##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data predictionet
###
##############################################################################
##############################################################################
* 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 3.14159265-2.6-1.40.19 (TeX Live 2018) (preloaded format=pdflatex)
\write18 enabled.
entering extended mode
LaTeX2e <2018-04-01> patch level 2
Babel <3.18> and hyphenation patterns for 84 language(s) loaded.
(./Rd2.tex (/usr/local/texlive/2018/texmf-dist/tex/latex/base/book.cls
Document Class: book 2014/09/29 v1.4h Standard LaTeX document class
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/bk10.clo))
(/Library/Frameworks/R.framework/Resources/share/texmf/tex/latex/Rd.sty
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/ifthen.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/tools/longtable.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/tools/bm.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/alltt.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/url/url.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/textcomp.sty
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/ts1enc.def
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/ts1enc.dfu)))
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/fontenc.sty
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/t1enc.def))
(/usr/local/texlive/2018/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/inconsolata/zi4.sty
`inconsolata-zi4' v1.112, 2017/01/04 Text macros for Inconsolata (msharpe)
(/usr/local/texlive/2018/texmf-dist/tex/latex/xkeyval/xkeyval.sty
(/usr/local/texlive/2018/texmf-dist/tex/generic/xkeyval/xkeyval.tex
(/usr/local/texlive/2018/texmf-dist/tex/generic/xkeyval/xkvutils.tex
(/usr/local/texlive/2018/texmf-dist/tex/generic/xkeyval/keyval.tex)))))
(/usr/local/texlive/2018/texmf-dist/tex/latex/graphics/color.sty
(/usr/local/texlive/2018/texmf-dist/tex/latex/graphics-cfg/color.cfg)
(/usr/local/texlive/2018/texmf-dist/tex/latex/graphics-def/pdftex.def))
(/usr/local/texlive/2018/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/local/texlive/2018/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
(/usr/local/texlive/2018/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty))
(/usr/local/texlive/2018/texmf-dist/tex/generic/ifxetex/ifxetex.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/oberdiek/auxhook.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/oberdiek/kvoptions.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/local/texlive/2018/texmf-dist/tex/latex/latexconfig/hyperref.cfg))
(/usr/local/texlive/2018/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/local/texlive/2018/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 377.
Package hyperref Warning: Option `pagebackref' has already been used,
(hyperref) setting the option has no effect on input line 377.
) (/usr/local/texlive/2018/texmf-dist/tex/latex/base/makeidx.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/inputenc.sty
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/latin1.def))
Writing index file Rd2.idx
No file Rd2.aux.
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/ts1cmr.fd)
(/usr/local/texlive/2018/texmf-dist/tex/latex/psnfss/t1ptm.fd)
(/usr/local/texlive/2018/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/local/texlive/2018/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/local/texlive/2018/texmf-dist/tex/generic/oberdiek/gettitlestring.sty))
(/usr/local/texlive/2018/texmf-dist/tex/latex/inconsolata/t1zi4.fd)
(/usr/local/texlive/2018/texmf-dist/tex/latex/psnfss/ts1ptm.fd)
(/usr/local/texlive/2018/texmf-dist/tex/latex/psnfss/t1phv.fd)
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/utf8.def) [1{/usr/local/texl
ive/2018/texmf-var/fonts/map/pdftex/updmap/pdftex.map}] [2]
Overfull \hbox (128.25635pt too wide) in paragraph at lines 137--137
[]\T1/zi4/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]))[]
[3] [4]
Overfull \hbox (146.21954pt too wide) in paragraph at lines 228--228
[]\T1/zi4/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 (578.21034pt too wide) in paragraph at lines 233--233
[]\T1/zi4/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]]
) })[]
Overfull \hbox (13.78735pt too wide) in paragraph at lines 254--255
[]\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.
[5] [6] [7]
Overfull \hbox (128.08014pt too wide) in paragraph at lines 412--412
[]\T1/zi4/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 423--424
[]\T1/ptm/m/n/10 type of pre-dic-tive model to fit; \T1/zi4/m/n/10 linear \T1/p
tm/m/n/10 for lin-ear re-gres-sion model, \T1/zi4/m/n/10 linear.penalized
Overfull \hbox (146.21954pt too wide) in paragraph at lines 438--438
[]\T1/zi4/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 (62.26862pt too wide) in paragraph at lines 446--446
[]\T1/zi4/m/n/9 goi <- dimnames(annot.ras)[[1]][order(abs(log2(annot.ras[ ,"fo
ld.change"])), decreasing=TRUE)[1:genen]][]
Overfull \hbox (234.75328pt too wide) in paragraph at lines 457--457
[]\T1/zi4/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)[]
Overfull \hbox (1117.99835pt too wide) in paragraph at lines 472--472
[]\T1/zi4/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 489--490
\T1/ptm/m/n/10 iden-tify all the sta-tis-ti-cally equiv-a-lent net-works, it \T
1/zi4/m/n/10 best \T1/ptm/m/n/10 only the top \T1/zi4/m/n/10 ensemble.maxnsol
[10]
Overfull \hbox (146.21954pt too wide) in paragraph at lines 521--521
[]\T1/zi4/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 (62.26862pt too wide) in paragraph at lines 529--529
[]\T1/zi4/m/n/9 goi <- dimnames(annot.ras)[[1]][order(abs(log2(annot.ras[ ,"fo
ld.change"])), decreasing=TRUE)[1:genen]][]
Overfull \hbox (261.75328pt too wide) in paragraph at lines 540--540
[]\T1/zi4/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 (126.76248pt too wide) in paragraph at lines 545--545
[]\T1/zi4/m/n/9 xnet <- network(x=mytopo, matrix.type="adjacency", directed=TR
UE, loops=FALSE, vertex.attrnames=dimnames(mytopo)[[1]])[]
Overfull \hbox (369.75328pt too wide) in paragraph at lines 546--546
[]\T1/zi4/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)[]
(/usr/local/texlive/2018/texmf-dist/tex/latex/inconsolata/ts1zi4.fd) [11]
Overfull \hbox (569.21034pt too wide) in paragraph at lines 557--557
[]\T1/zi4/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 (315.74408pt too wide) in paragraph at lines 561--561
[]\T1/zi4/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 (176.25328pt too wide) in paragraph at lines 566--566
[]\T1/zi4/m/n/9 ## Not run: xnet <- network(x=mytopo, matrix.type="adjacency",
directed=TRUE, loops=FALSE, vertex.attrnames=dimnames(mytopo)[[1]])[]
Overfull \hbox (419.24408pt too wide) in paragraph at lines 567--567
[]\T1/zi4/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)[]
Overfull \hbox (1282.96768pt too wide) in paragraph at lines 583--583
[]\T1/zi4/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 601--602
[]\T1/ptm/m/n/10 type of pre-dic-tive model to fit; \T1/zi4/m/n/10 linear \T1/p
tm/m/n/10 for lin-ear re-gres-sion model, \T1/zi4/m/n/10 linear.penalized
[13]
Overfull \hbox (146.21954pt too wide) in paragraph at lines 636--636
[]\T1/zi4/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 (62.26862pt too wide) in paragraph at lines 644--644
[]\T1/zi4/m/n/9 goi <- dimnames(annot.ras)[[1]][order(abs(log2(annot.ras[ ,"fo
ld.change"])), decreasing=TRUE)[1:genen]][]
Overfull \hbox (221.25328pt too wide) in paragraph at lines 655--655
[]\T1/zi4/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 (359.24101pt too wide) in paragraph at lines 668--668
[]\T1/zi4/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)[]
[14]
Overfull \hbox (161.42029pt too wide) in paragraph at lines 688--688
[]\T1/zi4/m/n/10 netinf.predict(net, data, categories, perturbations, subset,
predn, method=c("linear", "linear.penalized", "cpt"))[]
Overfull \hbox (146.21954pt too wide) in paragraph at lines 714--714
[]\T1/zi4/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 (62.26862pt too wide) in paragraph at lines 719--719
[]\T1/zi4/m/n/9 goi <- dimnames(annot.ras)[[1]][order(abs(log2(annot.ras[ ,"fo
ld.change"])), decreasing=TRUE)[1:genen]][]
Overfull \hbox (164.25635pt too wide) in paragraph at lines 725--725
[]\T1/zi4/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 (33.75635pt too wide) in paragraph at lines 734--734
[]\T1/zi4/m/n/9 plot(mydata[ ,goi[1]], mypreds, xlab="Observed gene expression
", ylab="Predicted gene expression")[]
Overfull \hbox (146.21954pt too wide) in paragraph at lines 786--786
[]\T1/zi4/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 (62.26862pt too wide) in paragraph at lines 791--791
[]\T1/zi4/m/n/9 goi <- dimnames(annot.ras)[[1]][order(abs(log2(annot.ras[ ,"fo
ld.change"])), decreasing=TRUE)[1:genen]][]
Overfull \hbox (278.25021pt too wide) in paragraph at lines 797--797
[]\T1/zi4/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)[]
[17]
Overfull \hbox (146.21954pt too wide) in paragraph at lines 892--892
[]\T1/zi4/m/n/9 ## load gene expression data for colon cancer data, list of ge
nes related to RAS signaling pathway and the corresponding priors[]
[18]
Overfull \hbox (62.26862pt too wide) in paragraph at lines 900--900
[]\T1/zi4/m/n/9 goi <- dimnames(annot.ras)[[1]][order(abs(log2(annot.ras[ ,"fo
ld.change"])), decreasing=TRUE)[1:genen]][]
Overfull \hbox (221.25328pt too wide) in paragraph at lines 911--911
[]\T1/zi4/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 (359.24101pt too wide) in paragraph at lines 924--924
[]\T1/zi4/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)[]
Overfull \hbox (1037.98813pt too wide) in paragraph at lines 944--944
[]\T1/zi4/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 (146.21954pt too wide) in paragraph at lines 986--986
[]\T1/zi4/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 (62.26862pt too wide) in paragraph at lines 994--994
[]\T1/zi4/m/n/9 goi <- dimnames(annot.ras)[[1]][order(abs(log2(annot.ras[ ,"fo
ld.change"])), decreasing=TRUE)[1:genen]][]
Overfull \hbox (218.25635pt too wide) in paragraph at lines 1005--1005
[]\T1/zi4/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 (359.24101pt too wide) in paragraph at lines 1018--1018
[]\T1/zi4/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/2018/texmf-dist/fonts/enc/dvips/inconsolata/i4-ts1.enc}{/us
r/local/texlive/2018/texmf-dist/fonts/enc/dvips/base/8r.enc}{/usr/local/texlive
/2018/texmf-dist/fonts/enc/dvips/inconsolata/i4-t1-0.enc}</usr/local/texlive/20
18/texmf-dist/fonts/type1/public/inconsolata/Inconsolata-zi4r.pfb></usr/local/t
exlive/2018/texmf-dist/fonts/type1/urw/helvetic/uhvr8a.pfb></usr/local/texlive/
2018/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></usr/local/texlive/2018/texmf
-dist/fonts/type1/urw/times/utmr8a.pfb></usr/local/texlive/2018/texmf-dist/font
s/type1/urw/times/utmr8a.pfb></usr/local/texlive/2018/texmf-dist/fonts/type1/ur
w/times/utmri8a.pfb>
Output written on Rd2.pdf (21 pages, 129942 bytes).
Transcript written on Rd2.log.
This is makeindex, version 2.15 [TeX Live 2018] (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 3.14159265-2.6-1.40.19 (TeX Live 2018) (preloaded format=pdflatex)
\write18 enabled.
entering extended mode
LaTeX2e <2018-04-01> patch level 2
Babel <3.18> and hyphenation patterns for 84 language(s) loaded.
(./Rd2.tex (/usr/local/texlive/2018/texmf-dist/tex/latex/base/book.cls
Document Class: book 2014/09/29 v1.4h Standard LaTeX document class
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/bk10.clo))
(/Library/Frameworks/R.framework/Resources/share/texmf/tex/latex/Rd.sty
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/ifthen.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/tools/longtable.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/tools/bm.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/alltt.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/url/url.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/textcomp.sty
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/ts1enc.def
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/ts1enc.dfu)))
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/fontenc.sty
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/t1enc.def))
(/usr/local/texlive/2018/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/inconsolata/zi4.sty
`inconsolata-zi4' v1.112, 2017/01/04 Text macros for Inconsolata (msharpe)
(/usr/local/texlive/2018/texmf-dist/tex/latex/xkeyval/xkeyval.sty
(/usr/local/texlive/2018/texmf-dist/tex/generic/xkeyval/xkeyval.tex
(/usr/local/texlive/2018/texmf-dist/tex/generic/xkeyval/xkvutils.tex
(/usr/local/texlive/2018/texmf-dist/tex/generic/xkeyval/keyval.tex)))))
(/usr/local/texlive/2018/texmf-dist/tex/latex/graphics/color.sty
(/usr/local/texlive/2018/texmf-dist/tex/latex/graphics-cfg/color.cfg)
(/usr/local/texlive/2018/texmf-dist/tex/latex/graphics-def/pdftex.def))
(/usr/local/texlive/2018/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/local/texlive/2018/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
(/usr/local/texlive/2018/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty))
(/usr/local/texlive/2018/texmf-dist/tex/generic/ifxetex/ifxetex.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/oberdiek/auxhook.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/oberdiek/kvoptions.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/local/texlive/2018/texmf-dist/tex/latex/latexconfig/hyperref.cfg))
(/usr/local/texlive/2018/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/local/texlive/2018/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 377.
Package hyperref Warning: Option `pagebackref' has already been used,
(hyperref) setting the option has no effect on input line 377.
) (/usr/local/texlive/2018/texmf-dist/tex/latex/base/makeidx.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/inputenc.sty
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/latin1.def))
Writing index file Rd2.idx
(./Rd2.aux) (/usr/local/texlive/2018/texmf-dist/tex/latex/base/ts1cmr.fd)
(/usr/local/texlive/2018/texmf-dist/tex/latex/psnfss/t1ptm.fd)
(/usr/local/texlive/2018/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/local/texlive/2018/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/local/texlive/2018/texmf-dist/tex/generic/oberdiek/gettitlestring.sty))
(./Rd2.out) (./Rd2.out)
(/usr/local/texlive/2018/texmf-dist/tex/latex/inconsolata/t1zi4.fd)
(/usr/local/texlive/2018/texmf-dist/tex/latex/psnfss/ts1ptm.fd)
(/usr/local/texlive/2018/texmf-dist/tex/latex/psnfss/t1phv.fd) (./Rd2.toc
[1{/usr/local/texlive/2018/texmf-var/fonts/map/pdftex/updmap/pdftex.map}])
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/utf8.def) [2]
Overfull \hbox (128.25635pt too wide) in paragraph at lines 137--137
[]\T1/zi4/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]))[]
[3] [4]
Overfull \hbox (146.21954pt too wide) in paragraph at lines 228--228
[]\T1/zi4/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 (578.21034pt too wide) in paragraph at lines 233--233
[]\T1/zi4/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]]
) })[]
[5]
Overfull \hbox (13.78735pt too wide) in paragraph at lines 254--255
[]\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.
[6] [7]
Overfull \hbox (128.08014pt too wide) in paragraph at lines 412--412
[]\T1/zi4/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 423--424
[]\T1/ptm/m/n/10 type of pre-dic-tive model to fit; \T1/zi4/m/n/10 linear \T1/p
tm/m/n/10 for lin-ear re-gres-sion model, \T1/zi4/m/n/10 linear.penalized
Overfull \hbox (146.21954pt too wide) in paragraph at lines 438--438
[]\T1/zi4/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 (62.26862pt too wide) in paragraph at lines 446--446
[]\T1/zi4/m/n/9 goi <- dimnames(annot.ras)[[1]][order(abs(log2(annot.ras[ ,"fo
ld.change"])), decreasing=TRUE)[1:genen]][]
[9]
Overfull \hbox (234.75328pt too wide) in paragraph at lines 457--457
[]\T1/zi4/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)[]
Overfull \hbox (1117.99835pt too wide) in paragraph at lines 472--472
[]\T1/zi4/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 489--490
\T1/ptm/m/n/10 iden-tify all the sta-tis-ti-cally equiv-a-lent net-works, it \T
1/zi4/m/n/10 best \T1/ptm/m/n/10 only the top \T1/zi4/m/n/10 ensemble.maxnsol
Overfull \hbox (146.21954pt too wide) in paragraph at lines 521--521
[]\T1/zi4/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 (62.26862pt too wide) in paragraph at lines 529--529
[]\T1/zi4/m/n/9 goi <- dimnames(annot.ras)[[1]][order(abs(log2(annot.ras[ ,"fo
ld.change"])), decreasing=TRUE)[1:genen]][]
Overfull \hbox (261.75328pt too wide) in paragraph at lines 540--540
[]\T1/zi4/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 (126.76248pt too wide) in paragraph at lines 545--545
[]\T1/zi4/m/n/9 xnet <- network(x=mytopo, matrix.type="adjacency", directed=TR
UE, loops=FALSE, vertex.attrnames=dimnames(mytopo)[[1]])[]
Overfull \hbox (369.75328pt too wide) in paragraph at lines 546--546
[]\T1/zi4/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)[]
(/usr/local/texlive/2018/texmf-dist/tex/latex/inconsolata/ts1zi4.fd)
Overfull \hbox (569.21034pt too wide) in paragraph at lines 557--557
[]\T1/zi4/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 (315.74408pt too wide) in paragraph at lines 561--561
[]\T1/zi4/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 (176.25328pt too wide) in paragraph at lines 566--566
[]\T1/zi4/m/n/9 ## Not run: xnet <- network(x=mytopo, matrix.type="adjacency",
directed=TRUE, loops=FALSE, vertex.attrnames=dimnames(mytopo)[[1]])[]
Overfull \hbox (419.24408pt too wide) in paragraph at lines 567--567
[]\T1/zi4/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)[]
[12]
Overfull \hbox (1282.96768pt too wide) in paragraph at lines 583--583
[]\T1/zi4/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 601--602
[]\T1/ptm/m/n/10 type of pre-dic-tive model to fit; \T1/zi4/m/n/10 linear \T1/p
tm/m/n/10 for lin-ear re-gres-sion model, \T1/zi4/m/n/10 linear.penalized
[13]
Overfull \hbox (146.21954pt too wide) in paragraph at lines 636--636
[]\T1/zi4/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 (62.26862pt too wide) in paragraph at lines 644--644
[]\T1/zi4/m/n/9 goi <- dimnames(annot.ras)[[1]][order(abs(log2(annot.ras[ ,"fo
ld.change"])), decreasing=TRUE)[1:genen]][]
[14]
Overfull \hbox (221.25328pt too wide) in paragraph at lines 655--655
[]\T1/zi4/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 (359.24101pt too wide) in paragraph at lines 668--668
[]\T1/zi4/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)[]
Overfull \hbox (161.42029pt too wide) in paragraph at lines 688--688
[]\T1/zi4/m/n/10 netinf.predict(net, data, categories, perturbations, subset,
predn, method=c("linear", "linear.penalized", "cpt"))[]
[15]
Overfull \hbox (146.21954pt too wide) in paragraph at lines 714--714
[]\T1/zi4/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 (62.26862pt too wide) in paragraph at lines 719--719
[]\T1/zi4/m/n/9 goi <- dimnames(annot.ras)[[1]][order(abs(log2(annot.ras[ ,"fo
ld.change"])), decreasing=TRUE)[1:genen]][]
Overfull \hbox (164.25635pt too wide) in paragraph at lines 725--725
[]\T1/zi4/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 (33.75635pt too wide) in paragraph at lines 734--734
[]\T1/zi4/m/n/9 plot(mydata[ ,goi[1]], mypreds, xlab="Observed gene expression
", ylab="Predicted gene expression")[]
[16]
Overfull \hbox (146.21954pt too wide) in paragraph at lines 786--786
[]\T1/zi4/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 (62.26862pt too wide) in paragraph at lines 791--791
[]\T1/zi4/m/n/9 goi <- dimnames(annot.ras)[[1]][order(abs(log2(annot.ras[ ,"fo
ld.change"])), decreasing=TRUE)[1:genen]][]
Overfull \hbox (278.25021pt too wide) in paragraph at lines 797--797
[]\T1/zi4/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)[]
[17] [18]
Overfull \hbox (146.21954pt too wide) in paragraph at lines 892--892
[]\T1/zi4/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 (62.26862pt too wide) in paragraph at lines 900--900
[]\T1/zi4/m/n/9 goi <- dimnames(annot.ras)[[1]][order(abs(log2(annot.ras[ ,"fo
ld.change"])), decreasing=TRUE)[1:genen]][]
Overfull \hbox (221.25328pt too wide) in paragraph at lines 911--911
[]\T1/zi4/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 (359.24101pt too wide) in paragraph at lines 924--924
[]\T1/zi4/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)[]
Overfull \hbox (1037.98813pt too wide) in paragraph at lines 944--944
[]\T1/zi4/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 (146.21954pt too wide) in paragraph at lines 986--986
[]\T1/zi4/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 (62.26862pt too wide) in paragraph at lines 994--994
[]\T1/zi4/m/n/9 goi <- dimnames(annot.ras)[[1]][order(abs(log2(annot.ras[ ,"fo
ld.change"])), decreasing=TRUE)[1:genen]][]
[21]
Overfull \hbox (218.25635pt too wide) in paragraph at lines 1005--1005
[]\T1/zi4/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 (359.24101pt too wide) in paragraph at lines 1018--1018
[]\T1/zi4/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/zi4/m/it' undefined
(Font) using `T1/zi4/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/2018/texmf-dist/fonts/enc/dvips/inconsolata/i4-ts1.enc}{/us
r/local/texlive/2018/texmf-dist/fonts/enc/dvips/base/8r.enc}{/usr/local/texlive
/2018/texmf-dist/fonts/enc/dvips/inconsolata/i4-t1-0.enc}</usr/local/texlive/20
18/texmf-dist/fonts/type1/public/inconsolata/Inconsolata-zi4r.pfb></usr/local/t
exlive/2018/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/local/te
xlive/2018/texmf-dist/fonts/type1/urw/helvetic/uhvr8a.pfb></usr/local/texlive/2
018/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></usr/local/texlive/2018/texmf-
dist/fonts/type1/urw/times/utmr8a.pfb></usr/local/texlive/2018/texmf-dist/fonts
/type1/urw/times/utmr8a.pfb></usr/local/texlive/2018/texmf-dist/fonts/type1/urw
/times/utmri8a.pfb>
Output written on Rd2.pdf (23 pages, 143063 bytes).
Transcript written on Rd2.log.
This is makeindex, version 2.15 [TeX Live 2018] (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 3.14159265-2.6-1.40.19 (TeX Live 2018) (preloaded format=pdflatex)
\write18 enabled.
entering extended mode
LaTeX2e <2018-04-01> patch level 2
Babel <3.18> and hyphenation patterns for 84 language(s) loaded.
(./Rd2.tex (/usr/local/texlive/2018/texmf-dist/tex/latex/base/book.cls
Document Class: book 2014/09/29 v1.4h Standard LaTeX document class
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/bk10.clo))
(/Library/Frameworks/R.framework/Resources/share/texmf/tex/latex/Rd.sty
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/ifthen.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/tools/longtable.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/tools/bm.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/alltt.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/url/url.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/textcomp.sty
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/ts1enc.def
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/ts1enc.dfu)))
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/fontenc.sty
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/t1enc.def))
(/usr/local/texlive/2018/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/inconsolata/zi4.sty
`inconsolata-zi4' v1.112, 2017/01/04 Text macros for Inconsolata (msharpe)
(/usr/local/texlive/2018/texmf-dist/tex/latex/xkeyval/xkeyval.sty
(/usr/local/texlive/2018/texmf-dist/tex/generic/xkeyval/xkeyval.tex
(/usr/local/texlive/2018/texmf-dist/tex/generic/xkeyval/xkvutils.tex
(/usr/local/texlive/2018/texmf-dist/tex/generic/xkeyval/keyval.tex)))))
(/usr/local/texlive/2018/texmf-dist/tex/latex/graphics/color.sty
(/usr/local/texlive/2018/texmf-dist/tex/latex/graphics-cfg/color.cfg)
(/usr/local/texlive/2018/texmf-dist/tex/latex/graphics-def/pdftex.def))
(/usr/local/texlive/2018/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/local/texlive/2018/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
(/usr/local/texlive/2018/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty))
(/usr/local/texlive/2018/texmf-dist/tex/generic/ifxetex/ifxetex.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/oberdiek/auxhook.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/oberdiek/kvoptions.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/local/texlive/2018/texmf-dist/tex/latex/latexconfig/hyperref.cfg))
(/usr/local/texlive/2018/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/local/texlive/2018/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 377.
Package hyperref Warning: Option `pagebackref' has already been used,
(hyperref) setting the option has no effect on input line 377.
) (/usr/local/texlive/2018/texmf-dist/tex/latex/base/makeidx.sty)
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/inputenc.sty
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/latin1.def))
Writing index file Rd2.idx
(./Rd2.aux) (/usr/local/texlive/2018/texmf-dist/tex/latex/base/ts1cmr.fd)
(/usr/local/texlive/2018/texmf-dist/tex/latex/psnfss/t1ptm.fd)
(/usr/local/texlive/2018/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/local/texlive/2018/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/local/texlive/2018/texmf-dist/tex/generic/oberdiek/gettitlestring.sty))
(./Rd2.out) (./Rd2.out)
(/usr/local/texlive/2018/texmf-dist/tex/latex/inconsolata/t1zi4.fd)
(/usr/local/texlive/2018/texmf-dist/tex/latex/psnfss/ts1ptm.fd)
(/usr/local/texlive/2018/texmf-dist/tex/latex/psnfss/t1phv.fd) (./Rd2.toc
[1{/usr/local/texlive/2018/texmf-var/fonts/map/pdftex/updmap/pdftex.map}])
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/utf8.def) [2]
Overfull \hbox (128.25635pt too wide) in paragraph at lines 137--137
[]\T1/zi4/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]))[]
[3] [4]
Overfull \hbox (146.21954pt too wide) in paragraph at lines 228--228
[]\T1/zi4/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 (578.21034pt too wide) in paragraph at lines 233--233
[]\T1/zi4/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]]
) })[]
[5]
Overfull \hbox (13.78735pt too wide) in paragraph at lines 254--255
[]\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.
[6] [7]
Overfull \hbox (128.08014pt too wide) in paragraph at lines 412--412
[]\T1/zi4/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 423--424
[]\T1/ptm/m/n/10 type of pre-dic-tive model to fit; \T1/zi4/m/n/10 linear \T1/p
tm/m/n/10 for lin-ear re-gres-sion model, \T1/zi4/m/n/10 linear.penalized
Overfull \hbox (146.21954pt too wide) in paragraph at lines 438--438
[]\T1/zi4/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 (62.26862pt too wide) in paragraph at lines 446--446
[]\T1/zi4/m/n/9 goi <- dimnames(annot.ras)[[1]][order(abs(log2(annot.ras[ ,"fo
ld.change"])), decreasing=TRUE)[1:genen]][]
[9]
Overfull \hbox (234.75328pt too wide) in paragraph at lines 457--457
[]\T1/zi4/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)[]
Overfull \hbox (1117.99835pt too wide) in paragraph at lines 472--472
[]\T1/zi4/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 489--490
\T1/ptm/m/n/10 iden-tify all the sta-tis-ti-cally equiv-a-lent net-works, it \T
1/zi4/m/n/10 best \T1/ptm/m/n/10 only the top \T1/zi4/m/n/10 ensemble.maxnsol
Overfull \hbox (146.21954pt too wide) in paragraph at lines 521--521
[]\T1/zi4/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 (62.26862pt too wide) in paragraph at lines 529--529
[]\T1/zi4/m/n/9 goi <- dimnames(annot.ras)[[1]][order(abs(log2(annot.ras[ ,"fo
ld.change"])), decreasing=TRUE)[1:genen]][]
Overfull \hbox (261.75328pt too wide) in paragraph at lines 540--540
[]\T1/zi4/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 (126.76248pt too wide) in paragraph at lines 545--545
[]\T1/zi4/m/n/9 xnet <- network(x=mytopo, matrix.type="adjacency", directed=TR
UE, loops=FALSE, vertex.attrnames=dimnames(mytopo)[[1]])[]
Overfull \hbox (369.75328pt too wide) in paragraph at lines 546--546
[]\T1/zi4/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)[]
(/usr/local/texlive/2018/texmf-dist/tex/latex/inconsolata/ts1zi4.fd)
Overfull \hbox (569.21034pt too wide) in paragraph at lines 557--557
[]\T1/zi4/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 (315.74408pt too wide) in paragraph at lines 561--561
[]\T1/zi4/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 (176.25328pt too wide) in paragraph at lines 566--566
[]\T1/zi4/m/n/9 ## Not run: xnet <- network(x=mytopo, matrix.type="adjacency",
directed=TRUE, loops=FALSE, vertex.attrnames=dimnames(mytopo)[[1]])[]
Overfull \hbox (419.24408pt too wide) in paragraph at lines 567--567
[]\T1/zi4/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)[]
[12]
Overfull \hbox (1282.96768pt too wide) in paragraph at lines 583--583
[]\T1/zi4/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 601--602
[]\T1/ptm/m/n/10 type of pre-dic-tive model to fit; \T1/zi4/m/n/10 linear \T1/p
tm/m/n/10 for lin-ear re-gres-sion model, \T1/zi4/m/n/10 linear.penalized
[13]
Overfull \hbox (146.21954pt too wide) in paragraph at lines 636--636
[]\T1/zi4/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 (62.26862pt too wide) in paragraph at lines 644--644
[]\T1/zi4/m/n/9 goi <- dimnames(annot.ras)[[1]][order(abs(log2(annot.ras[ ,"fo
ld.change"])), decreasing=TRUE)[1:genen]][]
[14]
Overfull \hbox (221.25328pt too wide) in paragraph at lines 655--655
[]\T1/zi4/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 (359.24101pt too wide) in paragraph at lines 668--668
[]\T1/zi4/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)[]
Overfull \hbox (161.42029pt too wide) in paragraph at lines 688--688
[]\T1/zi4/m/n/10 netinf.predict(net, data, categories, perturbations, subset,
predn, method=c("linear", "linear.penalized", "cpt"))[]
[15]
Overfull \hbox (146.21954pt too wide) in paragraph at lines 714--714
[]\T1/zi4/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 (62.26862pt too wide) in paragraph at lines 719--719
[]\T1/zi4/m/n/9 goi <- dimnames(annot.ras)[[1]][order(abs(log2(annot.ras[ ,"fo
ld.change"])), decreasing=TRUE)[1:genen]][]
Overfull \hbox (164.25635pt too wide) in paragraph at lines 725--725
[]\T1/zi4/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 (33.75635pt too wide) in paragraph at lines 734--734
[]\T1/zi4/m/n/9 plot(mydata[ ,goi[1]], mypreds, xlab="Observed gene expression
", ylab="Predicted gene expression")[]
[16]
Overfull \hbox (146.21954pt too wide) in paragraph at lines 786--786
[]\T1/zi4/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 (62.26862pt too wide) in paragraph at lines 791--791
[]\T1/zi4/m/n/9 goi <- dimnames(annot.ras)[[1]][order(abs(log2(annot.ras[ ,"fo
ld.change"])), decreasing=TRUE)[1:genen]][]
Overfull \hbox (278.25021pt too wide) in paragraph at lines 797--797
[]\T1/zi4/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)[]
[17] [18]
Overfull \hbox (146.21954pt too wide) in paragraph at lines 892--892
[]\T1/zi4/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 (62.26862pt too wide) in paragraph at lines 900--900
[]\T1/zi4/m/n/9 goi <- dimnames(annot.ras)[[1]][order(abs(log2(annot.ras[ ,"fo
ld.change"])), decreasing=TRUE)[1:genen]][]
Overfull \hbox (221.25328pt too wide) in paragraph at lines 911--911
[]\T1/zi4/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 (359.24101pt too wide) in paragraph at lines 924--924
[]\T1/zi4/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)[]
Overfull \hbox (1037.98813pt too wide) in paragraph at lines 944--944
[]\T1/zi4/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 (146.21954pt too wide) in paragraph at lines 986--986
[]\T1/zi4/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 (62.26862pt too wide) in paragraph at lines 994--994
[]\T1/zi4/m/n/9 goi <- dimnames(annot.ras)[[1]][order(abs(log2(annot.ras[ ,"fo
ld.change"])), decreasing=TRUE)[1:genen]][]
[21]
Overfull \hbox (218.25635pt too wide) in paragraph at lines 1005--1005
[]\T1/zi4/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 (359.24101pt too wide) in paragraph at lines 1018--1018
[]\T1/zi4/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/zi4/m/it' undefined
(Font) using `T1/zi4/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/2018/texmf-dist/fonts/enc/dvips/inconsolata/i4-ts1.enc}{/us
r/local/texlive/2018/texmf-dist/fonts/enc/dvips/base/8r.enc}{/usr/local/texlive
/2018/texmf-dist/fonts/enc/dvips/inconsolata/i4-t1-0.enc}</usr/local/texlive/20
18/texmf-dist/fonts/type1/public/inconsolata/Inconsolata-zi4r.pfb></usr/local/t
exlive/2018/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/local/te
xlive/2018/texmf-dist/fonts/type1/urw/helvetic/uhvr8a.pfb></usr/local/texlive/2
018/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></usr/local/texlive/2018/texmf-
dist/fonts/type1/urw/times/utmr8a.pfb></usr/local/texlive/2018/texmf-dist/fonts
/type1/urw/times/utmr8a.pfb></usr/local/texlive/2018/texmf-dist/fonts/type1/urw
/times/utmri8a.pfb>
Output written on Rd2.pdf (23 pages, 142997 bytes).
Transcript written on Rd2.log.
Saving output to ‘/private/tmp/RtmpG63eMA/Rbuild13d7a1ae7429a/predictionet/build/predictionet.pdf’ ...
Done
* creating vignettes ... OK
* cleaning src
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘predictionet_1.33.0.tar.gz’
