex.def
(/usr/local/texlive/2012/texmf-dist/tex/generic/oberdiek/infwarerr.sty)
(/usr/local/texlive/2012/texmf-dist/tex/generic/oberdiek/ltxcmds.sty)))
(/usr/local/texlive/2012/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/local/texlive/2012/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
(/usr/local/texlive/2012/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty))
(/usr/local/texlive/2012/texmf-dist/tex/generic/ifxetex/ifxetex.sty)
(/usr/local/texlive/2012/texmf-dist/tex/latex/oberdiek/kvoptions.sty)
(/usr/local/texlive/2012/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/local/texlive/2012/texmf-dist/tex/latex/latexconfig/hyperref.cfg))

Package hyperref Message: Driver (autodetected): hpdftex.

(/usr/local/texlive/2012/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/local/texlive/2012/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty))

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


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

) (/usr/local/texlive/2012/texmf-dist/tex/latex/base/makeidx.sty)
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/inputenc.sty
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/t1enc.dfu)
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/ot1enc.dfu)
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/omsenc.dfu)
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/ts1enc.dfu))
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/latin1.def))
Writing index file Rd2.idx
No file Rd2.aux.
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/ts1cmr.fd)
(/usr/local/texlive/2012/texmf-dist/tex/latex/psnfss/t1ptm.fd)
(/usr/local/texlive/2012/texmf-dist/tex/context/base/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/local/texlive/2012/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/local/texlive/2012/texmf-dist/tex/generic/oberdiek/gettitlestring.sty))
(/usr/local/texlive/2012/texmf-dist/tex/latex/inconsolata/t1fi4.fd)
(/usr/local/texlive/2012/texmf-dist/tex/latex/psnfss/t1phv.fd)
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def) [1{/usr/local/texl
ive/2012/texmf-var/fonts/map/pdftex/updmap/pdftex.map}]
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def) [2]
Overfull \hbox (140.28088pt too wide) in paragraph at lines 117--117
 []\T1/fi4/m/n/9 mytopo <- matrix(sample(0:1, 100, replace=TRUE, prob=c(0.7,0.3
)), nrow=10, dimnames=list(LETTERS[1:10], LETTERS[1:10]))[] 
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def) [3]
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def) [4]
Overfull \hbox (176.28088pt too wide) in paragraph at lines 208--208
 []\T1/fi4/m/n/9 ## load gene expression data for colon cancer data, list of ge
nes related to RAS signaling pathway and the corresponding priors[] 

Overfull \hbox (612.78088pt too wide) in paragraph at lines 213--213
 []\T1/fi4/m/n/9 cuts.discr <- lapply(apply(rbind("nbcat"=categories, data.ras)
, 2, function(x) { y <- x[1]; x <- x[-1]; return(list(quantile(x=x, probs=seq(0
, 1, length.out=y+1), na.rm=TRUE)[-c(1, y+1)])) }), function(x) { return(x[[1]]
) })[] 
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (13.78735pt too wide) in paragraph at lines 234--235
[]\T1/ptm/m/n/10 Inferred topol-ogy, an edge be-tween to vari-ables X and Y cor
-re-sponds to net[X,Y]=1. 
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def) [5]
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def) [6]
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def) [7]
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (144.78088pt too wide) in paragraph at lines 392--392
 []\T1/fi4/m/n/10 net2pred(net, data, categories, predn, perturbations, method 
= c("linear", "linear.penalized", "cpt"), seed)[] 
[8]
Overfull \hbox (25.18864pt too wide) in paragraph at lines 403--404
[]\T1/ptm/m/n/10 type of pre-dic-tive model to fit; \T1/fi4/m/n/10 linear \T1/p
tm/m/n/10 for lin-ear re-gres-sion model, \T1/fi4/m/n/10 linear.penalized

Overfull \hbox (176.28088pt too wide) in paragraph at lines 418--418
 []\T1/fi4/m/n/9 ## load gene expression data for colon cancer data, list of ge
nes related to RAS signaling pathway and the corresponding priors[] 

Overfull \hbox (0.78088pt too wide) in paragraph at lines 421--421
 []\T1/fi4/m/n/9 pert <- matrix(0, nrow=nrow(data.ras), ncol=ncol(data.ras), di
mnames=dimnames(data.ras))[] 

Overfull \hbox (68.28088pt too wide) in paragraph at lines 426--426
 []\T1/fi4/m/n/9 goi <- dimnames(annot.ras)[[1]][order(abs(log2(annot.ras[ ,"fo
ld.change"])), decreasing=TRUE)[1:genen]][] 

Overfull \hbox (248.28088pt too wide) in paragraph at lines 437--437
 []\T1/fi4/m/n/9 mynet <- netinf(data=mydata, perturbations=mypert, priors=mypr
iors, priors.count=TRUE, priors.weight=0.5, maxparents=3, method="regrnet", see
d)[] 
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (1174.78088pt too wide) in paragraph at lines 452--452
 []\T1/fi4/m/n/10 netinf(data, categories, perturbations, priors, predn, priors
.count = TRUE, priors.weight = 0.5, maxparents = 3, subset, method = c("regrnet
", "bayesnet"), ensemble = FALSE, ensemble.model = c("full","best"), ensemble.m
axnsol = 3, causal=TRUE, seed, bayesnet.maxcomplexity=0, bayesnet.maxiter=100, 
verbose = FALSE)[] 
[9]
Overfull \hbox (30.51768pt too wide) in paragraph at lines 469--470
\T1/ptm/m/n/10 iden-tify all the sta-tis-ti-cally equiv-a-lent net-works, it \T
1/fi4/m/n/10 best \T1/ptm/m/n/10 only the top \T1/fi4/m/n/10 ensemble.maxnsol
[10]
Overfull \hbox (176.28088pt too wide) in paragraph at lines 501--501
 []\T1/fi4/m/n/9 ## load gene expression data for colon cancer data, list of ge
nes related to RAS signaling pathway and the corresponding priors[] 

Overfull \hbox (0.78088pt too wide) in paragraph at lines 504--504
 []\T1/fi4/m/n/9 pert <- matrix(0, nrow=nrow(data.ras), ncol=ncol(data.ras), di
mnames=dimnames(data.ras))[] 

Overfull \hbox (68.28088pt too wide) in paragraph at lines 509--509
 []\T1/fi4/m/n/9 goi <- dimnames(annot.ras)[[1]][order(abs(log2(annot.ras[ ,"fo
ld.change"])), decreasing=TRUE)[1:genen]][] 

Overfull \hbox (275.28088pt too wide) in paragraph at lines 520--520
 []\T1/fi4/m/n/9 mynet <- netinf(data=mydata, perturbations=mypert, priors=mypr
iors, priors.count=TRUE, priors.weight=0.5, maxparents=3, method="regrnet", see
d=54321)[] 

Overfull \hbox (135.78088pt too wide) in paragraph at lines 525--525
 []\T1/fi4/m/n/9 xnet <- network(x=mytopo, matrix.type="adjacency", directed=TR
UE, loops=FALSE, vertex.attrnames=dimnames(mytopo)[[1]])[] 

Overfull \hbox (383.28088pt too wide) in paragraph at lines 526--526
 []\T1/fi4/m/n/9 plot.network(x=xnet, displayisolates=TRUE, displaylabels=TRUE,
 boxed.labels=FALSE, label.pos=0, arrowhead.cex=2, vertex.cex=4, vertex.col="ro
yalblue", jitter=FALSE, pad=0.5)[] 
[11]
Overfull \hbox (603.78088pt too wide) in paragraph at lines 537--537
 []\T1/fi4/m/n/9 cuts.discr <- lapply(apply(rbind("nbcat"=categories, mydata), 
2, function(x) { y <- x[1]; x <- x[-1]; return(list(quantile(x=x, probs=seq(0, 
1, length.out=y+1), na.rm=TRUE)[-c(1, y+1)])) }), function(x) { return(x[[1]]) 
})[] 

Overfull \hbox (333.78088pt too wide) in paragraph at lines 541--541
 []\T1/fi4/m/n/9 ## Not run: mynet <- netinf(data=mydata, perturbations=mypert,
 priors=mypriors, priors.count=TRUE, priors.weight=0.5, maxparents=3, method="b
ayesnet", seed=54321)[] 

Overfull \hbox (189.78088pt too wide) in paragraph at lines 546--546
 []\T1/fi4/m/n/9 ## Not run: xnet <- network(x=mytopo, matrix.type="adjacency",
 directed=TRUE, loops=FALSE, vertex.attrnames=dimnames(mytopo)[[1]])[] 

Overfull \hbox (437.28088pt too wide) in paragraph at lines 547--547
 []\T1/fi4/m/n/9 ## Not run: plot.network(x=xnet, displayisolates=TRUE, display
labels=TRUE, boxed.labels=FALSE, label.pos=0, arrowhead.cex=2, vertex.cex=4, ve
rtex.col="royalblue", jitter=FALSE, pad=0.5)[] 
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (1354.78088pt too wide) in paragraph at lines 563--563
 []\T1/fi4/m/n/10 netinf.cv(data, categories, perturbations, priors, predn, pri
ors.count = TRUE, priors.weight = 0.5, maxparents = 3, subset, method = c("regr
net", "bayesnet"), ensemble = FALSE, ensemble.maxnsol=3, predmodel = c("linear"
, "linear.penalized", "cpt"), nfold = 10, causal = TRUE, seed, bayesnet.maxcomp
lexity = 0, bayesnet.maxiter = 100, verbose = FALSE)[] 
[12]
Overfull \hbox (25.18864pt too wide) in paragraph at lines 581--582
[]\T1/ptm/m/n/10 type of pre-dic-tive model to fit; \T1/fi4/m/n/10 linear \T1/p
tm/m/n/10 for lin-ear re-gres-sion model, \T1/fi4/m/n/10 linear.penalized
[13]
Overfull \hbox (176.28088pt too wide) in paragraph at lines 616--616
 []\T1/fi4/m/n/9 ## load gene expression data for colon cancer data, list of ge
nes related to RAS signaling pathway and the corresponding priors[] 

Overfull \hbox (0.78088pt too wide) in paragraph at lines 619--619
 []\T1/fi4/m/n/9 pert <- matrix(0, nrow=nrow(data.ras), ncol=ncol(data.ras), di
mnames=dimnames(data.ras))[] 

Overfull \hbox (68.28088pt too wide) in paragraph at lines 624--624
 []\T1/fi4/m/n/9 goi <- dimnames(annot.ras)[[1]][order(abs(log2(annot.ras[ ,"fo
ld.change"])), decreasing=TRUE)[1:genen]][] 

Overfull \hbox (234.78088pt too wide) in paragraph at lines 635--635
 []\T1/fi4/m/n/9 res <- netinf.cv(data=mydata, categories=3, perturbations=mype
rt, priors=mypriors, priors.weight=0.5, method="regrnet", nfold=3, seed=54321)[
] 

Overfull \hbox (378.78088pt too wide) in paragraph at lines 648--648
 []\T1/fi4/m/n/9 ## Not run: res <- netinf.cv(data=mydata, categories=3, pertur
bations=mypert, priors=mypriors, priors.count=TRUE, priors.weight=0.5, method="
bayesnet", nfold=3, seed=54321)[] 
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def) [14]
Overfull \hbox (174.78088pt too wide) in paragraph at lines 668--668
 []\T1/fi4/m/n/10 netinf.predict(net, data, categories, perturbations, subset, 
predn, method=c("linear", "linear.penalized", "cpt"))[] 

Overfull \hbox (176.28088pt too wide) in paragraph at lines 694--694
 []\T1/fi4/m/n/9 ## load gene expression data for colon cancer data, list of ge
nes related to RAS signaling pathway and the corresponding priors[] 

Overfull \hbox (68.28088pt too wide) in paragraph at lines 699--699
 []\T1/fi4/m/n/9 goi <- dimnames(annot.ras)[[1]][order(abs(log2(annot.ras[ ,"fo
ld.change"])), decreasing=TRUE)[1:genen]][] 

Overfull \hbox (176.28088pt too wide) in paragraph at lines 705--705
 []\T1/fi4/m/n/9 mynet <- netinf(data=mydata, priors=mypriors, priors.count=TRU
E, priors.weight=0.5, maxparents=3, method="regrnet", seed=54321)[] 
[15]
Overfull \hbox (45.78088pt too wide) in paragraph at lines 714--714
 []\T1/fi4/m/n/9 plot(mydata[ ,goi[1]], mypreds, xlab="Observed gene expression
", ylab="Predicted gene expression")[] 
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (176.28088pt too wide) in paragraph at lines 766--766
 []\T1/fi4/m/n/9 ## load gene expression data for colon cancer data, list of ge
nes related to RAS signaling pathway and the corresponding priors[] 
[16]
Overfull \hbox (68.28088pt too wide) in paragraph at lines 771--771
 []\T1/fi4/m/n/9 goi <- dimnames(annot.ras)[[1]][order(abs(log2(annot.ras[ ,"fo
ld.change"])), decreasing=TRUE)[1:genen]][] 

Overfull \hbox (293.28088pt too wide) in paragraph at lines 777--777
 []\T1/fi4/m/n/9 mynet <- netinf.cv(data=mydata, categories=3, priors=mypriors,
 priors.count=TRUE, priors.weight=0.5, maxparents=3, method="regrnet", nfold=3,
 seed=54321)[] 
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def) [17]
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (176.28088pt too wide) in paragraph at lines 872--872
 []\T1/fi4/m/n/9 ## load gene expression data for colon cancer data, list of ge
nes related to RAS signaling pathway and the corresponding priors[] 

Overfull \hbox (0.78088pt too wide) in paragraph at lines 875--875
 []\T1/fi4/m/n/9 pert <- matrix(0, nrow=nrow(data.ras), ncol=ncol(data.ras), di
mnames=dimnames(data.ras))[] 
[18]
Overfull \hbox (68.28088pt too wide) in paragraph at lines 880--880
 []\T1/fi4/m/n/9 goi <- dimnames(annot.ras)[[1]][order(abs(log2(annot.ras[ ,"fo
ld.change"])), decreasing=TRUE)[1:genen]][] 

Overfull \hbox (234.78088pt too wide) in paragraph at lines 891--891
 []\T1/fi4/m/n/9 res <- netinf.cv(data=mydata, categories=3, perturbations=mype
rt, priors=mypriors, priors.weight=0.5, method="regrnet", nfold=3, seed=54321)[
] 

Overfull \hbox (378.78088pt too wide) in paragraph at lines 904--904
 []\T1/fi4/m/n/9 ## Not run: res <- netinf.cv(data=mydata, categories=3, pertur
bations=mypert, priors=mypriors, priors.count=TRUE, priors.weight=0.5, method="
bayesnet", nfold=3, seed=54321)[] 
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (1099.78088pt too wide) in paragraph at lines 924--924
 []\T1/fi4/m/n/10 predictionet.stability.cv(data, categories, perturbations, pr
iors, predn, priors.count = TRUE, priors.weight = 0.5, maxparents = 3, subset, 
method = c("regrnet", "bayesnet"), ensemble = FALSE, ensemble.maxnsol = 3, nfol
d = 10, causal = TRUE, seed, bayesnet.maxcomplexity = 0, bayesnet.maxiter = 100
)[] 
[19]
Overfull \hbox (176.28088pt too wide) in paragraph at lines 966--966
 []\T1/fi4/m/n/9 ## load gene expression data for colon cancer data, list of ge
nes related to RAS signaling pathway and the corresponding priors[] 
[20]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 969--969
 []\T1/fi4/m/n/9 pert <- matrix(0, nrow=nrow(data.ras), ncol=ncol(data.ras), di
mnames=dimnames(data.ras))[] 

Overfull \hbox (68.28088pt too wide) in paragraph at lines 974--974
 []\T1/fi4/m/n/9 goi <- dimnames(annot.ras)[[1]][order(abs(log2(annot.ras[ ,"fo
ld.change"])), decreasing=TRUE)[1:genen]][] 

Overfull \hbox (230.28088pt too wide) in paragraph at lines 985--985
 []\T1/fi4/m/n/9 res <-netinf.cv(data=mydata, categories=3, perturbations=myper
t, priors=mypriors, priors.weight=0.5, method="regrnet", nfold=3, seed=54321)[]
 

Overfull \hbox (378.78088pt too wide) in paragraph at lines 998--998
 []\T1/fi4/m/n/9 ## Not run: res <- netinf.cv(data=mydata, categories=3, pertur
bations=mypert, priors=mypriors, priors.count=TRUE, priors.weight=0.5, method="
bayesnet", nfold=3, seed=54321)[] 
No file Rd2.ind.
[21] (./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.igraph} has been referenced but does not exist, replaced by a fixed one

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

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

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

{/usr/local/texlive/2012/texmf-dist/fonts/enc/dvips/base/8r.enc}{/usr/local/tex
live/2012/texmf-dist/fonts/enc/dvips/inconsolata/fi4-ec.enc}</usr/local/texlive
/2012/texmf-dist/fonts/type1/public/inconsolata/Inconsolata.pfb></usr/local/tex
live/2012/texmf-dist/fonts/type1/urw/helvetic/uhvr8a.pfb></usr/local/texlive/20
12/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></usr/local/texlive/2012/texmf-d
ist/fonts/type1/urw/times/utmr8a.pfb></usr/local/texlive/2012/texmf-dist/fonts/
type1/urw/times/utmr8a.pfb></usr/local/texlive/2012/texmf-dist/fonts/type1/urw/
times/utmri8a.pfb>
Output written on Rd2.pdf (21 pages, 113603 bytes).
Transcript written on Rd2.log.
This is makeindex, version 2.15 [TeX Live 2012] (kpathsea + Thai support).
Scanning input file ./Rd2.idx....done (56 entries accepted, 0 rejected).
Sorting entries....done (331 comparisons).
Generating output file ./Rd2.ind....done (101 lines written, 2 warnings).
Output written in ./Rd2.ind.
Transcript written in ./Rd2.ilg.
This is pdfTeX, Version 3.1415926-2.4-1.40.13 (TeX Live 2012)
 \write18 enabled.
entering extended mode
(/private/tmp/RtmpjS8fF5/Rbuild2393318dd8c7/predictionet/.Rd2pdf9107/Rd2.tex
LaTeX2e <2011/06/27>
Babel <v3.8m> and hyphenation patterns for english, dumylang, nohyphenation, ge
rman-x-2012-05-30, ngerman-x-2012-05-30, afrikaans, ancientgreek, ibycus, arabi
c, armenian, basque, bulgarian, catalan, pinyin, coptic, croatian, czech, danis
h, dutch, ukenglish, usenglishmax, esperanto, estonian, ethiopic, farsi, finnis
h, french, friulan, galician, german, ngerman, swissgerman, monogreek, greek, h
ungarian, icelandic, assamese, bengali, gujarati, hindi, kannada, malayalam, ma
rathi, oriya, panjabi, tamil, telugu, indonesian, interlingua, irish, italian, 
kurmanji, latin, latvian, lithuanian, mongolian, mongolianlmc, bokmal, nynorsk,
 polish, portuguese, romanian, romansh, russian, sanskrit, serbian, serbianc, s
lovak, slovenian, spanish, swedish, turkish, turkmen, ukrainian, uppersorbian, 
welsh, loaded.
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/book.cls
Document Class: book 2007/10/19 v1.4h Standard LaTeX document class
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/bk10.clo))
(/Library/Frameworks/R.framework/Resources/share/texmf/tex/latex/Rd.sty
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/ifthen.sty)
(/usr/local/texlive/2012/texmf-dist/tex/latex/tools/longtable.sty)
(/usr/local/texlive/2012/texmf-dist/tex/latex/tools/bm.sty)
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/alltt.sty)
(/usr/local/texlive/2012/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/local/texlive/2012/texmf-dist/tex/latex/url/url.sty) NOT loading ae
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/fontenc.sty
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/t1enc.def))
(/usr/local/texlive/2012/texmf-dist/tex/latex/psnfss/times.sty)
NOT loading lmodern
(/usr/local/texlive/2012/texmf-dist/tex/latex/inconsolata/inconsolata.sty
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/textcomp.sty
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/ts1enc.def))
(/usr/local/texlive/2012/texmf-dist/tex/latex/graphics/keyval.sty))
(/usr/local/texlive/2012/texmf-dist/tex/latex/graphics/color.sty
(/usr/local/texlive/2012/texmf-dist/tex/latex/latexconfig/color.cfg)
(/usr/local/texlive/2012/texmf-dist/tex/latex/pdftex-def/pdftex.def
(/usr/local/texlive/2012/texmf-dist/tex/generic/oberdiek/infwarerr.sty)
(/usr/local/texlive/2012/texmf-dist/tex/generic/oberdiek/ltxcmds.sty)))
(/usr/local/texlive/2012/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/local/texlive/2012/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
(/usr/local/texlive/2012/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty))
(/usr/local/texlive/2012/texmf-dist/tex/generic/ifxetex/ifxetex.sty)
(/usr/local/texlive/2012/texmf-dist/tex/latex/oberdiek/kvoptions.sty)
(/usr/local/texlive/2012/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/local/texlive/2012/texmf-dist/tex/latex/latexconfig/hyperref.cfg))

Package hyperref Message: Driver (autodetected): hpdftex.

(/usr/local/texlive/2012/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/local/texlive/2012/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty))

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


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

) (/usr/local/texlive/2012/texmf-dist/tex/latex/base/makeidx.sty)
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/inputenc.sty
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/t1enc.dfu)
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/ot1enc.dfu)
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/omsenc.dfu)
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/ts1enc.dfu))
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/latin1.def))
Writing index file Rd2.idx
(./Rd2.aux) (/usr/local/texlive/2012/texmf-dist/tex/latex/base/ts1cmr.fd)
(/usr/local/texlive/2012/texmf-dist/tex/latex/psnfss/t1ptm.fd)
(/usr/local/texlive/2012/texmf-dist/tex/context/base/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/local/texlive/2012/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/local/texlive/2012/texmf-dist/tex/generic/oberdiek/gettitlestring.sty))
(./Rd2.out) (./Rd2.out)
(/usr/local/texlive/2012/texmf-dist/tex/latex/inconsolata/t1fi4.fd)
(/usr/local/texlive/2012/texmf-dist/tex/latex/psnfss/t1phv.fd) (./Rd2.toc
[1{/usr/local/texlive/2012/texmf-var/fonts/map/pdftex/updmap/pdftex.map}])
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def) [2]
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (140.28088pt too wide) in paragraph at lines 117--117
 []\T1/fi4/m/n/9 mytopo <- matrix(sample(0:1, 100, replace=TRUE, prob=c(0.7,0.3
)), nrow=10, dimnames=list(LETTERS[1:10], LETTERS[1:10]))[] 
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def) [3]
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def) [4]
Overfull \hbox (176.28088pt too wide) in paragraph at lines 208--208
 []\T1/fi4/m/n/9 ## load gene expression data for colon cancer data, list of ge
nes related to RAS signaling pathway and the corresponding priors[] 

Overfull \hbox (612.78088pt too wide) in paragraph at lines 213--213
 []\T1/fi4/m/n/9 cuts.discr <- lapply(apply(rbind("nbcat"=categories, data.ras)
, 2, function(x) { y <- x[1]; x <- x[-1]; return(list(quantile(x=x, probs=seq(0
, 1, length.out=y+1), na.rm=TRUE)[-c(1, y+1)])) }), function(x) { return(x[[1]]
) })[] 
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def) [5]
Overfull \hbox (13.78735pt too wide) in paragraph at lines 234--235
[]\T1/ptm/m/n/10 Inferred topol-ogy, an edge be-tween to vari-ables X and Y cor
-re-sponds to net[X,Y]=1. 
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def) [6]
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def) [7]
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (144.78088pt too wide) in paragraph at lines 392--392
 []\T1/fi4/m/n/10 net2pred(net, data, categories, predn, perturbations, method 
= c("linear", "linear.penalized", "cpt"), seed)[] 
[8]
Overfull \hbox (25.18864pt too wide) in paragraph at lines 403--404
[]\T1/ptm/m/n/10 type of pre-dic-tive model to fit; \T1/fi4/m/n/10 linear \T1/p
tm/m/n/10 for lin-ear re-gres-sion model, \T1/fi4/m/n/10 linear.penalized

Overfull \hbox (176.28088pt too wide) in paragraph at lines 418--418
 []\T1/fi4/m/n/9 ## load gene expression data for colon cancer data, list of ge
nes related to RAS signaling pathway and the corresponding priors[] 

Overfull \hbox (0.78088pt too wide) in paragraph at lines 421--421
 []\T1/fi4/m/n/9 pert <- matrix(0, nrow=nrow(data.ras), ncol=ncol(data.ras), di
mnames=dimnames(data.ras))[] 

Overfull \hbox (68.28088pt too wide) in paragraph at lines 426--426
 []\T1/fi4/m/n/9 goi <- dimnames(annot.ras)[[1]][order(abs(log2(annot.ras[ ,"fo
ld.change"])), decreasing=TRUE)[1:genen]][] 
[9]
Overfull \hbox (248.28088pt too wide) in paragraph at lines 437--437
 []\T1/fi4/m/n/9 mynet <- netinf(data=mydata, perturbations=mypert, priors=mypr
iors, priors.count=TRUE, priors.weight=0.5, maxparents=3, method="regrnet", see
d)[] 
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (1174.78088pt too wide) in paragraph at lines 452--452
 []\T1/fi4/m/n/10 netinf(data, categories, perturbations, priors, predn, priors
.count = TRUE, priors.weight = 0.5, maxparents = 3, subset, method = c("regrnet
", "bayesnet"), ensemble = FALSE, ensemble.model = c("full","best"), ensemble.m
axnsol = 3, causal=TRUE, seed, bayesnet.maxcomplexity=0, bayesnet.maxiter=100, 
verbose = FALSE)[] 
[10]
Overfull \hbox (30.51768pt too wide) in paragraph at lines 469--470
\T1/ptm/m/n/10 iden-tify all the sta-tis-ti-cally equiv-a-lent net-works, it \T
1/fi4/m/n/10 best \T1/ptm/m/n/10 only the top \T1/fi4/m/n/10 ensemble.maxnsol

Overfull \hbox (176.28088pt too wide) in paragraph at lines 501--501
 []\T1/fi4/m/n/9 ## load gene expression data for colon cancer data, list of ge
nes related to RAS signaling pathway and the corresponding priors[] 
[11]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 504--504
 []\T1/fi4/m/n/9 pert <- matrix(0, nrow=nrow(data.ras), ncol=ncol(data.ras), di
mnames=dimnames(data.ras))[] 

Overfull \hbox (68.28088pt too wide) in paragraph at lines 509--509
 []\T1/fi4/m/n/9 goi <- dimnames(annot.ras)[[1]][order(abs(log2(annot.ras[ ,"fo
ld.change"])), decreasing=TRUE)[1:genen]][] 

Overfull \hbox (275.28088pt too wide) in paragraph at lines 520--520
 []\T1/fi4/m/n/9 mynet <- netinf(data=mydata, perturbations=mypert, priors=mypr
iors, priors.count=TRUE, priors.weight=0.5, maxparents=3, method="regrnet", see
d=54321)[] 

Overfull \hbox (135.78088pt too wide) in paragraph at lines 525--525
 []\T1/fi4/m/n/9 xnet <- network(x=mytopo, matrix.type="adjacency", directed=TR
UE, loops=FALSE, vertex.attrnames=dimnames(mytopo)[[1]])[] 

Overfull \hbox (383.28088pt too wide) in paragraph at lines 526--526
 []\T1/fi4/m/n/9 plot.network(x=xnet, displayisolates=TRUE, displaylabels=TRUE,
 boxed.labels=FALSE, label.pos=0, arrowhead.cex=2, vertex.cex=4, vertex.col="ro
yalblue", jitter=FALSE, pad=0.5)[] 

Overfull \hbox (603.78088pt too wide) in paragraph at lines 537--537
 []\T1/fi4/m/n/9 cuts.discr <- lapply(apply(rbind("nbcat"=categories, mydata), 
2, function(x) { y <- x[1]; x <- x[-1]; return(list(quantile(x=x, probs=seq(0, 
1, length.out=y+1), na.rm=TRUE)[-c(1, y+1)])) }), function(x) { return(x[[1]]) 
})[] 

Overfull \hbox (333.78088pt too wide) in paragraph at lines 541--541
 []\T1/fi4/m/n/9 ## Not run: mynet <- netinf(data=mydata, perturbations=mypert,
 priors=mypriors, priors.count=TRUE, priors.weight=0.5, maxparents=3, method="b
ayesnet", seed=54321)[] 

Overfull \hbox (189.78088pt too wide) in paragraph at lines 546--546
 []\T1/fi4/m/n/9 ## Not run: xnet <- network(x=mytopo, matrix.type="adjacency",
 directed=TRUE, loops=FALSE, vertex.attrnames=dimnames(mytopo)[[1]])[] 

Overfull \hbox (437.28088pt too wide) in paragraph at lines 547--547
 []\T1/fi4/m/n/9 ## Not run: plot.network(x=xnet, displayisolates=TRUE, display
labels=TRUE, boxed.labels=FALSE, label.pos=0, arrowhead.cex=2, vertex.cex=4, ve
rtex.col="royalblue", jitter=FALSE, pad=0.5)[] 
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def) [12]
Overfull \hbox (1354.78088pt too wide) in paragraph at lines 563--563
 []\T1/fi4/m/n/10 netinf.cv(data, categories, perturbations, priors, predn, pri
ors.count = TRUE, priors.weight = 0.5, maxparents = 3, subset, method = c("regr
net", "bayesnet"), ensemble = FALSE, ensemble.maxnsol=3, predmodel = c("linear"
, "linear.penalized", "cpt"), nfold = 10, causal = TRUE, seed, bayesnet.maxcomp
lexity = 0, bayesnet.maxiter = 100, verbose = FALSE)[] 

Overfull \hbox (25.18864pt too wide) in paragraph at lines 581--582
[]\T1/ptm/m/n/10 type of pre-dic-tive model to fit; \T1/fi4/m/n/10 linear \T1/p
tm/m/n/10 for lin-ear re-gres-sion model, \T1/fi4/m/n/10 linear.penalized
[13]
Overfull \hbox (176.28088pt too wide) in paragraph at lines 616--616
 []\T1/fi4/m/n/9 ## load gene expression data for colon cancer data, list of ge
nes related to RAS signaling pathway and the corresponding priors[] 

Overfull \hbox (0.78088pt too wide) in paragraph at lines 619--619
 []\T1/fi4/m/n/9 pert <- matrix(0, nrow=nrow(data.ras), ncol=ncol(data.ras), di
mnames=dimnames(data.ras))[] 

Overfull \hbox (68.28088pt too wide) in paragraph at lines 624--624
 []\T1/fi4/m/n/9 goi <- dimnames(annot.ras)[[1]][order(abs(log2(annot.ras[ ,"fo
ld.change"])), decreasing=TRUE)[1:genen]][] 
[14]
Overfull \hbox (234.78088pt too wide) in paragraph at lines 635--635
 []\T1/fi4/m/n/9 res <- netinf.cv(data=mydata, categories=3, perturbations=mype
rt, priors=mypriors, priors.weight=0.5, method="regrnet", nfold=3, seed=54321)[
] 

Overfull \hbox (378.78088pt too wide) in paragraph at lines 648--648
 []\T1/fi4/m/n/9 ## Not run: res <- netinf.cv(data=mydata, categories=3, pertur
bations=mypert, priors=mypriors, priors.count=TRUE, priors.weight=0.5, method="
bayesnet", nfold=3, seed=54321)[] 
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (174.78088pt too wide) in paragraph at lines 668--668
 []\T1/fi4/m/n/10 netinf.predict(net, data, categories, perturbations, subset, 
predn, method=c("linear", "linear.penalized", "cpt"))[] 
[15]
Overfull \hbox (176.28088pt too wide) in paragraph at lines 694--694
 []\T1/fi4/m/n/9 ## load gene expression data for colon cancer data, list of ge
nes related to RAS signaling pathway and the corresponding priors[] 

Overfull \hbox (68.28088pt too wide) in paragraph at lines 699--699
 []\T1/fi4/m/n/9 goi <- dimnames(annot.ras)[[1]][order(abs(log2(annot.ras[ ,"fo
ld.change"])), decreasing=TRUE)[1:genen]][] 

Overfull \hbox (176.28088pt too wide) in paragraph at lines 705--705
 []\T1/fi4/m/n/9 mynet <- netinf(data=mydata, priors=mypriors, priors.count=TRU
E, priors.weight=0.5, maxparents=3, method="regrnet", seed=54321)[] 

Overfull \hbox (45.78088pt too wide) in paragraph at lines 714--714
 []\T1/fi4/m/n/9 plot(mydata[ ,goi[1]], mypreds, xlab="Observed gene expression
", ylab="Predicted gene expression")[] 
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def) [16]
Overfull \hbox (176.28088pt too wide) in paragraph at lines 766--766
 []\T1/fi4/m/n/9 ## load gene expression data for colon cancer data, list of ge
nes related to RAS signaling pathway and the corresponding priors[] 

Overfull \hbox (68.28088pt too wide) in paragraph at lines 771--771
 []\T1/fi4/m/n/9 goi <- dimnames(annot.ras)[[1]][order(abs(log2(annot.ras[ ,"fo
ld.change"])), decreasing=TRUE)[1:genen]][] 

Overfull \hbox (293.28088pt too wide) in paragraph at lines 777--777
 []\T1/fi4/m/n/9 mynet <- netinf.cv(data=mydata, categories=3, priors=mypriors,
 priors.count=TRUE, priors.weight=0.5, maxparents=3, method="regrnet", nfold=3,
 seed=54321)[] 
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def) [17]
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def) [18]
Overfull \hbox (176.28088pt too wide) in paragraph at lines 872--872
 []\T1/fi4/m/n/9 ## load gene expression data for colon cancer data, list of ge
nes related to RAS signaling pathway and the corresponding priors[] 

Overfull \hbox (0.78088pt too wide) in paragraph at lines 875--875
 []\T1/fi4/m/n/9 pert <- matrix(0, nrow=nrow(data.ras), ncol=ncol(data.ras), di
mnames=dimnames(data.ras))[] 

Overfull \hbox (68.28088pt too wide) in paragraph at lines 880--880
 []\T1/fi4/m/n/9 goi <- dimnames(annot.ras)[[1]][order(abs(log2(annot.ras[ ,"fo
ld.change"])), decreasing=TRUE)[1:genen]][] 

Overfull \hbox (234.78088pt too wide) in paragraph at lines 891--891
 []\T1/fi4/m/n/9 res <- netinf.cv(data=mydata, categories=3, perturbations=mype
rt, priors=mypriors, priors.weight=0.5, method="regrnet", nfold=3, seed=54321)[
] 
[19]
Overfull \hbox (378.78088pt too wide) in paragraph at lines 904--904
 []\T1/fi4/m/n/9 ## Not run: res <- netinf.cv(data=mydata, categories=3, pertur
bations=mypert, priors=mypriors, priors.count=TRUE, priors.weight=0.5, method="
bayesnet", nfold=3, seed=54321)[] 
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (1099.78088pt too wide) in paragraph at lines 924--924
 []\T1/fi4/m/n/10 predictionet.stability.cv(data, categories, perturbations, pr
iors, predn, priors.count = TRUE, priors.weight = 0.5, maxparents = 3, subset, 
method = c("regrnet", "bayesnet"), ensemble = FALSE, ensemble.maxnsol = 3, nfol
d = 10, causal = TRUE, seed, bayesnet.maxcomplexity = 0, bayesnet.maxiter = 100
)[] 
[20]
Overfull \hbox (176.28088pt too wide) in paragraph at lines 966--966
 []\T1/fi4/m/n/9 ## load gene expression data for colon cancer data, list of ge
nes related to RAS signaling pathway and the corresponding priors[] 

Overfull \hbox (0.78088pt too wide) in paragraph at lines 969--969
 []\T1/fi4/m/n/9 pert <- matrix(0, nrow=nrow(data.ras), ncol=ncol(data.ras), di
mnames=dimnames(data.ras))[] 

Overfull \hbox (68.28088pt too wide) in paragraph at lines 974--974
 []\T1/fi4/m/n/9 goi <- dimnames(annot.ras)[[1]][order(abs(log2(annot.ras[ ,"fo
ld.change"])), decreasing=TRUE)[1:genen]][] 
[21]
Overfull \hbox (230.28088pt too wide) in paragraph at lines 985--985
 []\T1/fi4/m/n/9 res <-netinf.cv(data=mydata, categories=3, perturbations=myper
t, priors=mypriors, priors.weight=0.5, method="regrnet", nfold=3, seed=54321)[]
 

Overfull \hbox (378.78088pt too wide) in paragraph at lines 998--998
 []\T1/fi4/m/n/9 ## Not run: res <- netinf.cv(data=mydata, categories=3, pertur
bations=mypert, priors=mypriors, priors.count=TRUE, priors.weight=0.5, method="
bayesnet", nfold=3, seed=54321)[] 
(./Rd2.ind [22]

LaTeX Font Warning: Font shape `T1/fi4/m/it' undefined
(Font)              using `T1/fi4/m/n' instead on input line 33.

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

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

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

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

{/usr/local/texlive/2012/texmf-dist/fonts/enc/dvips/base/8r.enc}{/usr/local/tex
live/2012/texmf-dist/fonts/enc/dvips/inconsolata/fi4-ec.enc}</usr/local/texlive
/2012/texmf-dist/fonts/type1/public/inconsolata/Inconsolata.pfb></usr/local/tex
live/2012/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/local/texl
ive/2012/texmf-dist/fonts/type1/urw/helvetic/uhvr8a.pfb></usr/local/texlive/201
2/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></usr/local/texlive/2012/texmf-di
st/fonts/type1/urw/times/utmr8a.pfb></usr/local/texlive/2012/texmf-dist/fonts/t
ype1/urw/times/utmr8a.pfb></usr/local/texlive/2012/texmf-dist/fonts/type1/urw/t
imes/utmri8a.pfb>
Output written on Rd2.pdf (23 pages, 126960 bytes).
Transcript written on Rd2.log.
This is makeindex, version 2.15 [TeX Live 2012] (kpathsea + Thai support).
Scanning input file ./Rd2.idx....done (56 entries accepted, 0 rejected).
Sorting entries....done (332 comparisons).
Generating output file ./Rd2.ind....done (101 lines written, 2 warnings).
Output written in ./Rd2.ind.
Transcript written in ./Rd2.ilg.
This is pdfTeX, Version 3.1415926-2.4-1.40.13 (TeX Live 2012)
 \write18 enabled.
entering extended mode
(/private/tmp/RtmpjS8fF5/Rbuild2393318dd8c7/predictionet/.Rd2pdf9107/Rd2.tex
LaTeX2e <2011/06/27>
Babel <v3.8m> and hyphenation patterns for english, dumylang, nohyphenation, ge
rman-x-2012-05-30, ngerman-x-2012-05-30, afrikaans, ancientgreek, ibycus, arabi
c, armenian, basque, bulgarian, catalan, pinyin, coptic, croatian, czech, danis
h, dutch, ukenglish, usenglishmax, esperanto, estonian, ethiopic, farsi, finnis
h, french, friulan, galician, german, ngerman, swissgerman, monogreek, greek, h
ungarian, icelandic, assamese, bengali, gujarati, hindi, kannada, malayalam, ma
rathi, oriya, panjabi, tamil, telugu, indonesian, interlingua, irish, italian, 
kurmanji, latin, latvian, lithuanian, mongolian, mongolianlmc, bokmal, nynorsk,
 polish, portuguese, romanian, romansh, russian, sanskrit, serbian, serbianc, s
lovak, slovenian, spanish, swedish, turkish, turkmen, ukrainian, uppersorbian, 
welsh, loaded.
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/book.cls
Document Class: book 2007/10/19 v1.4h Standard LaTeX document class
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/bk10.clo))
(/Library/Frameworks/R.framework/Resources/share/texmf/tex/latex/Rd.sty
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/ifthen.sty)
(/usr/local/texlive/2012/texmf-dist/tex/latex/tools/longtable.sty)
(/usr/local/texlive/2012/texmf-dist/tex/latex/tools/bm.sty)
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/alltt.sty)
(/usr/local/texlive/2012/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/local/texlive/2012/texmf-dist/tex/latex/url/url.sty) NOT loading ae
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/fontenc.sty
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/t1enc.def))
(/usr/local/texlive/2012/texmf-dist/tex/latex/psnfss/times.sty)
NOT loading lmodern
(/usr/local/texlive/2012/texmf-dist/tex/latex/inconsolata/inconsolata.sty
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/textcomp.sty
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/ts1enc.def))
(/usr/local/texlive/2012/texmf-dist/tex/latex/graphics/keyval.sty))
(/usr/local/texlive/2012/texmf-dist/tex/latex/graphics/color.sty
(/usr/local/texlive/2012/texmf-dist/tex/latex/latexconfig/color.cfg)
(/usr/local/texlive/2012/texmf-dist/tex/latex/pdftex-def/pdftex.def
(/usr/local/texlive/2012/texmf-dist/tex/generic/oberdiek/infwarerr.sty)
(/usr/local/texlive/2012/texmf-dist/tex/generic/oberdiek/ltxcmds.sty)))
(/usr/local/texlive/2012/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/local/texlive/2012/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
(/usr/local/texlive/2012/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty))
(/usr/local/texlive/2012/texmf-dist/tex/generic/ifxetex/ifxetex.sty)
(/usr/local/texlive/2012/texmf-dist/tex/latex/oberdiek/kvoptions.sty)
(/usr/local/texlive/2012/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/local/texlive/2012/texmf-dist/tex/latex/latexconfig/hyperref.cfg))

Package hyperref Message: Driver (autodetected): hpdftex.

(/usr/local/texlive/2012/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/local/texlive/2012/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty))

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


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

) (/usr/local/texlive/2012/texmf-dist/tex/latex/base/makeidx.sty)
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/inputenc.sty
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/t1enc.dfu)
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/ot1enc.dfu)
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/omsenc.dfu)
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/ts1enc.dfu))
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/latin1.def))
Writing index file Rd2.idx
(./Rd2.aux) (/usr/local/texlive/2012/texmf-dist/tex/latex/base/ts1cmr.fd)
(/usr/local/texlive/2012/texmf-dist/tex/latex/psnfss/t1ptm.fd)
(/usr/local/texlive/2012/texmf-dist/tex/context/base/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/local/texlive/2012/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/local/texlive/2012/texmf-dist/tex/generic/oberdiek/gettitlestring.sty))
(./Rd2.out) (./Rd2.out)
(/usr/local/texlive/2012/texmf-dist/tex/latex/inconsolata/t1fi4.fd)
(/usr/local/texlive/2012/texmf-dist/tex/latex/psnfss/t1phv.fd) (./Rd2.toc
[1{/usr/local/texlive/2012/texmf-var/fonts/map/pdftex/updmap/pdftex.map}])
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def) [2]
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (140.28088pt too wide) in paragraph at lines 117--117
 []\T1/fi4/m/n/9 mytopo <- matrix(sample(0:1, 100, replace=TRUE, prob=c(0.7,0.3
)), nrow=10, dimnames=list(LETTERS[1:10], LETTERS[1:10]))[] 
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def) [3]
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def) [4]
Overfull \hbox (176.28088pt too wide) in paragraph at lines 208--208
 []\T1/fi4/m/n/9 ## load gene expression data for colon cancer data, list of ge
nes related to RAS signaling pathway and the corresponding priors[] 

Overfull \hbox (612.78088pt too wide) in paragraph at lines 213--213
 []\T1/fi4/m/n/9 cuts.discr <- lapply(apply(rbind("nbcat"=categories, data.ras)
, 2, function(x) { y <- x[1]; x <- x[-1]; return(list(quantile(x=x, probs=seq(0
, 1, length.out=y+1), na.rm=TRUE)[-c(1, y+1)])) }), function(x) { return(x[[1]]
) })[] 
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def) [5]
Overfull \hbox (13.78735pt too wide) in paragraph at lines 234--235
[]\T1/ptm/m/n/10 Inferred topol-ogy, an edge be-tween to vari-ables X and Y cor
-re-sponds to net[X,Y]=1. 
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def) [6]
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def) [7]
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def)
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (144.78088pt too wide) in paragraph at lines 392--392
 []\T1/fi4/m/n/10 net2pred(net, data, categories, predn, perturbations, method 
= c("linear", "linear.penalized", "cpt"), seed)[] 
[8]
Overfull \hbox (25.18864pt too wide) in paragraph at lines 403--404
[]\T1/ptm/m/n/10 type of pre-dic-tive model to fit; \T1/fi4/m/n/10 linear \T1/p
tm/m/n/10 for lin-ear re-gres-sion model, \T1/fi4/m/n/10 linear.penalized

Overfull \hbox (176.28088pt too wide) in paragraph at lines 418--418
 []\T1/fi4/m/n/9 ## load gene expression data for colon cancer data, list of ge
nes related to RAS signaling pathway and the corresponding priors[] 

Overfull \hbox (0.78088pt too wide) in paragraph at lines 421--421
 []\T1/fi4/m/n/9 pert <- matrix(0, nrow=nrow(data.ras), ncol=ncol(data.ras), di
mnames=dimnames(data.ras))[] 

Overfull \hbox (68.28088pt too wide) in paragraph at lines 426--426
 []\T1/fi4/m/n/9 goi <- dimnames(annot.ras)[[1]][order(abs(log2(annot.ras[ ,"fo
ld.change"])), decreasing=TRUE)[1:genen]][] 
[9]
Overfull \hbox (248.28088pt too wide) in paragraph at lines 437--437
 []\T1/fi4/m/n/9 mynet <- netinf(data=mydata, perturbations=mypert, priors=mypr
iors, priors.count=TRUE, priors.weight=0.5, maxparents=3, method="regrnet", see
d)[] 
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (1174.78088pt too wide) in paragraph at lines 452--452
 []\T1/fi4/m/n/10 netinf(data, categories, perturbations, priors, predn, priors
.count = TRUE, priors.weight = 0.5, maxparents = 3, subset, method = c("regrnet
", "bayesnet"), ensemble = FALSE, ensemble.model = c("full","best"), ensemble.m
axnsol = 3, causal=TRUE, seed, bayesnet.maxcomplexity=0, bayesnet.maxiter=100, 
verbose = FALSE)[] 
[10]
Overfull \hbox (30.51768pt too wide) in paragraph at lines 469--470
\T1/ptm/m/n/10 iden-tify all the sta-tis-ti-cally equiv-a-lent net-works, it \T
1/fi4/m/n/10 best \T1/ptm/m/n/10 only the top \T1/fi4/m/n/10 ensemble.maxnsol

Overfull \hbox (176.28088pt too wide) in paragraph at lines 501--501
 []\T1/fi4/m/n/9 ## load gene expression data for colon cancer data, list of ge
nes related to RAS signaling pathway and the corresponding priors[] 
[11]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 504--504
 []\T1/fi4/m/n/9 pert <- matrix(0, nrow=nrow(data.ras), ncol=ncol(data.ras), di
mnames=dimnames(data.ras))[] 

Overfull \hbox (68.28088pt too wide) in paragraph at lines 509--509
 []\T1/fi4/m/n/9 goi <- dimnames(annot.ras)[[1]][order(abs(log2(annot.ras[ ,"fo
ld.change"])), decreasing=TRUE)[1:genen]][] 

Overfull \hbox (275.28088pt too wide) in paragraph at lines 520--520
 []\T1/fi4/m/n/9 mynet <- netinf(data=mydata, perturbations=mypert, priors=mypr
iors, priors.count=TRUE, priors.weight=0.5, maxparents=3, method="regrnet", see
d=54321)[] 

Overfull \hbox (135.78088pt too wide) in paragraph at lines 525--525
 []\T1/fi4/m/n/9 xnet <- network(x=mytopo, matrix.type="adjacency", directed=TR
UE, loops=FALSE, vertex.attrnames=dimnames(mytopo)[[1]])[] 

Overfull \hbox (383.28088pt too wide) in paragraph at lines 526--526
 []\T1/fi4/m/n/9 plot.network(x=xnet, displayisolates=TRUE, displaylabels=TRUE,
 boxed.labels=FALSE, label.pos=0, arrowhead.cex=2, vertex.cex=4, vertex.col="ro
yalblue", jitter=FALSE, pad=0.5)[] 

Overfull \hbox (603.78088pt too wide) in paragraph at lines 537--537
 []\T1/fi4/m/n/9 cuts.discr <- lapply(apply(rbind("nbcat"=categories, mydata), 
2, function(x) { y <- x[1]; x <- x[-1]; return(list(quantile(x=x, probs=seq(0, 
1, length.out=y+1), na.rm=TRUE)[-c(1, y+1)])) }), function(x) { return(x[[1]]) 
})[] 

Overfull \hbox (333.78088pt too wide) in paragraph at lines 541--541
 []\T1/fi4/m/n/9 ## Not run: mynet <- netinf(data=mydata, perturbations=mypert,
 priors=mypriors, priors.count=TRUE, priors.weight=0.5, maxparents=3, method="b
ayesnet", seed=54321)[] 

Overfull \hbox (189.78088pt too wide) in paragraph at lines 546--546
 []\T1/fi4/m/n/9 ## Not run: xnet <- network(x=mytopo, matrix.type="adjacency",
 directed=TRUE, loops=FALSE, vertex.attrnames=dimnames(mytopo)[[1]])[] 

Overfull \hbox (437.28088pt too wide) in paragraph at lines 547--547
 []\T1/fi4/m/n/9 ## Not run: plot.network(x=xnet, displayisolates=TRUE, display
labels=TRUE, boxed.labels=FALSE, label.pos=0, arrowhead.cex=2, vertex.cex=4, ve
rtex.col="royalblue", jitter=FALSE, pad=0.5)[] 
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def) [12]
Overfull \hbox (1354.78088pt too wide) in paragraph at lines 563--563
 []\T1/fi4/m/n/10 netinf.cv(data, categories, perturbations, priors, predn, pri
ors.count = TRUE, priors.weight = 0.5, maxparents = 3, subset, method = c("regr
net", "bayesnet"), ensemble = FALSE, ensemble.maxnsol=3, predmodel = c("linear"
, "linear.penalized", "cpt"), nfold = 10, causal = TRUE, seed, bayesnet.maxcomp
lexity = 0, bayesnet.maxiter = 100, verbose = FALSE)[] 

Overfull \hbox (25.18864pt too wide) in paragraph at lines 581--582
[]\T1/ptm/m/n/10 type of pre-dic-tive model to fit; \T1/fi4/m/n/10 linear \T1/p
tm/m/n/10 for lin-ear re-gres-sion model, \T1/fi4/m/n/10 linear.penalized
[13]
Overfull \hbox (176.28088pt too wide) in paragraph at lines 616--616
 []\T1/fi4/m/n/9 ## load gene expression data for colon cancer data, list of ge
nes related to RAS signaling pathway and the corresponding priors[] 

Overfull \hbox (0.78088pt too wide) in paragraph at lines 619--619
 []\T1/fi4/m/n/9 pert <- matrix(0, nrow=nrow(data.ras), ncol=ncol(data.ras), di
mnames=dimnames(data.ras))[] 

Overfull \hbox (68.28088pt too wide) in paragraph at lines 624--624
 []\T1/fi4/m/n/9 goi <- dimnames(annot.ras)[[1]][order(abs(log2(annot.ras[ ,"fo
ld.change"])), decreasing=TRUE)[1:genen]][] 
[14]
Overfull \hbox (234.78088pt too wide) in paragraph at lines 635--635
 []\T1/fi4/m/n/9 res <- netinf.cv(data=mydata, categories=3, perturbations=mype
rt, priors=mypriors, priors.weight=0.5, method="regrnet", nfold=3, seed=54321)[
] 

Overfull \hbox (378.78088pt too wide) in paragraph at lines 648--648
 []\T1/fi4/m/n/9 ## Not run: res <- netinf.cv(data=mydata, categories=3, pertur
bations=mypert, priors=mypriors, priors.count=TRUE, priors.weight=0.5, method="
bayesnet", nfold=3, seed=54321)[] 
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (174.78088pt too wide) in paragraph at lines 668--668
 []\T1/fi4/m/n/10 netinf.predict(net, data, categories, perturbations, subset, 
predn, method=c("linear", "linear.penalized", "cpt"))[] 
[15]
Overfull \hbox (176.28088pt too wide) in paragraph at lines 694--694
 []\T1/fi4/m/n/9 ## load gene expression data for colon cancer data, list of ge
nes related to RAS signaling pathway and the corresponding priors[] 

Overfull \hbox (68.28088pt too wide) in paragraph at lines 699--699
 []\T1/fi4/m/n/9 goi <- dimnames(annot.ras)[[1]][order(abs(log2(annot.ras[ ,"fo
ld.change"])), decreasing=TRUE)[1:genen]][] 

Overfull \hbox (176.28088pt too wide) in paragraph at lines 705--705
 []\T1/fi4/m/n/9 mynet <- netinf(data=mydata, priors=mypriors, priors.count=TRU
E, priors.weight=0.5, maxparents=3, method="regrnet", seed=54321)[] 

Overfull \hbox (45.78088pt too wide) in paragraph at lines 714--714
 []\T1/fi4/m/n/9 plot(mydata[ ,goi[1]], mypreds, xlab="Observed gene expression
", ylab="Predicted gene expression")[] 
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def) [16]
Overfull \hbox (176.28088pt too wide) in paragraph at lines 766--766
 []\T1/fi4/m/n/9 ## load gene expression data for colon cancer data, list of ge
nes related to RAS signaling pathway and the corresponding priors[] 

Overfull \hbox (68.28088pt too wide) in paragraph at lines 771--771
 []\T1/fi4/m/n/9 goi <- dimnames(annot.ras)[[1]][order(abs(log2(annot.ras[ ,"fo
ld.change"])), decreasing=TRUE)[1:genen]][] 

Overfull \hbox (293.28088pt too wide) in paragraph at lines 777--777
 []\T1/fi4/m/n/9 mynet <- netinf.cv(data=mydata, categories=3, priors=mypriors,
 priors.count=TRUE, priors.weight=0.5, maxparents=3, method="regrnet", nfold=3,
 seed=54321)[] 
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def) [17]
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def) [18]
Overfull \hbox (176.28088pt too wide) in paragraph at lines 872--872
 []\T1/fi4/m/n/9 ## load gene expression data for colon cancer data, list of ge
nes related to RAS signaling pathway and the corresponding priors[] 

Overfull \hbox (0.78088pt too wide) in paragraph at lines 875--875
 []\T1/fi4/m/n/9 pert <- matrix(0, nrow=nrow(data.ras), ncol=ncol(data.ras), di
mnames=dimnames(data.ras))[] 

Overfull \hbox (68.28088pt too wide) in paragraph at lines 880--880
 []\T1/fi4/m/n/9 goi <- dimnames(annot.ras)[[1]][order(abs(log2(annot.ras[ ,"fo
ld.change"])), decreasing=TRUE)[1:genen]][] 

Overfull \hbox (234.78088pt too wide) in paragraph at lines 891--891
 []\T1/fi4/m/n/9 res <- netinf.cv(data=mydata, categories=3, perturbations=mype
rt, priors=mypriors, priors.weight=0.5, method="regrnet", nfold=3, seed=54321)[
] 
[19]
Overfull \hbox (378.78088pt too wide) in paragraph at lines 904--904
 []\T1/fi4/m/n/9 ## Not run: res <- netinf.cv(data=mydata, categories=3, pertur
bations=mypert, priors=mypriors, priors.count=TRUE, priors.weight=0.5, method="
bayesnet", nfold=3, seed=54321)[] 
(/usr/local/texlive/2012/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (1099.78088pt too wide) in paragraph at lines 924--924
 []\T1/fi4/m/n/10 predictionet.stability.cv(data, categories, perturbations, pr
iors, predn, priors.count = TRUE, priors.weight = 0.5, maxparents = 3, subset, 
method = c("regrnet", "bayesnet"), ensemble = FALSE, ensemble.maxnsol = 3, nfol
d = 10, causal = TRUE, seed, bayesnet.maxcomplexity = 0, bayesnet.maxiter = 100
)[] 
[20]
Overfull \hbox (176.28088pt too wide) in paragraph at lines 966--966
 []\T1/fi4/m/n/9 ## load gene expression data for colon cancer data, list of ge
nes related to RAS signaling pathway and the corresponding priors[] 

Overfull \hbox (0.78088pt too wide) in paragraph at lines 969--969
 []\T1/fi4/m/n/9 pert <- matrix(0, nrow=nrow(data.ras), ncol=ncol(data.ras), di
mnames=dimnames(data.ras))[] 

Overfull \hbox (68.28088pt too wide) in paragraph at lines 974--974
 []\T1/fi4/m/n/9 goi <- dimnames(annot.ras)[[1]][order(abs(log2(annot.ras[ ,"fo
ld.change"])), decreasing=TRUE)[1:genen]][] 
[21]
Overfull \hbox (230.28088pt too wide) in paragraph at lines 985--985
 []\T1/fi4/m/n/9 res <-netinf.cv(data=mydata, categories=3, perturbations=myper
t, priors=mypriors, priors.weight=0.5, method="regrnet", nfold=3, seed=54321)[]
 

Overfull \hbox (378.78088pt too wide) in paragraph at lines 998--998
 []\T1/fi4/m/n/9 ## Not run: res <- netinf.cv(data=mydata, categories=3, pertur
bations=mypert, priors=mypriors, priors.count=TRUE, priors.weight=0.5, method="
bayesnet", nfold=3, seed=54321)[] 
(./Rd2.ind [22]

LaTeX Font Warning: Font shape `T1/fi4/m/it' undefined
(Font)              using `T1/fi4/m/n' instead on input line 33.

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

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

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

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

{/usr/local/texlive/2012/texmf-dist/fonts/enc/dvips/base/8r.enc}{/usr/local/tex
live/2012/texmf-dist/fonts/enc/dvips/inconsolata/fi4-ec.enc}</usr/local/texlive
/2012/texmf-dist/fonts/type1/public/inconsolata/Inconsolata.pfb></usr/local/tex
live/2012/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/local/texl
ive/2012/texmf-dist/fonts/type1/urw/helvetic/uhvr8a.pfb></usr/local/texlive/201
2/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></usr/local/texlive/2012/texmf-di
st/fonts/type1/urw/times/utmr8a.pfb></usr/local/texlive/2012/texmf-dist/fonts/t
ype1/urw/times/utmr8a.pfb></usr/local/texlive/2012/texmf-dist/fonts/type1/urw/t
imes/utmri8a.pfb>
Output written on Rd2.pdf (23 pages, 126966 bytes).
Transcript written on Rd2.log.
Saving output to '/private/tmp/RtmpjS8fF5/Rbuild2393318dd8c7/predictionet/build/predictionet.pdf' ...
Done
* creating vignettes ... OK
* cleaning src
* 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 'predictionet_1.5.0.tar.gz'