############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/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 378. 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(/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'! 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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 138--138 []\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 229--229 []\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 234--234 []\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 255--256 []\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 413--413 []\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 424--425 []\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 439--439 []\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 447--447 []\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 458--458 []\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 473--473 []\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 490--491 \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 522--522 []\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 530--530 []\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 541--541 []\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 546--546 []\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 547--547 []\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 558--558 []\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 562--562 []\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 567--567 []\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 568--568 []\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 584--584 []\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 602--603 []\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 637--637 []\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 645--645 []\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 656--656 []\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 669--669 []\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 689--689 []\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 715--715 []\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 720--720 []\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 726--726 []\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 735--735 []\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 787--787 []\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 792--792 []\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 798--798 []\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 893--893 []\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 901--901 []\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 912--912 []\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 925--925 []\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 945--945 []\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 987--987 []\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 995--995 []\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 1006--1006 []\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 1019--1019 []\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/RtmpFwhKx0/Rbuildc6d4114d6196/predictionet/.Rd2pdf50900/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} Output written on Rd2.pdf (21 pages, 125242 bytes). 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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 378. 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Found on input line 46. ) (/private/tmp/RtmpFwhKx0/Rbuildc6d4114d6196/predictionet/.Rd2pdf50900/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 138--138 []\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 229--229 []\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 234--234 []\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 255--256 []\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 413--413 []\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 424--425 []\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 439--439 []\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 447--447 []\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 458--458 []\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 473--473 []\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 490--491 \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 522--522 []\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 530--530 []\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 541--541 []\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 546--546 []\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 547--547 []\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 558--558 []\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 562--562 []\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 567--567 []\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 568--568 []\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 584--584 []\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 602--603 []\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 637--637 []\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 645--645 []\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 656--656 []\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 669--669 []\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 689--689 []\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 715--715 []\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 720--720 []\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 726--726 []\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 735--735 []\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 787--787 []\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 792--792 []\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 798--798 []\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 893--893 []\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 901--901 []\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 912--912 []\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 925--925 []\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 945--945 []\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 987--987 []\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 995--995 []\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 1006--1006 []\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 1019--1019 []\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/RtmpFwhKx0/Rbuildc6d4114d6196/predictionet/.Rd2pdf50900/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} Output written on Rd2.pdf (22 pages, 127183 bytes). Transcript written on Rd2.log. This is makeindex, version 2.15 [TeX Live 2019] (kpathsea + Thai support). 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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 378. Package hyperref Warning: Option `pagebackref' has already been used, (hyperref) setting the option has no effect on input line 378. ) (/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/RtmpFwhKx0/Rbuildc6d4114d6196/predictionet/.Rd2pdf50900/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/RtmpFwhKx0/Rbuildc6d4114d6196/predictionet/.Rd2pdf50900/Rd2.out) (/private/tmp/RtmpFwhKx0/Rbuildc6d4114d6196/predictionet/.Rd2pdf50900/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/RtmpFwhKx0/Rbuildc6d4114d6196/predictionet/.Rd2pdf50900/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 138--138 []\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 229--229 []\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 234--234 []\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 255--256 []\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 413--413 []\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 424--425 []\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 439--439 []\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 447--447 []\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 458--458 []\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 473--473 []\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 490--491 \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 522--522 []\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 530--530 []\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 541--541 []\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 546--546 []\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 547--547 []\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 558--558 []\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 562--562 []\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 567--567 []\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 568--568 []\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 584--584 []\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 602--603 []\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 637--637 []\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 645--645 []\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 656--656 []\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 669--669 []\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 689--689 []\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 715--715 []\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 720--720 []\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 726--726 []\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 735--735 []\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 787--787 []\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 792--792 []\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 798--798 []\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 893--893 []\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 901--901 []\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 912--912 []\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 925--925 []\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 945--945 []\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 987--987 []\T1/zi4/m/n/9 ## 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[23]) (/private/tmp/RtmpFwhKx0/Rbuildc6d4114d6196/predictionet/.Rd2pdf50900/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} Output written on Rd2.pdf (23 pages, 138245 bytes). Transcript written on Rd2.log. This is makeindex, version 2.15 [TeX Live 2019] (kpathsea + Thai support). 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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 378. Package hyperref Warning: Option `pagebackref' has already been used, (hyperref) setting the option has no effect on input line 378. ) (/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/RtmpFwhKx0/Rbuildc6d4114d6196/predictionet/.Rd2pdf50900/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/RtmpFwhKx0/Rbuildc6d4114d6196/predictionet/.Rd2pdf50900/Rd2.out) (/private/tmp/RtmpFwhKx0/Rbuildc6d4114d6196/predictionet/.Rd2pdf50900/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/RtmpFwhKx0/Rbuildc6d4114d6196/predictionet/.Rd2pdf50900/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 138--138 []\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 229--229 []\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 234--234 []\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 255--256 []\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 413--413 []\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 424--425 []\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 439--439 []\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 447--447 []\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 458--458 []\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 473--473 []\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 490--491 \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 522--522 []\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 530--530 []\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 541--541 []\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 546--546 []\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 547--547 []\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 558--558 []\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 562--562 []\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 567--567 []\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 568--568 []\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 584--584 []\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 602--603 []\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 637--637 []\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 645--645 []\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 656--656 []\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 669--669 []\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 689--689 []\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 715--715 []\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 720--720 []\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 726--726 []\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 735--735 []\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 787--787 []\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 792--792 []\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 798--798 []\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 893--893 []\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 901--901 []\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 912--912 []\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 925--925 []\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 945--945 []\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 987--987 []\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 995--995 []\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 1006--1006 []\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 1019--1019 []\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/RtmpFwhKx0/Rbuildc6d4114d6196/predictionet/.Rd2pdf50900/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/RtmpFwhKx0/Rbuildc6d4114d6196/predictionet/.Rd2pdf50900/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} Output written on Rd2.pdf (23 pages, 138271 bytes). Transcript written on Rd2.log. Saving output to ‘/private/tmp/RtmpFwhKx0/Rbuildc6d4114d6196/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_1.40.0.tar.gz’