##############################################################################
##############################################################################
###
### 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 3.14159265-2.6-1.40.20 (TeX Live 2019) (preloaded format=pdflatex)
restricted \write18 enabled.
entering extended mode
LaTeX2e <2020-02-02> patch level 5
L3 programming layer <2020-02-25>
(./Rd2.tex (/usr/local/texlive/2019/texmf-dist/tex/latex/base/book.cls
Document Class: book 2019/12/20 v1.4l Standard LaTeX document class
(/usr/local/texlive/2019/texmf-dist/tex/latex/base/bk10.clo))
(/Library/Frameworks/R.framework/Resources/share/texmf/tex/latex/Rd.sty
(/usr/local/texlive/2019/texmf-dist/tex/latex/base/ifthen.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/tools/longtable.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/tools/bm.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/base/alltt.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/url/url.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/base/textcomp.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/base/fontenc.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/inconsolata/zi4.sty
`inconsolata-zi4' v1.12, 2019/05/17 Text macros for Inconsolata (msharpe)
(/usr/local/texlive/2019/texmf-dist/tex/latex/xkeyval/xkeyval.sty
(/usr/local/texlive/2019/texmf-dist/tex/generic/xkeyval/xkeyval.tex
(/usr/local/texlive/2019/texmf-dist/tex/generic/xkeyval/xkvutils.tex
(/usr/local/texlive/2019/texmf-dist/tex/generic/xkeyval/keyval.tex)))))
(/usr/local/texlive/2019/texmf-dist/tex/latex/graphics/color.sty
(/usr/local/texlive/2019/texmf-dist/tex/latex/graphics-cfg/color.cfg)
(/usr/local/texlive/2019/texmf-dist/tex/latex/graphics-def/pdftex.def))
(/usr/local/texlive/2019/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/local/texlive/2019/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty)
(/usr/local/texlive/2019/texmf-dist/tex/generic/iftex/iftex.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/pdftexcmds/pdftexcmds.sty
(/usr/local/texlive/2019/texmf-dist/tex/generic/infwarerr/infwarerr.sty))
(/usr/local/texlive/2019/texmf-dist/tex/generic/kvsetkeys/kvsetkeys.sty)
(/usr/local/texlive/2019/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty)
(/usr/local/texlive/2019/texmf-dist/tex/generic/pdfescape/pdfescape.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/hycolor/hycolor.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/letltxmacro/letltxmacro.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/auxhook/auxhook.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/kvoptions/kvoptions.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/local/texlive/2019/texmf-dist/tex/generic/intcalc/intcalc.sty)
(/usr/local/texlive/2019/texmf-dist/tex/generic/etexcmds/etexcmds.sty)
(/usr/local/texlive/2019/texmf-dist/tex/generic/bitset/bitset.sty
(/usr/local/texlive/2019/texmf-dist/tex/generic/bigintcalc/bigintcalc.sty))
(/usr/local/texlive/2019/texmf-dist/tex/generic/atbegshi/atbegshi.sty))
(/usr/local/texlive/2019/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/local/texlive/2019/texmf-dist/tex/latex/atveryend/atveryend.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty
(/usr/local/texlive/2019/texmf-dist/tex/generic/uniquecounter/uniquecounter.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/2019/texmf-dist/tex/latex/base/makeidx.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/base/inputenc.sty
(/usr/local/texlive/2019/texmf-dist/tex/latex/base/latin1.def))
Writing index file Rd2.idx
(/usr/local/texlive/2019/texmf-dist/tex/latex/l3backend/l3backend-pdfmode.def)
No file Rd2.aux.
(/usr/local/texlive/2019/texmf-dist/tex/latex/psnfss/t1ptm.fd)
(/usr/local/texlive/2019/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/local/texlive/2019/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/local/texlive/2019/texmf-dist/tex/latex/refcount/refcount.sty)
(/usr/local/texlive/2019/texmf-dist/tex/generic/gettitlestring/gettitlestring.s
ty)) (/usr/local/texlive/2019/texmf-dist/tex/latex/inconsolata/t1zi4.fd)
(/usr/local/texlive/2019/texmf-dist/tex/latex/psnfss/ts1ptm.fd)
(/usr/local/texlive/2019/texmf-dist/tex/latex/psnfss/t1phv.fd
LaTeX Warning: Font shape declaration has incorrect series value `mc'.
It should not contain an `m'! Please correct it.
Found on input line 20.
LaTeX Warning: Font shape declaration has incorrect series value `mc'.
It should not contain an `m'! Please correct it.
Found on input line 23.
LaTeX Warning: Font shape declaration has incorrect series value `mc'.
It should not contain an `m'! Please correct it.
Found on input line 26.
LaTeX Warning: Font shape declaration has incorrect series value `mc'.
It should not contain an `m'! Please correct it.
Found on input line 46.
) (/usr/local/texlive/2019/texmf-dist/tex/latex/base/utf8.def) [1{/usr/local/te
xlive/2019/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/2019/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]
(/private/tmp/Rtmpu4t6iY/Rbuild5f1b35368caf/predictionet/.Rd2pdf24347/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/2019/texmf-dist/fonts/enc/dvips/inconsolata/i4-ts1.enc}{/us
r/local/texlive/2019/texmf-dist/fonts/enc/dvips/base/8r.enc}{/usr/local/texlive
/2019/texmf-dist/fonts/enc/dvips/inconsolata/i4-t1-0.enc}</usr/local/texlive/20
19/texmf-dist/fonts/type1/public/inconsolata/Inconsolata-zi4r.pfb></usr/local/t
exlive/2019/texmf-dist/fonts/type1/urw/helvetic/uhvr8a.pfb></usr/local/texlive/
2019/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></usr/local/texlive/2019/texmf
-dist/fonts/type1/urw/times/utmr8a.pfb></usr/local/texlive/2019/texmf-dist/font
s/type1/urw/times/utmr8a.pfb></usr/local/texlive/2019/texmf-dist/fonts/type1/ur
w/times/utmri8a.pfb>
Output written on Rd2.pdf (21 pages, 125107 bytes).
Transcript written on Rd2.log.
This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019) (preloaded format=pdflatex)
restricted \write18 enabled.
entering extended mode
LaTeX2e <2020-02-02> patch level 5
L3 programming layer <2020-02-25>
(./Rd2.tex (/usr/local/texlive/2019/texmf-dist/tex/latex/base/book.cls
Document Class: book 2019/12/20 v1.4l Standard LaTeX document class
(/usr/local/texlive/2019/texmf-dist/tex/latex/base/bk10.clo))
(/Library/Frameworks/R.framework/Resources/share/texmf/tex/latex/Rd.sty
(/usr/local/texlive/2019/texmf-dist/tex/latex/base/ifthen.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/tools/longtable.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/tools/bm.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/base/alltt.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/url/url.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/base/textcomp.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/base/fontenc.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/inconsolata/zi4.sty
`inconsolata-zi4' v1.12, 2019/05/17 Text macros for Inconsolata (msharpe)
(/usr/local/texlive/2019/texmf-dist/tex/latex/xkeyval/xkeyval.sty
(/usr/local/texlive/2019/texmf-dist/tex/generic/xkeyval/xkeyval.tex
(/usr/local/texlive/2019/texmf-dist/tex/generic/xkeyval/xkvutils.tex
(/usr/local/texlive/2019/texmf-dist/tex/generic/xkeyval/keyval.tex)))))
(/usr/local/texlive/2019/texmf-dist/tex/latex/graphics/color.sty
(/usr/local/texlive/2019/texmf-dist/tex/latex/graphics-cfg/color.cfg)
(/usr/local/texlive/2019/texmf-dist/tex/latex/graphics-def/pdftex.def))
(/usr/local/texlive/2019/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/local/texlive/2019/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty)
(/usr/local/texlive/2019/texmf-dist/tex/generic/iftex/iftex.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/pdftexcmds/pdftexcmds.sty
(/usr/local/texlive/2019/texmf-dist/tex/generic/infwarerr/infwarerr.sty))
(/usr/local/texlive/2019/texmf-dist/tex/generic/kvsetkeys/kvsetkeys.sty)
(/usr/local/texlive/2019/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty)
(/usr/local/texlive/2019/texmf-dist/tex/generic/pdfescape/pdfescape.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/hycolor/hycolor.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/letltxmacro/letltxmacro.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/auxhook/auxhook.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/kvoptions/kvoptions.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/local/texlive/2019/texmf-dist/tex/generic/intcalc/intcalc.sty)
(/usr/local/texlive/2019/texmf-dist/tex/generic/etexcmds/etexcmds.sty)
(/usr/local/texlive/2019/texmf-dist/tex/generic/bitset/bitset.sty
(/usr/local/texlive/2019/texmf-dist/tex/generic/bigintcalc/bigintcalc.sty))
(/usr/local/texlive/2019/texmf-dist/tex/generic/atbegshi/atbegshi.sty))
(/usr/local/texlive/2019/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/local/texlive/2019/texmf-dist/tex/latex/atveryend/atveryend.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty
(/usr/local/texlive/2019/texmf-dist/tex/generic/uniquecounter/uniquecounter.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/2019/texmf-dist/tex/latex/base/makeidx.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/base/inputenc.sty
(/usr/local/texlive/2019/texmf-dist/tex/latex/base/latin1.def))
Writing index file Rd2.idx
(/usr/local/texlive/2019/texmf-dist/tex/latex/l3backend/l3backend-pdfmode.def)
(/private/tmp/Rtmpu4t6iY/Rbuild5f1b35368caf/predictionet/.Rd2pdf24347/Rd2.aux)
(/usr/local/texlive/2019/texmf-dist/tex/latex/psnfss/t1ptm.fd)
(/usr/local/texlive/2019/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/local/texlive/2019/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/local/texlive/2019/texmf-dist/tex/latex/refcount/refcount.sty)
(/usr/local/texlive/2019/texmf-dist/tex/generic/gettitlestring/gettitlestring.s
ty))
(/private/tmp/Rtmpu4t6iY/Rbuild5f1b35368caf/predictionet/.Rd2pdf24347/Rd2.out)
(/private/tmp/Rtmpu4t6iY/Rbuild5f1b35368caf/predictionet/.Rd2pdf24347/Rd2.out)
(/usr/local/texlive/2019/texmf-dist/tex/latex/inconsolata/t1zi4.fd)
(/usr/local/texlive/2019/texmf-dist/tex/latex/psnfss/ts1ptm.fd)
(/usr/local/texlive/2019/texmf-dist/tex/latex/psnfss/t1phv.fd
LaTeX Warning: Font shape declaration has incorrect series value `mc'.
It should not contain an `m'! Please correct it.
Found on input line 20.
LaTeX Warning: Font shape declaration has incorrect series value `mc'.
It should not contain an `m'! Please correct it.
Found on input line 23.
LaTeX Warning: Font shape declaration has incorrect series value `mc'.
It should not contain an `m'! Please correct it.
Found on input line 26.
LaTeX Warning: Font shape declaration has incorrect series value `mc'.
It should not contain an `m'! Please correct it.
Found on input line 46.
) (/private/tmp/Rtmpu4t6iY/Rbuild5f1b35368caf/predictionet/.Rd2pdf24347/Rd2.toc
[1{/usr/local/texlive/2019/texmf-var/fonts/map/pdftex/updmap/pdftex.map}])
(/usr/local/texlive/2019/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/2019/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)[]
No file Rd2.ind.
[22]
(/private/tmp/Rtmpu4t6iY/Rbuild5f1b35368caf/predictionet/.Rd2pdf24347/Rd2.aux)
)
(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/2019/texmf-dist/fonts/enc/dvips/inconsolata/i4-ts1.enc}{/us
r/local/texlive/2019/texmf-dist/fonts/enc/dvips/base/8r.enc}{/usr/local/texlive
/2019/texmf-dist/fonts/enc/dvips/inconsolata/i4-t1-0.enc}</usr/local/texlive/20
19/texmf-dist/fonts/type1/public/inconsolata/Inconsolata-zi4r.pfb></usr/local/t
exlive/2019/texmf-dist/fonts/type1/urw/helvetic/uhvr8a.pfb></usr/local/texlive/
2019/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></usr/local/texlive/2019/texmf
-dist/fonts/type1/urw/times/utmr8a.pfb></usr/local/texlive/2019/texmf-dist/font
s/type1/urw/times/utmr8a.pfb></usr/local/texlive/2019/texmf-dist/fonts/type1/ur
w/times/utmri8a.pfb>
Output written on Rd2.pdf (22 pages, 127058 bytes).
Transcript written on Rd2.log.
This is makeindex, version 2.15 [TeX Live 2019] (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 3.14159265-2.6-1.40.20 (TeX Live 2019) (preloaded format=pdflatex)
restricted \write18 enabled.
entering extended mode
LaTeX2e <2020-02-02> patch level 5
L3 programming layer <2020-02-25>
(./Rd2.tex (/usr/local/texlive/2019/texmf-dist/tex/latex/base/book.cls
Document Class: book 2019/12/20 v1.4l Standard LaTeX document class
(/usr/local/texlive/2019/texmf-dist/tex/latex/base/bk10.clo))
(/Library/Frameworks/R.framework/Resources/share/texmf/tex/latex/Rd.sty
(/usr/local/texlive/2019/texmf-dist/tex/latex/base/ifthen.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/tools/longtable.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/tools/bm.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/base/alltt.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/url/url.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/base/textcomp.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/base/fontenc.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/inconsolata/zi4.sty
`inconsolata-zi4' v1.12, 2019/05/17 Text macros for Inconsolata (msharpe)
(/usr/local/texlive/2019/texmf-dist/tex/latex/xkeyval/xkeyval.sty
(/usr/local/texlive/2019/texmf-dist/tex/generic/xkeyval/xkeyval.tex
(/usr/local/texlive/2019/texmf-dist/tex/generic/xkeyval/xkvutils.tex
(/usr/local/texlive/2019/texmf-dist/tex/generic/xkeyval/keyval.tex)))))
(/usr/local/texlive/2019/texmf-dist/tex/latex/graphics/color.sty
(/usr/local/texlive/2019/texmf-dist/tex/latex/graphics-cfg/color.cfg)
(/usr/local/texlive/2019/texmf-dist/tex/latex/graphics-def/pdftex.def))
(/usr/local/texlive/2019/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/local/texlive/2019/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty)
(/usr/local/texlive/2019/texmf-dist/tex/generic/iftex/iftex.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/pdftexcmds/pdftexcmds.sty
(/usr/local/texlive/2019/texmf-dist/tex/generic/infwarerr/infwarerr.sty))
(/usr/local/texlive/2019/texmf-dist/tex/generic/kvsetkeys/kvsetkeys.sty)
(/usr/local/texlive/2019/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty)
(/usr/local/texlive/2019/texmf-dist/tex/generic/pdfescape/pdfescape.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/hycolor/hycolor.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/letltxmacro/letltxmacro.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/auxhook/auxhook.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/kvoptions/kvoptions.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/local/texlive/2019/texmf-dist/tex/generic/intcalc/intcalc.sty)
(/usr/local/texlive/2019/texmf-dist/tex/generic/etexcmds/etexcmds.sty)
(/usr/local/texlive/2019/texmf-dist/tex/generic/bitset/bitset.sty
(/usr/local/texlive/2019/texmf-dist/tex/generic/bigintcalc/bigintcalc.sty))
(/usr/local/texlive/2019/texmf-dist/tex/generic/atbegshi/atbegshi.sty))
(/usr/local/texlive/2019/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/local/texlive/2019/texmf-dist/tex/latex/atveryend/atveryend.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty
(/usr/local/texlive/2019/texmf-dist/tex/generic/uniquecounter/uniquecounter.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/2019/texmf-dist/tex/latex/base/makeidx.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/base/inputenc.sty
(/usr/local/texlive/2019/texmf-dist/tex/latex/base/latin1.def))
Writing index file Rd2.idx
(/usr/local/texlive/2019/texmf-dist/tex/latex/l3backend/l3backend-pdfmode.def)
(/private/tmp/Rtmpu4t6iY/Rbuild5f1b35368caf/predictionet/.Rd2pdf24347/Rd2.aux)
(/usr/local/texlive/2019/texmf-dist/tex/latex/psnfss/t1ptm.fd)
(/usr/local/texlive/2019/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/local/texlive/2019/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/local/texlive/2019/texmf-dist/tex/latex/refcount/refcount.sty)
(/usr/local/texlive/2019/texmf-dist/tex/generic/gettitlestring/gettitlestring.s
ty))
(/private/tmp/Rtmpu4t6iY/Rbuild5f1b35368caf/predictionet/.Rd2pdf24347/Rd2.out)
(/private/tmp/Rtmpu4t6iY/Rbuild5f1b35368caf/predictionet/.Rd2pdf24347/Rd2.out)
(/usr/local/texlive/2019/texmf-dist/tex/latex/inconsolata/t1zi4.fd)
(/usr/local/texlive/2019/texmf-dist/tex/latex/psnfss/ts1ptm.fd)
(/usr/local/texlive/2019/texmf-dist/tex/latex/psnfss/t1phv.fd
LaTeX Warning: Font shape declaration has incorrect series value `mc'.
It should not contain an `m'! Please correct it.
Found on input line 20.
LaTeX Warning: Font shape declaration has incorrect series value `mc'.
It should not contain an `m'! Please correct it.
Found on input line 23.
LaTeX Warning: Font shape declaration has incorrect series value `mc'.
It should not contain an `m'! Please correct it.
Found on input line 26.
LaTeX Warning: Font shape declaration has incorrect series value `mc'.
It should not contain an `m'! Please correct it.
Found on input line 46.
) (/private/tmp/Rtmpu4t6iY/Rbuild5f1b35368caf/predictionet/.Rd2pdf24347/Rd2.toc
[1{/usr/local/texlive/2019/texmf-var/fonts/map/pdftex/updmap/pdftex.map}])
(/usr/local/texlive/2019/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/2019/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)[]
(/private/tmp/Rtmpu4t6iY/Rbuild5f1b35368caf/predictionet/.Rd2pdf24347/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])
(/private/tmp/Rtmpu4t6iY/Rbuild5f1b35368caf/predictionet/.Rd2pdf24347/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/2019/texmf-dist/fonts/enc/dvips/inconsolata/i4-ts1.enc}{/us
r/local/texlive/2019/texmf-dist/fonts/enc/dvips/base/8r.enc}{/usr/local/texlive
/2019/texmf-dist/fonts/enc/dvips/inconsolata/i4-t1-0.enc}</usr/local/texlive/20
19/texmf-dist/fonts/type1/public/inconsolata/Inconsolata-zi4r.pfb></usr/local/t
exlive/2019/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/local/te
xlive/2019/texmf-dist/fonts/type1/urw/helvetic/uhvr8a.pfb></usr/local/texlive/2
019/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></usr/local/texlive/2019/texmf-
dist/fonts/type1/urw/times/utmr8a.pfb></usr/local/texlive/2019/texmf-dist/fonts
/type1/urw/times/utmr8a.pfb></usr/local/texlive/2019/texmf-dist/fonts/type1/urw
/times/utmri8a.pfb>
Output written on Rd2.pdf (23 pages, 138109 bytes).
Transcript written on Rd2.log.
This is makeindex, version 2.15 [TeX Live 2019] (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 3.14159265-2.6-1.40.20 (TeX Live 2019) (preloaded format=pdflatex)
restricted \write18 enabled.
entering extended mode
LaTeX2e <2020-02-02> patch level 5
L3 programming layer <2020-02-25>
(./Rd2.tex (/usr/local/texlive/2019/texmf-dist/tex/latex/base/book.cls
Document Class: book 2019/12/20 v1.4l Standard LaTeX document class
(/usr/local/texlive/2019/texmf-dist/tex/latex/base/bk10.clo))
(/Library/Frameworks/R.framework/Resources/share/texmf/tex/latex/Rd.sty
(/usr/local/texlive/2019/texmf-dist/tex/latex/base/ifthen.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/tools/longtable.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/tools/bm.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/base/alltt.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/url/url.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/base/textcomp.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/base/fontenc.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/inconsolata/zi4.sty
`inconsolata-zi4' v1.12, 2019/05/17 Text macros for Inconsolata (msharpe)
(/usr/local/texlive/2019/texmf-dist/tex/latex/xkeyval/xkeyval.sty
(/usr/local/texlive/2019/texmf-dist/tex/generic/xkeyval/xkeyval.tex
(/usr/local/texlive/2019/texmf-dist/tex/generic/xkeyval/xkvutils.tex
(/usr/local/texlive/2019/texmf-dist/tex/generic/xkeyval/keyval.tex)))))
(/usr/local/texlive/2019/texmf-dist/tex/latex/graphics/color.sty
(/usr/local/texlive/2019/texmf-dist/tex/latex/graphics-cfg/color.cfg)
(/usr/local/texlive/2019/texmf-dist/tex/latex/graphics-def/pdftex.def))
(/usr/local/texlive/2019/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/local/texlive/2019/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty)
(/usr/local/texlive/2019/texmf-dist/tex/generic/iftex/iftex.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/pdftexcmds/pdftexcmds.sty
(/usr/local/texlive/2019/texmf-dist/tex/generic/infwarerr/infwarerr.sty))
(/usr/local/texlive/2019/texmf-dist/tex/generic/kvsetkeys/kvsetkeys.sty)
(/usr/local/texlive/2019/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty)
(/usr/local/texlive/2019/texmf-dist/tex/generic/pdfescape/pdfescape.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/hycolor/hycolor.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/letltxmacro/letltxmacro.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/auxhook/auxhook.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/kvoptions/kvoptions.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/local/texlive/2019/texmf-dist/tex/generic/intcalc/intcalc.sty)
(/usr/local/texlive/2019/texmf-dist/tex/generic/etexcmds/etexcmds.sty)
(/usr/local/texlive/2019/texmf-dist/tex/generic/bitset/bitset.sty
(/usr/local/texlive/2019/texmf-dist/tex/generic/bigintcalc/bigintcalc.sty))
(/usr/local/texlive/2019/texmf-dist/tex/generic/atbegshi/atbegshi.sty))
(/usr/local/texlive/2019/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/local/texlive/2019/texmf-dist/tex/latex/atveryend/atveryend.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty
(/usr/local/texlive/2019/texmf-dist/tex/generic/uniquecounter/uniquecounter.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/2019/texmf-dist/tex/latex/base/makeidx.sty)
(/usr/local/texlive/2019/texmf-dist/tex/latex/base/inputenc.sty
(/usr/local/texlive/2019/texmf-dist/tex/latex/base/latin1.def))
Writing index file Rd2.idx
(/usr/local/texlive/2019/texmf-dist/tex/latex/l3backend/l3backend-pdfmode.def)
(/private/tmp/Rtmpu4t6iY/Rbuild5f1b35368caf/predictionet/.Rd2pdf24347/Rd2.aux)
(/usr/local/texlive/2019/texmf-dist/tex/latex/psnfss/t1ptm.fd)
(/usr/local/texlive/2019/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/local/texlive/2019/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/local/texlive/2019/texmf-dist/tex/latex/refcount/refcount.sty)
(/usr/local/texlive/2019/texmf-dist/tex/generic/gettitlestring/gettitlestring.s
ty))
(/private/tmp/Rtmpu4t6iY/Rbuild5f1b35368caf/predictionet/.Rd2pdf24347/Rd2.out)
(/private/tmp/Rtmpu4t6iY/Rbuild5f1b35368caf/predictionet/.Rd2pdf24347/Rd2.out)
(/usr/local/texlive/2019/texmf-dist/tex/latex/inconsolata/t1zi4.fd)
(/usr/local/texlive/2019/texmf-dist/tex/latex/psnfss/ts1ptm.fd)
(/usr/local/texlive/2019/texmf-dist/tex/latex/psnfss/t1phv.fd
LaTeX Warning: Font shape declaration has incorrect series value `mc'.
It should not contain an `m'! Please correct it.
Found on input line 20.
LaTeX Warning: Font shape declaration has incorrect series value `mc'.
It should not contain an `m'! Please correct it.
Found on input line 23.
LaTeX Warning: Font shape declaration has incorrect series value `mc'.
It should not contain an `m'! Please correct it.
Found on input line 26.
LaTeX Warning: Font shape declaration has incorrect series value `mc'.
It should not contain an `m'! Please correct it.
Found on input line 46.
) (/private/tmp/Rtmpu4t6iY/Rbuild5f1b35368caf/predictionet/.Rd2pdf24347/Rd2.toc
[1{/usr/local/texlive/2019/texmf-var/fonts/map/pdftex/updmap/pdftex.map}])
(/usr/local/texlive/2019/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/2019/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)[]
(/private/tmp/Rtmpu4t6iY/Rbuild5f1b35368caf/predictionet/.Rd2pdf24347/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])
(/private/tmp/Rtmpu4t6iY/Rbuild5f1b35368caf/predictionet/.Rd2pdf24347/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/2019/texmf-dist/fonts/enc/dvips/inconsolata/i4-ts1.enc}{/us
r/local/texlive/2019/texmf-dist/fonts/enc/dvips/base/8r.enc}{/usr/local/texlive
/2019/texmf-dist/fonts/enc/dvips/inconsolata/i4-t1-0.enc}</usr/local/texlive/20
19/texmf-dist/fonts/type1/public/inconsolata/Inconsolata-zi4r.pfb></usr/local/t
exlive/2019/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/local/te
xlive/2019/texmf-dist/fonts/type1/urw/helvetic/uhvr8a.pfb></usr/local/texlive/2
019/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></usr/local/texlive/2019/texmf-
dist/fonts/type1/urw/times/utmr8a.pfb></usr/local/texlive/2019/texmf-dist/fonts
/type1/urw/times/utmr8a.pfb></usr/local/texlive/2019/texmf-dist/fonts/type1/urw
/times/utmri8a.pfb>
Output written on Rd2.pdf (23 pages, 138130 bytes).
Transcript written on Rd2.log.
Saving output to ‘/private/tmp/Rtmpu4t6iY/Rbuild5f1b35368caf/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_1.34.0.tar.gz’
