[Distr-commits] r857 - branches/distr-2.4/pkg/distr/tests/Examples branches/distr-2.4/pkg/distrEx/tests/Examples pkg/SweaveListingUtils/tests/Examples pkg/distr/man pkg/distr/tests/Examples pkg/distrEllipse/tests/Examples pkg/distrEx/tests/Examples pkg/distrMod/man pkg/distrMod/tests/Examples pkg/distrSim/tests/Examples pkg/distrTEst/tests/Examples pkg/distrTeach/man pkg/distrTeach/tests/Examples pkg/startupmsg/tests/Examples
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sun Jan 13 12:08:20 CET 2013
Author: stamats
Date: 2013-01-13 12:08:18 +0100 (Sun, 13 Jan 2013)
New Revision: 857
Modified:
branches/distr-2.4/pkg/distr/tests/Examples/distr-Ex.Rout.save
branches/distr-2.4/pkg/distrEx/tests/Examples/distrEx-Ex.Rout.save
pkg/SweaveListingUtils/tests/Examples/SweaveListingUtils-Ex.Rout.save
pkg/distr/man/operators-methods.Rd
pkg/distr/man/qqplot.Rd
pkg/distr/tests/Examples/distr-Ex.Rout.save
pkg/distrEllipse/tests/Examples/distrEllipse-Ex.Rout.save
pkg/distrEx/tests/Examples/distrEx-Ex.Rout.save
pkg/distrMod/man/MDEstimator.Rd
pkg/distrMod/man/MLEstimator.Rd
pkg/distrMod/tests/Examples/distrMod-Ex.Rout.save
pkg/distrSim/tests/Examples/distrSim-Ex.Rout.save
pkg/distrTEst/tests/Examples/distrTEst-Ex.Rout.save
pkg/distrTeach/man/IllustCLT.Rd
pkg/distrTeach/tests/Examples/distrTeach-Ex.Rout.save
pkg/startupmsg/tests/Examples/startupmsg-Ex.Rout.save
Log:
update of trunk
Modified: branches/distr-2.4/pkg/distr/tests/Examples/distr-Ex.Rout.save
===================================================================
--- branches/distr-2.4/pkg/distr/tests/Examples/distr-Ex.Rout.save 2013-01-12 02:58:38 UTC (rev 856)
+++ branches/distr-2.4/pkg/distr/tests/Examples/distr-Ex.Rout.save 2013-01-13 11:08:18 UTC (rev 857)
@@ -2279,8 +2279,8 @@
else d0 <- df1(x)/stand
return(d0)
}
-<bytecode: 0x3a97850>
-<environment: 0x4f3daf8>
+<bytecode: 0x3f8e9b0>
+<environment: 0x4ee6850>
$pfun
function (q, lower.tail = TRUE, log.p = FALSE)
@@ -2295,7 +2295,7 @@
else p0/nm
return(p0)
}
-<environment: 0x52b8678>
+<environment: 0x537e520>
$qfun
function (p, lower.tail = TRUE, log.p = FALSE)
@@ -2313,7 +2313,7 @@
else q.l(1 - p01)
return(as.numeric(q0))
}
-<environment: 0x510df50>
+<environment: 0x48b1180>
>
> rp2 <- function(n){rpois(n, lambda = 1)^2}
@@ -2359,8 +2359,8 @@
else d0 <- df1(x)/stand
return(d0)
}
-<bytecode: 0x3a97850>
-<environment: 0x5e0ab00>
+<bytecode: 0x3f8e9b0>
+<environment: 0x68d2c88>
$pfun
function (q, lower.tail = TRUE, log.p = FALSE)
@@ -2375,7 +2375,7 @@
else p0/nm
return(p0)
}
-<environment: 0x52b8a80>
+<environment: 0x537f900>
$qfun
function (p, lower.tail = TRUE, log.p = FALSE)
@@ -2393,7 +2393,7 @@
else q.l(1 - p01)
return(as.numeric(q0))
}
-<environment: 0x4f4e198>
+<environment: 0x5dc29f8>
>
> rp2 <- function(n){rpois(n, lambda = 1)^2}
@@ -4122,11 +4122,11 @@
> F <- ( Norm() + Binom() + Pois() + Exp() ) * 2 - 10
> system.time(r(F)(10^6))
user system elapsed
- 0.708 0.028 0.739
+ 0.712 0.016 0.732
> simplifyr(F, size = 10^6)
> system.time(r(F)(10^6))
user system elapsed
- 0.048 0.000 0.048
+ 0.040 0.008 0.048
>
>
>
@@ -4166,7 +4166,7 @@
> ### * <FOOTER>
> ###
> cat("Time elapsed: ", proc.time() - get("ptime", pos = 'CheckExEnv'),"\n")
-Time elapsed: 33.75 0.204 34.238 0 0
+Time elapsed: 29.229 0.22 29.643 0.004 0
> grDevices::dev.off()
pdf
2
Modified: branches/distr-2.4/pkg/distrEx/tests/Examples/distrEx-Ex.Rout.save
===================================================================
--- branches/distr-2.4/pkg/distrEx/tests/Examples/distrEx-Ex.Rout.save 2013-01-12 02:58:38 UTC (rev 856)
+++ branches/distr-2.4/pkg/distrEx/tests/Examples/distrEx-Ex.Rout.save 2013-01-13 11:08:18 UTC (rev 857)
@@ -894,7 +894,7 @@
}
0 + cond %*% 1 + 1 * r(n, ...)
}
-<environment: 0x7253578>
+<environment: 0x6a66ee8>
> d(D1)
function (x, cond, log = FALSE, ...)
{
@@ -916,7 +916,7 @@
else d0 <- d0/1
return(d0)
}
-<environment: 0x7253578>
+<environment: 0x6a66ee8>
> p(D1)
function (q, cond, lower.tail = TRUE, log.p = FALSE, ...)
{
@@ -943,7 +943,7 @@
p0 <- log(p0)
return(p0)
}
-<environment: 0x7253578>
+<environment: 0x6a66ee8>
> q(D1)
function (p, cond, lower.tail = TRUE, log.p = FALSE, ...)
{
@@ -967,7 +967,7 @@
argList <- c(argList, dots)
1 * do.call(q, argList) + 0 + as.vector(cond %*% 1)
}
-<environment: 0x7253578>
+<environment: 0x6a66ee8>
> param(D1)
name: parameter of a linear regression model
theta: 1
@@ -1764,7 +1764,7 @@
> ### * <FOOTER>
> ###
> cat("Time elapsed: ", proc.time() - get("ptime", pos = 'CheckExEnv'),"\n")
-Time elapsed: 11.58 0.136 11.79 0 0.004
+Time elapsed: 9.352 0.112 9.515 0 0.008
> grDevices::dev.off()
null device
1
Modified: pkg/SweaveListingUtils/tests/Examples/SweaveListingUtils-Ex.Rout.save
===================================================================
--- pkg/SweaveListingUtils/tests/Examples/SweaveListingUtils-Ex.Rout.save 2013-01-12 02:58:38 UTC (rev 856)
+++ pkg/SweaveListingUtils/tests/Examples/SweaveListingUtils-Ex.Rout.save 2013-01-13 11:08:18 UTC (rev 857)
@@ -1,6 +1,6 @@
-R version 2.15.1 Patched (2012-06-29 r59688) -- "Roasted Marshmallows"
-Copyright (C) 2012 The R Foundation for Statistical Computing
+R Under development (unstable) (2013-01-09 r61595) -- "Unsuffered Consequences"
+Copyright (C) 2013 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -31,6 +31,13 @@
:SweaveListingUtils> Utilities for Sweave together with
:SweaveListingUtils> TeX listings package (version 0.6)
:SweaveListingUtils>
+:SweaveListingUtils> NOTE: Support for this package
+:SweaveListingUtils> will stop soon.
+:SweaveListingUtils>
+:SweaveListingUtils> Package 'knitr' is providing the
+:SweaveListingUtils> same functionality in a better
+:SweaveListingUtils> way.
+:SweaveListingUtils>
:SweaveListingUtils> Some functions from package 'base'
:SweaveListingUtils> are intentionally masked ---see
:SweaveListingUtils> SweaveListingMASK().
@@ -50,18 +57,29 @@
Attaching package: ‘SweaveListingUtils’
-The following object(s) are masked from ‘package:base’:
+The following object is masked from ‘package:base’:
library, require
>
> assign(".oldSearch", search(), pos = 'CheckExEnv')
+> assign(".ExTimings", "SweaveListingUtils-Ex.timings", pos = 'CheckExEnv')
+> cat("name\tuser\tsystem\telapsed\n", file=get(".ExTimings", pos = 'CheckExEnv'))
+> assign(".format_ptime",
++ function(x) {
++ if(!is.na(x[4L])) x[1L] <- x[1L] + x[4L]
++ if(!is.na(x[5L])) x[2L] <- x[2L] + x[5L]
++ format(x[1L:3L])
++ },
++ pos = 'CheckExEnv')
+>
> cleanEx()
> nameEx("SweaveListingMASK")
> ### * SweaveListingMASK
>
> flush(stderr()); flush(stdout())
>
+> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: SweaveListingMASK
> ### Title: Masking of/by other functions in package "SweaveListingUtils"
> ### Aliases: SweaveListingMASK MASKING
@@ -102,12 +120,16 @@
>
>
>
+>
+> assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
+> cat("SweaveListingMASK", get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("SweaveListingOptions")
> ### * SweaveListingOptions
>
> flush(stderr()); flush(stdout())
>
+> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: SweaveListingOptions
> ### Title: Function to change the global options of the package
> ### 'SweaveListingUtils'
@@ -295,12 +317,16 @@
>
>
>
+>
+> assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
+> cat("SweaveListingOptions", get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("SweaveListingPreparations")
> ### * SweaveListingPreparations
>
> flush(stderr()); flush(stdout())
>
+> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: SweaveListingPreparations
> ### Title: SweaveListingPreparations
> ### Aliases: SweaveListingPreparations
@@ -462,61 +488,59 @@
smooth,simulate,shapiro.test,setNames,selfStart,%
se.contrast,screeplot,scatter.smooth,runmed,rstudent.lm,%
rstudent.glm,rstandard.lm,rstandard.glm,rmultinom,residuals.lm,%
-residuals.glm,residuals.default,reshapeWide,reshapeLong,reshape,%
-reorder,rect.hclust,read.ftable,rWishart,r2dtable,%
-quasipoisson,quasibinomial,quantile.default,quade.test,qqnorm.default,%
-qbirthday,prop.trend.test,prop.test,promax,printCoefmat,%
-print.ts,print.terms,print.logLik,print.lm,print.integrate,%
-print.infl,print.glm,print.ftable,print.formula,print.family,%
-print.density,print.coefmat,print.anova,princomp,predict.poly,%
-predict.mlm,predict.lm,predict.glm,prcomp,ppr,%
-power.t.test,power.prop.test,power.anova.test,polym,poisson.test,%
-plot.ts,plot.stepfun,plot.spec.phase,plot.spec.coherency,plot.spec,%
-plot.mlm,plot.lm,plot.ecdf,plot.density,plot.TukeyHSD,%
-plclust,pbirthday,pairwise.wilcox.test,pairwise.table,pairwise.t.test,%
-pairwise.prop.test,pacf,p.adjust.methods,p.adjust,order.dendrogram,%
-optimHess,oneway.test,numericDeriv,nobs,nls.control,%
-nls,nlminb,naresid,naprint,napredict,%
-na.pass,na.omit,na.fail,na.exclude,na.contiguous,%
-na.action,mood.test,monthplot,model.weights,model.tables,%
-model.response,model.offset,model.matrix.lm,model.matrix.default,model.matrix,%
-model.frame.lm,model.frame.glm,model.frame.default,model.frame.aovlist,model.frame,%
-model.extract,medpolish,median.default,mcnemar.test,mauchly.test,%
-mauchley.test,mantelhaen.test,manova,makepredictcall,makeARIMA,%
-make.link,ls.print,ls.diag,logLik,loess.smooth,%
-loess.control,loess,loadings,lm.wfit.null,lm.wfit,%
-lm.influence,lm.fit.null,lm.fit,lines.ts,line,%
-lag.plot,lag,ksmooth,ks.test,kruskal.test,%
-knots,kmeans,kernel,kernapply,isoreg,%
-is.tskernel,is.ts,is.stepfun,is.mts,is.leaf,%
-is.empty.model,inverse.gaussian,interaction.plot,integrate,influence.measures,%
-heatmap,hclust,hatvalues.lm,hatvalues,glm.fit.null,%
-glm.fit,glm.control,get_all_vars,getInitial,getCall,%
-friedman.test,fligner.test,fitted.values,fisher.test,filter,%
-factor.scope,factanal,expand.model.frame,estVar,embed,%
-eff.aovlist,ecdf,dummy.coef,drop.terms,drop.scope,%
-dmultinom,dist,diffinv,diff.ts,dfbeta,%
-df.residual,df.kernel,deriv3.formula,deriv3.default,deriv3,%
-deriv.formula,deriv.default,density.default,dendrapply,delete.response,%
-decompose,cutree,cpgram,cov2cor,cov.wt,%
-cor.test,cophenetic,cooks.distance,contrasts<-,contr.treatment,%
-contr.sum,contr.poly,contr.helmert,contr.SAS,constrOptim,%
-confint.default,confint,complete.cases,cmdscale,clearNames,%
-chisq.test,ccf,case.names,cancor,bw.ucv,%
-bw.nrd0,bw.nrd,bw.bcv,bw.SJ,biplot,%
-binom.test,bartlett.test,bandwidth.kernel,asOneSidedFormula,as.ts,%
-as.stepfun,as.hclust,as.formula,as.dist,as.dendrogram,%
-arima0.diag,arima0,arima.sim,arima,ar.yw,%
-ar.ols,ar.mle,ar.burg,ar,ansari.test,%
-anovalist.lm,anova.mlm,anova.lmlist,anova.lm,anova.glmlist,%
-anova.glm,aggregate.ts,aggregate.default,aggregate.data.frame,addmargins,%
-add.scope,acf2AR,acf,TukeyHSD.aov,TukeyHSD,%
-StructTS,SSweibull,SSmicmen,SSlogis,SSgompertz,%
-SSfpl,SSfol,SSbiexp,SSasympOrig,SSasympOff,%
-SSasymp,SSD,PP.test,NLSstRtAsymptote,NLSstLfAsymptote,%
-NLSstClosestX,NLSstAsymptotic,KalmanSmooth,KalmanRun,KalmanLike,%
-KalmanForecast,HoltWinters,Box.test,BIC,ARMAtoMA,%
-ARMAacf,AIC%
+residuals.glm,residuals.default,reshape,reorder,rect.hclust,%
+read.ftable,rWishart,r2dtable,quasipoisson,quasibinomial,%
+quantile.default,quade.test,qqnorm.default,qbirthday,prop.trend.test,%
+prop.test,promax,printCoefmat,print.ts,print.terms,%
+print.logLik,print.lm,print.integrate,print.infl,print.glm,%
+print.ftable,print.formula,print.family,print.density,print.anova,%
+princomp,predict.poly,predict.mlm,predict.lm,predict.glm,%
+prcomp,ppr,power.t.test,power.prop.test,power.anova.test,%
+polym,poisson.test,plot.ts,plot.stepfun,plot.spec.phase,%
+plot.spec.coherency,plot.spec,plot.mlm,plot.lm,plot.ecdf,%
+plot.density,plot.TukeyHSD,plclust,pbirthday,pairwise.wilcox.test,%
+pairwise.table,pairwise.t.test,pairwise.prop.test,pacf,p.adjust.methods,%
+p.adjust,order.dendrogram,optimHess,oneway.test,numericDeriv,%
+nobs,nls.control,nls,nlminb,naresid,%
+naprint,napredict,na.pass,na.omit,na.fail,%
+na.exclude,na.contiguous,na.action,mood.test,monthplot,%
+model.weights,model.tables,model.response,model.offset,model.matrix.lm,%
+model.matrix.default,model.matrix,model.frame.lm,model.frame.glm,model.frame.default,%
+model.frame.aovlist,model.frame,model.extract,medpolish,median.default,%
+mcnemar.test,mauchly.test,mantelhaen.test,manova,makepredictcall,%
+makeARIMA,make.link,ls.print,ls.diag,logLik,%
+loess.smooth,loess.control,loess,loadings,lm.wfit,%
+lm.influence,lm.fit,lines.ts,line,lag.plot,%
+lag,ksmooth,ks.test,kruskal.test,knots,%
+kmeans,kernel,kernapply,isoreg,is.tskernel,%
+is.ts,is.stepfun,is.mts,is.leaf,is.empty.model,%
+inverse.gaussian,interaction.plot,integrate,influence.measures,heatmap,%
+hclust,hatvalues.lm,hatvalues,glm.fit,glm.control,%
+get_all_vars,getInitial,getCall,friedman.test,fligner.test,%
+fitted.values,fisher.test,filter,factor.scope,factanal,%
+expand.model.frame,estVar,embed,eff.aovlist,ecdf,%
+dummy.coef,drop.terms,drop.scope,dmultinom,dist,%
+diffinv,diff.ts,dfbeta,df.residual,df.kernel,%
+deriv3.formula,deriv3.default,deriv3,deriv.formula,deriv.default,%
+density.default,dendrapply,delete.response,decompose,cutree,%
+cpgram,cov2cor,cov.wt,cor.test,cophenetic,%
+cooks.distance,contrasts<-,contr.treatment,contr.sum,contr.poly,%
+contr.helmert,contr.SAS,constrOptim,confint.default,confint,%
+complete.cases,cmdscale,chisq.test,ccf,case.names,%
+cancor,bw.ucv,bw.nrd0,bw.nrd,bw.bcv,%
+bw.SJ,biplot,binom.test,bartlett.test,bandwidth.kernel,%
+asOneSidedFormula,as.ts,as.stepfun,as.hclust,as.formula,%
+as.dist,as.dendrogram,arima0.diag,arima0,arima.sim,%
+arima,ar.yw,ar.ols,ar.mle,ar.burg,%
+ar,ansari.test,anova.mlm,anova.lmlist,anova.lm,%
+anova.glmlist,anova.glm,aggregate.ts,aggregate.default,aggregate.data.frame,%
+addmargins,add.scope,acf2AR,acf,TukeyHSD.aov,%
+TukeyHSD,StructTS,SSweibull,SSmicmen,SSlogis,%
+SSgompertz,SSfpl,SSfol,SSbiexp,SSasympOrig,%
+SSasympOff,SSasymp,SSD,PP.test,NLSstRtAsymptote,%
+NLSstLfAsymptote,NLSstClosestX,NLSstAsymptotic,KalmanSmooth,KalmanRun,%
+KalmanLike,KalmanForecast,HoltWinters,Box.test,BIC,%
+ARMAtoMA,ARMAacf,AIC%
},%
keywordstyle={[4]{\bf\color{RRecomdcolor}}},%
%
@@ -542,62 +566,62 @@
topo.colors,tiff,terrain.colors,svg,setPS,%
setGraphicsEventHandlers,setGraphicsEventEnv,setEPS,savePlot,rgb2hsv,%
replayPlot,recordPlot,recordGraphics,quartzFonts,quartzFont,%
-quartz.options,quartz,ps.options,postscriptFonts,postscriptFont,%
-png,pdfFonts,pdf.options,pdf,nclass.scott,%
-nclass.Sturges,nclass.FD,n2mfrow,make.rgb,jpeg,%
-is.raster,heat.colors,hcl,grey.colors,gray.colors,%
-graphics.off,getGraphicsEventEnv,getGraphicsEvent,extendrange,embedFonts,%
-deviceIsInteractive,devAskNewPage,dev.size,dev.set,dev.print,%
-dev.prev,dev.off,dev.next,dev.new,dev.list,%
-dev.interactive,dev.hold,dev.flush,dev.cur,dev.copy2pdf,%
-dev.copy2eps,dev.copy,dev.control,dev.capture,dev.capabilities,%
-densCols,convertColor,contourLines,colorspaces,colorRampPalette,%
-colorRamp,colorConverter,col2rgb,cm.colors,check.options,%
-cairo_ps,cairo_pdf,boxplot.stats,bmp,blues9,%
-bitmap,axisTicks,as.raster,as.graphicsAnnot,adjustcolor,%
-X11Fonts,X11Font,X11.options,Type1Font,Hershey,%
-CIDFont%
+quartz.save,quartz.options,quartz,ps.options,postscriptFonts,%
+postscriptFont,png,pdfFonts,pdf.options,pdf,%
+nclass.scott,nclass.Sturges,nclass.FD,n2mfrow,make.rgb,%
+jpeg,is.raster,heat.colors,hcl,grey.colors,%
+gray.colors,graphics.off,getGraphicsEventEnv,getGraphicsEvent,extendrange,%
+embedFonts,deviceIsInteractive,devAskNewPage,dev.size,dev.set,%
+dev.print,dev.prev,dev.off,dev.next,dev.new,%
+dev.list,dev.interactive,dev.hold,dev.flush,dev.cur,%
+dev.copy2pdf,dev.copy2eps,dev.copy,dev.control,dev.capture,%
+dev.capabilities,densCols,convertColor,contourLines,colorspaces,%
+colorRampPalette,colorRamp,colorConverter,col2rgb,cm.colors,%
+check.options,cairo_ps,cairo_pdf,boxplot.stats,bmp,%
+blues9,bitmap,axisTicks,as.raster,as.graphicsAnnot,%
+adjustcolor,X11Fonts,X11Font,X11.options,Type1Font,%
+Hershey,CIDFont%
},%
keywordstyle={[6]{\bf\color{RRecomdcolor}}},%
%
% --------------------------
% Registration of package utils [recommended or base]
% --------------------------
-morekeywords={[7]zip.file.extract,wsbrowser,write.table,write.socket,write.csv2,%
-write.csv,vignette,url.show,upgrade,update.packages,%
-update.packageStatus,unzip,untar,unstack,type.convert,%
-txtProgressBar,toLatex,toBibtex,timestamp,tar,%
-tail.matrix,tail,summaryRprof,strOptions,str,%
-stack,setTxtProgressBar,setRepositories,setBreakpoint,sessionInfo,%
-select.list,savehistory,rtags,removeSource,remove.packages,%
-relist,recover,readCitationFile,read.table,read.socket,%
-read.fwf,read.fortran,read.delim2,read.delim,read.csv2,%
-read.csv,read.DIF,rc.status,rc.settings,rc.options,%
-rc.getOption,promptPackage,promptData,personList,person,%
-packageVersion,packageStatus,packageDescription,package.skeleton,package.contents,%
-old.packages,object.size,nsl,news,new.packages,%
-modifyList,mirror2html,memory.size,memory.limit,makeRweaveLatexCodeRunner,%
-make.socket,make.packages.html,maintainer,lsf.str,ls.str,%
-localeToCharset,loadhistory,limitedLabels,is.relistable,installed.packages,%
-install.packages,history,help.start,help.search,help.request,%
-head.matrix,head,globalVariables,glob2rx,getTxtProgressBar,%
-getSrcref,getSrcLocation,getSrcFilename,getSrcDirectory,getS3method,%
+morekeywords={[7]write.table,write.socket,write.csv2,write.csv,vignette,%
+url.show,upgrade,update.packages,update.packageStatus,unzip,%
+untar,unstack,type.convert,txtProgressBar,toLatex,%
+toBibtex,timestamp,tar,tail.matrix,tail,%
+summaryRprof,strOptions,str,stack,setTxtProgressBar,%
+setRepositories,setBreakpoint,sessionInfo,select.list,savehistory,%
+rtags,removeSource,remove.packages,relist,recover,%
+readCitationFile,read.table,read.socket,read.fwf,read.fortran,%
+read.delim2,read.delim,read.csv2,read.csv,read.DIF,%
+rc.status,rc.settings,rc.options,rc.getOption,promptPackage,%
+promptData,process.events,personList,person,packageVersion,%
+packageStatus,packageDescription,package.skeleton,old.packages,object.size,%
+nsl,news,new.packages,modifyList,mirror2html,%
+memory.size,memory.limit,makeRweaveLatexCodeRunner,make.socket,make.packages.html,%
+maintainer,lsf.str,ls.str,localeToCharset,loadhistory,%
+limitedLabels,is.relistable,installed.packages,install.packages,history,%
+help.start,help.search,help.request,head.matrix,head,%
+globalVariables,glob2rx,getTxtProgressBar,getSrcref,getSrcLocation,%
+getSrcFilename,getSrcDirectory,getS3method,getParseText,getParseData,%
getFromNamespace,getCRANmirrors,getAnywhere,formatUL,formatOL,%
flush.console,fixInNamespace,findLineNum,file_test,file.edit,%
dump.frames,download.packages,download.file,de.setup,de.restore,%
de.ncols,data.entry,create.post,count.fields,contrib.url,%
-compareVersion,combn,close.socket,citation,citHeader,%
-citFooter,citEntry,chooseCRANmirror,chooseBioCmirror,checkCRAN,%
-capture.output,bug.report,browseVignettes,browseURL,browseEnv,%
-bibentry,available.packages,assignInNamespace,assignInMyNamespace,aspell_write_personal_dictionary_file,%
-aspell_package_vignettes,aspell_package_Rd_files,aspell,as.roman,as.relistable,%
-as.personList,as.person,argsAnywhere,aregexec,alarm,%
-adist,View,URLencode,URLdecode,SweaveSyntaxNoweb,%
-SweaveSyntaxLatex,SweaveSyntConv,SweaveHooks,Sweave,Stangle,%
-RweaveTryStop,RweaveLatexWritedoc,RweaveLatexSetup,RweaveLatexOptions,RweaveLatexFinish,%
-RweaveLatex,RweaveEvalWithOpt,RweaveChunkPrefix,RtangleWritedoc,RtangleSetup,%
-Rtangle,Rprofmem,Rprof,RSiteSearch,RShowDoc,%
-CRAN.packages%
+compareVersion,combn,close.socket,citeNatbib,cite,%
+citation,citHeader,citFooter,citEntry,chooseCRANmirror,%
+chooseBioCmirror,checkCRAN,capture.output,bug.report,browseVignettes,%
+browseURL,browseEnv,bibentry,available.packages,assignInNamespace,%
+assignInMyNamespace,aspell_write_personal_dictionary_file,aspell_package_vignettes,aspell_package_Rd_files,aspell_package_R_files,%
+aspell_package_C_files,aspell,as.roman,as.relistable,as.personList,%
+as.person,argsAnywhere,aregexec,alarm,adist,%
+View,URLencode,URLdecode,SweaveSyntaxNoweb,SweaveSyntaxLatex,%
+SweaveSyntConv,SweaveHooks,Sweave,Stangle,RweaveTryStop,%
+RweaveLatexWritedoc,RweaveLatexSetup,RweaveLatexOptions,RweaveLatexFinish,RweaveLatex,%
+RweaveEvalWithOpt,RweaveChunkPrefix,RtangleWritedoc,RtangleSetup,Rtangle,%
+Rprofmem,Rprof,RSiteSearch,RShowDoc,CRAN.packages%
},%
keywordstyle={[7]{\bf\color{RRecomdcolor}}},%
%
@@ -631,48 +655,48 @@
% --------------------------
% Registration of package methods [recommended or base]
% --------------------------
-morekeywords={[9]validSlotNames,validObject,unRematchDefinition,trySilent,tryNew,%
-traceOn,traceOff,testVirtual,testInheritedMethods,superClassDepth,%
-substituteFunctionArgs,substituteDirect,slotsFromS3,slotNames,slot<-,%
-slot,signature,sigToEnv,showMlist,showMethods,%
-showExtends,showDefault,showClass,setValidity,setReplaceMethod,%
-setRefClass,setPrimitiveMethods,setPackageName,setOldClass,setMethod,%
-setLoadActions,setLoadAction,setIs,setGroupGeneric,setGenericImplicit,%
-setGeneric,setDataPart,setClassUnion,setClass,setAs,%
-sessionData,selectSuperClasses,selectMethod,seemsS4Object,sealClass,%
-resetGeneric,resetClass,requireMethods,representation,removeMethodsObject,%
-removeMethods,removeMethod,removeGeneric,removeClass,rematchDefinition,%
-registerImplicitGenerics,reconcilePropertiesAndPrototype,rbind2,prototype,promptMethods,%
-promptClass,prohibitGeneric,possibleExtends,packageSlot<-,packageSlot,%
-newEmptyObject,newClassRepresentation,newBasic,multipleClasses,mlistMetaName,%
-missingArg,methodsPackageMetaName,methodSignatureMatrix,method.skeleton,metaNameUndo,%
-mergeMethods,matchSignature,makeStandardGeneric,makePrototypeFromClassDef,makeMethodsList,%
-makeGeneric,makeExtends,makeClassRepresentation,loadMethod,listFromMlist,%
-listFromMethods,linearizeMlist,languageEl<-,languageEl,isXS3Class,%
-isVirtualClass,isSealedMethod,isSealedClass,isGroup,isGrammarSymbol,%
-isGeneric,isClassUnion,isClassDef,isClass,insertSource,%
-insertMethod,insertClassMethods,initialize,initRefFields,initFieldArgs,%
-inheritedSlotNames,implicitGeneric,hasMethods,hasMethod,hasLoadAction,%
-hasArg,getVirtual,getValidity,getSubclasses,getSlots,%
-getRefClass,getPrototype,getProperties,getPackageName,getMethodsMetaData,%
-getMethodsForDispatch,getMethods,getMethod,getLoadActions,getGroupMembers,%
-getGroup,getGenerics,getGeneric,getFunction,getExtends,%
-getDataPart,getClasses,getClassPackage,getClassName,getClassDef,%
-getClass,getAllSuperClasses,getAllMethods,getAccess,generic.skeleton,%
-functionBody<-,functionBody,formalArgs,fixPre1.8,findUnique,%
-findMethods,findMethodSignatures,findMethod,findFunction,findClass,%
-finalDefaultMethod,extends,existsMethod,existsFunction,evalqOnLoad,%
-evalSource,evalOnLoad,emptyMethodsList,empty.dump,elNamed<-,%
-elNamed,el<-,el,dumpMethods,dumpMethod,%
-doPrimitiveMethod,defaultPrototype,defaultDumpName,conformMethod,completeSubclasses,%
-completeExtends,completeClassDefinition,coerce<-,coerce,classesToAM,%
-className,classMetaName,classLabel,checkSlotAssignment,cbind2,%
-canCoerce,callNextMethod,callGeneric,cacheMethod,cacheMetaData,%
-cacheGenericsMetaData,body<-,balanceMethodsList,assignMethodsMetaData,assignClassDef,%
-asMethodDefinition,as<-,allNames,allGenerics,addNextMethod,%
-Summary,SignatureMethod,S3Part<-,S3Part,S3Class<-,%
-S3Class,Quote,MethodsListSelect,MethodsList,MethodAddCoerce,%
-Math2,Logic,Complex,Compare,Arith%
+morekeywords={[9]validSlotNames,validObject,unRematchDefinition,tryNew,traceOn,%
+traceOff,testVirtual,testInheritedMethods,superClassDepth,substituteFunctionArgs,%
+substituteDirect,slotsFromS3,slotNames,slot<-,slot,%
+signature,sigToEnv,showMlist,showMethods,showExtends,%
+showDefault,showClass,setValidity,setReplaceMethod,setRefClass,%
+setPrimitiveMethods,setPackageName,setOldClass,setMethod,setLoadActions,%
+setLoadAction,setIs,setGroupGeneric,setGenericImplicit,setGeneric,%
+setDataPart,setClassUnion,setClass,setAs,selectSuperClasses,%
+selectMethod,seemsS4Object,sealClass,resetGeneric,resetClass,%
+requireMethods,representation,removeMethodsObject,removeMethods,removeMethod,%
+removeGeneric,removeClass,rematchDefinition,registerImplicitGenerics,reconcilePropertiesAndPrototype,%
+rbind2,prototype,promptMethods,promptClass,prohibitGeneric,%
+possibleExtends,packageSlot<-,packageSlot,newEmptyObject,newClassRepresentation,%
+newBasic,multipleClasses,mlistMetaName,missingArg,methodsPackageMetaName,%
+methodSignatureMatrix,method.skeleton,metaNameUndo,mergeMethods,matchSignature,%
+makeStandardGeneric,makePrototypeFromClassDef,makeMethodsList,makeGeneric,makeExtends,%
+makeClassRepresentation,loadMethod,listFromMlist,listFromMethods,linearizeMlist,%
+languageEl<-,languageEl,isXS3Class,isVirtualClass,isSealedMethod,%
+isSealedClass,isGroup,isGrammarSymbol,isGeneric,isClassUnion,%
+isClassDef,isClass,insertSource,insertMethod,insertClassMethods,%
+initialize,initRefFields,initFieldArgs,inheritedSlotNames,implicitGeneric,%
+hasMethods,hasMethod,hasLoadAction,hasArg,getVirtual,%
+getValidity,getSubclasses,getSlots,getRefClass,getPrototype,%
+getProperties,getPackageName,getMethodsMetaData,getMethodsForDispatch,getMethods,%
+getMethod,getLoadActions,getGroupMembers,getGroup,getGenerics,%
+getGeneric,getFunction,getExtends,getDataPart,getClasses,%
+getClassPackage,getClassName,getClassDef,getClass,getAllSuperClasses,%
+getAllMethods,getAccess,generic.skeleton,functionBody<-,functionBody,%
+formalArgs,fixPre1.8,findUnique,findMethods,findMethodSignatures,%
+findMethod,findFunction,findClass,finalDefaultMethod,extends,%
+existsMethod,existsFunction,evalqOnLoad,evalSource,evalOnLoad,%
+emptyMethodsList,empty.dump,elNamed<-,elNamed,el<-,%
+el,dumpMethods,dumpMethod,doPrimitiveMethod,defaultPrototype,%
+defaultDumpName,conformMethod,completeSubclasses,completeExtends,completeClassDefinition,%
+coerce<-,coerce,classesToAM,className,classMetaName,%
+classLabel,checkSlotAssignment,cbind2,canCoerce,callNextMethod,%
+callGeneric,cacheMethod,cacheMetaData,cacheGenericsMetaData,body<-,%
+balanceMethodsList,assignMethodsMetaData,assignClassDef,asMethodDefinition,as<-,%
+allNames,allGenerics,addNextMethod,Summary,SignatureMethod,%
+S3Part<-,S3Part,S3Class<-,S3Class,Quote,%
+MethodsListSelect,MethodsList,MethodAddCoerce,Math2,Logic,%
+Complex,Compare,Arith%
},%
keywordstyle={[9]{\bf\color{RRecomdcolor}}},%
%
@@ -710,23 +734,23 @@
socketConnection,slice.index,sink.number,simplify2array,simpleWarning,%
simpleMessage,simpleError,simpleCondition,signalCondition,showConnections,%
shQuote,setTimeLimit,setSessionTimeLimit,setNamespaceInfo,setHook,%
-setCConverterStatus,set.seed,serialize,seq_len,seq_along,%
-seq.int,seq.default,seq.POSIXt,seq.Date,seek.connection,%
-seek,scale.default,saveRDS,save.image,sample.int,%
-sQuote,rowsum.default,rowsum.data.frame,rownames<-,rowSums,%
-rowMeans,row.names<-.default,row.names<-.data.frame,row.names<-,row.names.default,%
-row.names.data.frame,row.names,round.POSIXt,round.Date,rev.default,%
-retracemem,restartFormals,restartDescription,requireNamespace,replicate,%
+set.seed,serialize,seq_len,seq_along,seq.int,%
+seq.default,seq.POSIXt,seq.Date,seek.connection,seek,%
+scale.default,saveRDS,save.image,sample.int,sQuote,%
+rowsum.default,rowsum.data.frame,rownames<-,rowSums,rowMeans,%
+row.names<-.default,row.names<-.data.frame,row.names<-,row.names.default,row.names.data.frame,%
+row.names,round.POSIXt,round.Date,rev.default,retracemem,%
+restartFormals,restartDescription,requireNamespace,replicate,rep_len,%
rep.numeric_version,rep.int,rep.factor,rep.POSIXlt,rep.POSIXct,%
-rep.Date,removeTaskCallback,removeCConverter,regmatches<-,regmatches,%
-registerS3methods,registerS3method,regexec,reg.finalizer,readRenviron,%
-readRDS,readLines,readChar,readBin,read.dcf,%
-rcond,rbind.data.frame,rawToChar,rawToBits,rawShift,%
-rawConnectionValue,rawConnection,raw,rapply,range.default,%
-quarters.POSIXt,quarters.Date,quarters,qr.solve,qr.resid,%
-qr.qy,qr.qty,qr.fitted,qr.default,qr.coef,%
-qr.X,qr.R,qr.Q,pushBackLength,pushBack,%
-psigamma,prop.table,proc.time,print.warnings,print.table,%
+rep.Date,removeTaskCallback,regmatches<-,regmatches,registerS3methods,%
+registerS3method,regexec,reg.finalizer,readRenviron,readRDS,%
+readLines,readChar,readBin,read.dcf,rcond,%
+rbind.data.frame,rawToChar,rawToBits,rawShift,rawConnectionValue,%
+rawConnection,raw,rapply,range.default,quarters.POSIXt,%
+quarters.Date,quarters,qr.solve,qr.resid,qr.qy,%
+qr.qty,qr.fitted,qr.default,qr.coef,qr.X,%
+qr.R,qr.Q,pushBackLength,pushBack,psigamma,%
+provideDimnames,prop.table,proc.time,print.warnings,print.table,%
print.summaryDefault,print.summary.table,print.srcref,print.srcfile,print.simple.list,%
print.rle,print.restart,print.proc_time,print.packageInfo,print.octmode,%
print.numeric_version,print.noquote,print.listof,print.libraryIQR,print.hexmode,%
@@ -744,37 +768,36 @@
names<-,names.POSIXlt,mostattributes<-,months.POSIXt,months.Date,%
months,month.name,month.abb,mode<-,mget,%
message,merge.default,merge.data.frame,memory.profile,memDecompress,%
-memCompress,mem.limits,mean.difftime,mean.default,mean.data.frame,%
-mean.POSIXlt,mean.POSIXct,mean.Date,max.col,match.fun,%
-match.call,match.arg,mat.or.vec,margin.table,mapply,%
-manglePackageName,makeActiveBinding,make.unique,make.names,lower.tri,%
-logb,lockEnvironment,lockBinding,loadingNamespaceInfo,loadedNamespaces,%
-loadNamespace,list2env,list.files,list.dirs,library.dynam.unload,%
-library.dynam,lfactorial,levels<-.factor,levels<-,levels.default,%
-letters,length<-.factor,length<-,length.POSIXlt,lazyLoadDBfetch,%
-lazyLoadDBexec,lazyLoad,labels.default,l10n_info,kappa.tri,%
-kappa.qr,kappa.lm,kappa.default,julian.POSIXt,julian.Date,%
-julian,isdebugged,isatty,isTRUE,isSymmetric.matrix,%
-isSymmetric,isSeekable,isS4,isRestart,isOpen,%
-isNamespace,isIncomplete,isBaseNamespace,is.vector,is.unsorted,%
-is.table,is.symbol,is.single,is.recursive,is.real,%
-is.raw,is.qr,is.primitive,is.pairlist,is.package_version,%
-is.ordered,is.object,is.numeric_version,is.numeric.difftime,is.numeric.POSIXt,%
-is.numeric.Date,is.numeric,is.null,is.nan,is.name,%
-is.na<-.factor,is.na<-.default,is.na<-,is.na.numeric_version,is.na.data.frame,%
-is.na.POSIXlt,is.na,is.matrix,is.logical,is.loaded,%
-is.list,is.language,is.integer,is.infinite,is.function,%
-is.finite,is.factor,is.expression,is.environment,is.element,%
-is.double,is.data.frame,is.complex,is.character,is.call,%
-is.atomic,is.array,is.R,invokeRestartInteractively,invokeRestart,%
-inverse.rle,intToUtf8,intToBits,importIntoEnv,identity,%
-identical,icuSetCollate,iconvlist,iconv,gzfile,%
-gzcon,grepl,grepRaw,gregexpr,gettextf,%
-gettext,getTaskCallbackNames,getSrcLines,getRversion,getNumCConverters,%
-getNativeSymbolInfo,getNamespaceVersion,getNamespaceUsers,getNamespaceName,getNamespaceInfo,%
-getNamespaceImports,getNamespaceExports,getNamespace,getLoadedDLLs,getHook,%
-getExportedValue,getElement,getDLLRegisteredRoutines.character,getDLLRegisteredRoutines.DLLInfo,getDLLRegisteredRoutines,%
-getConnection,getCallingDLLe,getCallingDLL,getCConverterStatus,getCConverterDescriptions,%
+memCompress,mem.limits,mean.difftime,mean.default,mean.POSIXlt,%
+mean.POSIXct,mean.Date,max.col,match.fun,match.call,%
+match.arg,mat.or.vec,margin.table,mapply,manglePackageName,%
+makeActiveBinding,make.unique,make.names,lower.tri,logb,%
+lockEnvironment,lockBinding,loadingNamespaceInfo,loadedNamespaces,loadNamespace,%
+list2env,list.files,list.dirs,library.dynam.unload,library.dynam,%
+lfactorial,levels<-.factor,levels<-,levels.default,letters,%
+length<-.factor,length<-,length.POSIXlt,lazyLoadDBfetch,lazyLoadDBexec,%
+lazyLoad,labels.default,l10n_info,kappa.qr,kappa.lm,%
+kappa.default,julian.POSIXt,julian.Date,julian,isdebugged,%
+isatty,isTRUE,isSymmetric.matrix,isSymmetric,isSeekable,%
+isS4,isRestart,isOpen,isNamespace,isIncomplete,%
+isBaseNamespace,is.vector,is.unsorted,is.table,is.symbol,%
+is.single,is.recursive,is.real,is.raw,is.qr,%
+is.primitive,is.pairlist,is.package_version,is.ordered,is.object,%
+is.numeric_version,is.numeric.difftime,is.numeric.POSIXt,is.numeric.Date,is.numeric,%
+is.null,is.nan,is.name,is.na<-.factor,is.na<-.default,%
+is.na<-,is.na.numeric_version,is.na.data.frame,is.na.POSIXlt,is.na,%
+is.matrix,is.logical,is.loaded,is.list,is.language,%
+is.integer,is.infinite,is.function,is.finite,is.factor,%
+is.expression,is.environment,is.element,is.double,is.data.frame,%
+is.complex,is.character,is.call,is.atomic,is.array,%
+is.R,invokeRestartInteractively,invokeRestart,inverse.rle,intToUtf8,%
+intToBits,importIntoEnv,identity,identical,icuSetCollate,%
+iconvlist,iconv,gzfile,gzcon,grepl,%
+grepRaw,gregexpr,gettextf,gettext,getTaskCallbackNames,%
+getSrcLines,getRversion,getNativeSymbolInfo,getNamespaceVersion,getNamespaceUsers,%
+getNamespaceName,getNamespaceInfo,getNamespaceImports,getNamespaceExports,getNamespace,%
+getLoadedDLLs,getHook,getExportedValue,getElement,getDLLRegisteredRoutines.character,%
+getDLLRegisteredRoutines.DLLInfo,getDLLRegisteredRoutines,getConnection,getCallingDLLe,getCallingDLL,%
getAllConnections,gctorture2,gc.time,formatDL,format.summaryDefault,%
format.pval,format.packageInfo,format.octmode,format.numeric_version,format.libraryIQR,%
format.info,format.hexmode,format.factor,format.difftime,format.default,%
@@ -796,52 +819,54 @@
cut.POSIXt,cut.Date,contributors,conditionMessage.condition,conditionMessage,%
conditionCall.condition,conditionCall,computeRestarts,comment<-,colnames<-,%
colSums,colMeans,closeAllConnections,close.srcfilealias,close.srcfile,%
-close.connection,class<-,chol.default,check_tzones,chartr,%
-charToRaw,char.expand,cbind.data.frame,casefold,capabilities,%
-callCC,c.numeric_version,c.noquote,c.POSIXlt,c.POSIXct,%
-c.Date,bzfile,by.default,by.data.frame,browserText,%
-browserSetDebug,browserCondition,bquote,body<-,bindtextdomain,%
-bindingIsLocked,bindingIsActive,baseenv,attributes<-,attr<-,%
-attr.all.equal,attachNamespace,assign,asS4,asS3,%
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/distr -r 857
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