##############################################################################
##############################################################################
###
### 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 3.14159265-2.6-1.40.17 (TeX Live 2016) (preloaded format=pdflatex)
\write18 enabled.
entering extended mode
(./Rd2.tex
LaTeX2e <2016/03/31>
Babel <3.9r> and hyphenation patterns for 83 language(s) loaded.
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/book.cls
Document Class: book 2014/09/29 v1.4h Standard LaTeX document class
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/bk10.clo))
(/Library/Frameworks/R.framework/Resources/share/texmf/tex/latex/Rd.sty
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/ifthen.sty)
(/usr/local/texlive/2016/texmf-dist/tex/latex/tools/longtable.sty)
(/usr/local/texlive/2016/texmf-dist/tex/latex/tools/bm.sty)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/alltt.sty)
(/usr/local/texlive/2016/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/local/texlive/2016/texmf-dist/tex/latex/url/url.sty)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/textcomp.sty
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/ts1enc.def))
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/fontenc.sty
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/t1enc.def))
(/usr/local/texlive/2016/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/local/texlive/2016/texmf-dist/tex/latex/inconsolata/zi4.sty
`inconsolata-zi4' v1.10, 2016/02/22 Text macros for Inconsolata (msharpe)
(/usr/local/texlive/2016/texmf-dist/tex/latex/graphics/keyval.sty))
(/usr/local/texlive/2016/texmf-dist/tex/latex/graphics/color.sty
(/usr/local/texlive/2016/texmf-dist/tex/latex/graphics-cfg/color.cfg)
(/usr/local/texlive/2016/texmf-dist/tex/latex/pdftex-def/pdftex.def
(/usr/local/texlive/2016/texmf-dist/tex/generic/oberdiek/infwarerr.sty)
(/usr/local/texlive/2016/texmf-dist/tex/generic/oberdiek/ltxcmds.sty)))
(/usr/local/texlive/2016/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/local/texlive/2016/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
(/usr/local/texlive/2016/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty))
(/usr/local/texlive/2016/texmf-dist/tex/generic/ifxetex/ifxetex.sty)
(/usr/local/texlive/2016/texmf-dist/tex/latex/oberdiek/auxhook.sty)
(/usr/local/texlive/2016/texmf-dist/tex/latex/oberdiek/kvoptions.sty)
(/usr/local/texlive/2016/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/local/texlive/2016/texmf-dist/tex/latex/latexconfig/hyperref.cfg))
Package hyperref Message: Driver (autodetected): hpdftex.
(/usr/local/texlive/2016/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/local/texlive/2016/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty))
Package hyperref Warning: Option `hyperindex' has already been used,
(hyperref) setting the option has no effect on input line 366.
Package hyperref Warning: Option `pagebackref' has already been used,
(hyperref) setting the option has no effect on input line 366.
) (/usr/local/texlive/2016/texmf-dist/tex/latex/base/makeidx.sty)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/inputenc.sty
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/t1enc.dfu)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/ot1enc.dfu)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/omsenc.dfu)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/ts1enc.dfu))
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/latin1.def))
Writing index file Rd2.idx
No file Rd2.aux.
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/ts1cmr.fd)
(/usr/local/texlive/2016/texmf-dist/tex/latex/psnfss/t1ptm.fd)
(/usr/local/texlive/2016/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/local/texlive/2016/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/local/texlive/2016/texmf-dist/tex/generic/oberdiek/gettitlestring.sty))
(/usr/local/texlive/2016/texmf-dist/tex/latex/inconsolata/t1zi4.fd)
(/usr/local/texlive/2016/texmf-dist/tex/latex/psnfss/ts1ptm.fd)
(/usr/local/texlive/2016/texmf-dist/tex/latex/psnfss/t1phv.fd)
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [1{/usr/local/texl
ive/2016/texmf-var/fonts/map/pdftex/updmap/pdftex.map}]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [2]
Overfull \hbox (133.08093pt too wide) in paragraph at lines 132--132
[]\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]))[]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [3]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [4]
Overfull \hbox (158.281pt too wide) in paragraph at lines 223--223
[]\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 (592.08102pt too wide) in paragraph at lines 228--228
[]\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]]
) })[]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (13.78735pt too wide) in paragraph at lines 249--250
[]\T1/ptm/m/n/10 Inferred topol-ogy, an edge be-tween to vari-ables X and Y cor
-re-sponds to net[X,Y]=1.
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [5]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [6]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [7]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (134.78088pt too wide) in paragraph at lines 407--407
[]\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 418--419
[]\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 (158.281pt too wide) in paragraph at lines 433--433
[]\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 (64.68091pt too wide) in paragraph at lines 441--441
[]\T1/zi4/m/n/9 goi <- dimnames(annot.ras)[[1]][order(abs(log2(annot.ras[ ,"fo
ld.change"])), decreasing=TRUE)[1:genen]][]
Overfull \hbox (240.18094pt too wide) in paragraph at lines 452--452
[]\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)[]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (1140.78088pt too wide) in paragraph at lines 467--467
[]\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 484--485
\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 (158.281pt too wide) in paragraph at lines 516--516
[]\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 (64.68091pt too wide) in paragraph at lines 524--524
[]\T1/zi4/m/n/9 goi <- dimnames(annot.ras)[[1]][order(abs(log2(annot.ras[ ,"fo
ld.change"])), decreasing=TRUE)[1:genen]][]
Overfull \hbox (267.18094pt too wide) in paragraph at lines 535--535
[]\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 (130.38092pt too wide) in paragraph at lines 540--540
[]\T1/zi4/m/n/9 xnet <- network(x=mytopo, matrix.type="adjacency", directed=TR
UE, loops=FALSE, vertex.attrnames=dimnames(mytopo)[[1]])[]
Overfull \hbox (375.18094pt too wide) in paragraph at lines 541--541
[]\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/2016/texmf-dist/tex/latex/inconsolata/ts1zi4.fd) [11]
Overfull \hbox (583.08102pt too wide) in paragraph at lines 552--552
[]\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 (322.98096pt too wide) in paragraph at lines 556--556
[]\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 (181.68094pt too wide) in paragraph at lines 561--561
[]\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 (426.48096pt too wide) in paragraph at lines 562--562
[]\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)[]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (1311.78088pt too wide) in paragraph at lines 578--578
[]\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 596--597
[]\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 (158.281pt too wide) in paragraph at lines 631--631
[]\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 (64.68091pt too wide) in paragraph at lines 639--639
[]\T1/zi4/m/n/9 goi <- dimnames(annot.ras)[[1]][order(abs(log2(annot.ras[ ,"fo
ld.change"])), decreasing=TRUE)[1:genen]][]
Overfull \hbox (226.68094pt too wide) in paragraph at lines 650--650
[]\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 (367.08096pt too wide) in paragraph at lines 663--663
[]\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)[]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [14]
Overfull \hbox (166.78088pt too wide) in paragraph at lines 683--683
[]\T1/zi4/m/n/10 netinf.predict(net, data, categories, perturbations, subset,
predn, method=c("linear", "linear.penalized", "cpt"))[]
Overfull \hbox (158.281pt too wide) in paragraph at lines 709--709
[]\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 (64.68091pt too wide) in paragraph at lines 714--714
[]\T1/zi4/m/n/9 goi <- dimnames(annot.ras)[[1]][order(abs(log2(annot.ras[ ,"fo
ld.change"])), decreasing=TRUE)[1:genen]][]
Overfull \hbox (169.08093pt too wide) in paragraph at lines 720--720
[]\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 (38.58093pt too wide) in paragraph at lines 729--729
[]\T1/zi4/m/n/9 plot(mydata[ ,goi[1]], mypreds, xlab="Observed gene expression
", ylab="Predicted gene expression")[]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (158.281pt too wide) in paragraph at lines 781--781
[]\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 (64.68091pt too wide) in paragraph at lines 786--786
[]\T1/zi4/m/n/9 goi <- dimnames(annot.ras)[[1]][order(abs(log2(annot.ras[ ,"fo
ld.change"])), decreasing=TRUE)[1:genen]][]
Overfull \hbox (284.28094pt too wide) in paragraph at lines 792--792
[]\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)[]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def) [17]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (158.281pt too wide) in paragraph at lines 887--887
[]\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 (64.68091pt too wide) in paragraph at lines 895--895
[]\T1/zi4/m/n/9 goi <- dimnames(annot.ras)[[1]][order(abs(log2(annot.ras[ ,"fo
ld.change"])), decreasing=TRUE)[1:genen]][]
Overfull \hbox (226.68094pt too wide) in paragraph at lines 906--906
[]\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 (367.08096pt too wide) in paragraph at lines 919--919
[]\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)[]
(/usr/local/texlive/2016/texmf-dist/tex/latex/base/utf8.def)
Overfull \hbox (1062.78088pt too wide) in paragraph at lines 939--939
[]\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 (158.281pt too wide) in paragraph at lines 981--981
[]\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 (64.68091pt too wide) in paragraph at lines 989--989
[]\T1/zi4/m/n/9 goi <- dimnames(annot.ras)[[1]][order(abs(log2(annot.ras[ ,"fo
ld.change"])), decreasing=TRUE)[1:genen]][]
Overfull \hbox (223.08093pt too wide) in paragraph at lines 1000--1000
[]\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 (367.08096pt too wide) in paragraph at lines 1013--1013
[]\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/2016/texmf-dist/fonts/enc/dvips/inconsolata/i4-ts1.enc}{/us
r/local/texlive/2016/texmf-dist/fonts/enc/dvips/base/8r.enc}{/usr/local/texlive
/2016/texmf-dist/fonts/enc/dvips/inconsolata/i4-t1-0.enc}</usr/local/texlive/20
16/texmf-dist/fonts/type1/public/inconsolata/Inconsolata-zi4r.pfb></usr/local/t
exlive/2016/texmf-dist/fonts/type1/urw/helvetic/uhvr8a.pfb></usr/local/texlive/
2016/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></usr/local/texlive/2016/texmf
-dist/fonts/type1/urw/times/utmr8a.pfb></usr/local/texlive/2016/texmf-dist/font
s/type1/urw/times/utmr8a.pfb></usr/local/texlive/2016/texmf-dist/fonts/type1/ur
w/times/utmri8a.pfb>
Output written on Rd2.pdf (21 pages, 129812 bytes).
Transcript written on Rd2.log.
Saving output to ‘/private/tmp/RtmpUQLK0z/Rbuild10c5a5bf390a2/predictionet/build/predictionet.pdf’ ...
Done
* creating vignettes ... OK
* cleaning src
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* looking to see if a ‘data/datalist’ file should be added
* building ‘predictionet_1.20.0.tar.gz’
