- using R Under development (unstable) (2012-02-27 r58511)
- using platform: x86_64-pc-mingw32 (64-bit)
- using session charset: ISO8859-1
- checking for file 'SweaveListingUtils/DESCRIPTION' ... OK
- this is package 'SweaveListingUtils' version '0.5.5'
- package encoding: latin1
- checking package namespace information ... OK
- checking package dependencies ... OK
- checking if this is a source package ... OK
- checking if there is a namespace ... OK
- checking whether package 'SweaveListingUtils' can be installed ... OK
- checking installed package size ... OK
- checking package directory ... OK
- checking for portable file names ... OK
- checking DESCRIPTION meta-information ... OK
- checking top-level files ... OK
- checking index information ... OK
- checking package subdirectories ... OK
- checking R files for non-ASCII characters ... OK
- checking R files for syntax errors ... OK
- loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
- loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
- checking for unstated dependencies in R code ... OK
- checking S3 generic/method consistency ... OK
- checking replacement functions ... OK
- checking foreign function calls ... OK
- checking R code for possible problems ... OK
- checking Rd files ... OK
- checking Rd metadata ... OK
- checking Rd cross-references ... OK
- checking for missing documentation entries ... OK
- checking for code/documentation mismatches ... OK
- checking Rd \usage sections ... OK
- checking Rd contents ... OK
- checking for unstated dependencies in examples ... OK
- checking sizes of PDF files under 'inst/doc' ... OK
- checking installed files from 'inst/doc' ... OK
- checking examples ...
** running examples for arch 'i386' ... OK
** checking differences from 'SweaveListingUtils-Ex_i386.Rout' to 'SweaveListingUtils-Ex.Rout.save' ...
2c2
< :startupmsg> Utilities for start-up messages (version 0.7.2)
---
> :startupmsg> Utilities for start-up messages (version 0.7.3)
78c78,79
< ... nothing discovered so far ...>
---
> ... nothing discovered so far ...
> >
399c400
< \newcommand{\pkgversion}{{\tt 2.3.3}}
---
> \newcommand{\pkgversion}{{\tt 2.3.4}}
453,495c454,495
< 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%
---
> pacf,p.adjust.methods,p.adjust,order.dendrogram,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%
517,533c517,532
< morekeywords={[6]xyz.coords,xyTable,xy.coords,xfig,windowsFonts,%
< windowsFont,windows.options,windows,win.print,win.metafile,%
< win.graph,trans3d,topo.colors,tiff,terrain.colors,%
< svg,setPS,setGraphicsEventHandlers,setGraphicsEventEnv,setEPS,%
< savePlot,rgb2hsv,replayPlot,recordPlot,recordGraphics,%
< ps.options,postscriptFonts,postscriptFont,png,pdfFonts,%
< pdf.options,pdf,nclass.scott,nclass.Sturges,nclass.FD,%
< n2mfrow,msgWindow,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,bringToTop,boxplot.stats,bmp,blues9,%
---
> morekeywords={[6]xyz.coords,xyTable,xy.coords,xfig,trans3d,%
> 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,%
535c534,535
< Type1Font,Hershey,CIDFont%
---
> X11Fonts,X11Font,X11.options,Type1Font,Hershey,%
> CIDFont%
542,565c542,560
< morekeywords={[7]zip.unpack,zip.file.extract,wsbrowser,writeClipboard,write.table,%
< write.socket,write.csv2,write.csv,winProgressBar,winMenuNames,%
< winMenuItems,winMenuDelItem,winMenuDel,winMenuAddItem,winMenuAdd,%
< winDialogString,winDialog,win.version,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,shortPathName,setWindowTitle,%
< setWinProgressBar,setTxtProgressBar,setStatusBar,setRepositories,setInternet2,%
< setBreakpoint,sessionInfo,select.list,savehistory,rtags,%
< removeSource,remove.packages,relist,recover,readRegistry,%
< readClipboard,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,news,new.packages,modifyList,mirror2html,%
< memory.size,memory.limit,makeRweaveLatexCodeRunner,make.socket,make.packages.html,%
< maintainer,lsf.str,ls.str,localeToCharset,loadhistory,%
< loadRconsole,limitedLabels,is.relistable,installed.packages,install.packages,%
< history,help.start,help.search,help.request,head.matrix,%
< head,glob2rx,getWindowsHandles,getWindowsHandle,getWindowTitle,%
< getWinProgressBar,getTxtProgressBar,getSrcref,getSrcLocation,getSrcFilename,%
< getSrcDirectory,getS3method,getIdentification,getFromNamespace,getClipboardFormats,%
---
> 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,glob2rx,getTxtProgressBar,getSrcref,%
> getSrcLocation,getSrcFilename,getSrcDirectory,getS3method,getFromNamespace,%
571,581c566,575
< citEntry,chooseCRANmirror,chooseBioCmirror,choose.files,choose.dir,%
< 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,arrangeWindows,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,Filters,DLL.version,CRAN.packages%
---
> citEntry,chooseCRANmirror,chooseBioCmirror,checkCRAN,capture.output,%
> bug.report,browseVignettes,browseURL,browseEnv,bibentry,%
> available.packages,assignInNamespace,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%
665,709c659,704
< writeChar,writeBin,write.dcf,within.list,within.data.frame,%
< within,withVisible,withRestarts,withCallingHandlers,with.default,%
< with,which.min,which.max,weekdays.POSIXt,weekdays.Date,%
< weekdays,version,vapply,utf8ToInt,upper.tri,%
< unz,untracemem,unsplit,unserialize,unlockBinding,%
< unloadNamespace,unix.time,units<-.difftime,units<-,units.difftime,%
< units,unique.numeric_version,unique.matrix,unique.default,unique.data.frame,%
< unique.array,unique.POSIXlt,tryCatch,truncate.connection,truncate,%
< trunc.POSIXt,trunc.Date,transform.default,transform.data.frame,tracingState,%
< tracemem,toupper,topenv,tolower,toString.default,%
< toString,textConnectionValue,textConnection,testPlatformEquivalence,tempdir,%
< tcrossprod,taskCallbackManager,t.default,t.data.frame,system2,%
< system.time,system.file,sys.status,sys.source,sys.save.image,%
< sys.parents,sys.parent,sys.on.exit,sys.nframe,sys.load.image,%
< sys.function,sys.frames,sys.frame,sys.calls,sys.call,%
< suppressWarnings,suppressPackageStartupMessages,suppressMessages,summary.table,summary.srcref,%
< summary.srcfile,summary.matrix,summary.factor,summary.default,summary.data.frame,%
< summary.connection,summary.POSIXlt,summary.POSIXct,summary.Date,substring<-,%
< substr<-,subset.matrix,subset.default,subset.data.frame,strwrap,%
< strtrim,strtoi,strptime,strftime,storage.mode<-,%
< storage.mode,stopifnot,stdout,stdin,stderr,%
< standardGeneric,srcref,srcfilecopy,srcfilealias,srcfile,%
< sprintf,split<-.default,split<-.data.frame,split<-,split.default,%
< split.data.frame,split.POSIXct,split.Date,sort.list,sort.int,%
< sort.default,sort.POSIXlt,solve.qr,solve.default,socketSelect,%
< socketConnection,slice.index,sink.number,simplify2array,simpleWarning,%
< simpleMessage,simpleError,simpleCondition,signalCondition,showConnections,%
< shell.exec,shell,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,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,%
---
> writeChar,writeBin,write.table0,write.dcf,within.list,%
> within.data.frame,within,withVisible,withRestarts,withCallingHandlers,%
> with.default,with,which.min,which.max,weekdays.POSIXt,%
> weekdays.Date,weekdays,version,vapply,utf8ToInt,%
> upper.tri,unz,untracemem,unsplit,unserialize,%
> unlockBinding,unloadNamespace,unix.time,units<-.difftime,units<-,%
> units.difftime,units,unique.numeric_version,unique.matrix,unique.default,%
> unique.data.frame,unique.array,unique.POSIXlt,tryCatch,truncate.connection,%
> truncate,trunc.POSIXt,trunc.Date,transform.default,transform.data.frame,%
> tracingState,tracemem,toupper,topenv,tolower,%
> toString.default,toString,textConnectionValue,textConnection,testPlatformEquivalence,%
> tempdir,tcrossprod,taskCallbackManager,t.default,t.data.frame,%
> system2,system.time,system.file,sys.status,sys.source,%
> sys.save.image,sys.parents,sys.parent,sys.on.exit,sys.nframe,%
> sys.load.image,sys.function,sys.frames,sys.frame,sys.calls,%
> sys.call,symbol.For,symbol.C,suppressWarnings,suppressPackageStartupMessages,%
> suppressMessages,summary.table,summary.srcref,summary.srcfile,summary.matrix,%
> summary.factor,summary.default,summary.data.frame,summary.connection,summary.POSIXlt,%
> summary.POSIXct,summary.Date,substring<-,substr<-,subset.matrix,%
> subset.default,subset.data.frame,strwrap,strtrim,strtoi,%
> strptime,strftime,storage.mode<-,storage.mode,stopifnot,%
> stdout,stdin,stderr,standardGeneric,srcref,%
> srcfilecopy,srcfilealias,srcfile,sprintf,split<-.default,%
> split<-.data.frame,split<-,split.default,split.data.frame,split.POSIXct,%
> split.Date,source.url,sort.list,sort.int,sort.default,%
> sort.POSIXlt,solve.qr,solve.default,socketSelect,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,%
> scan.url,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.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.table.url,%
> 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,printNoClass,%
718c713
< path.package,path.expand,paste0,parseNamespaceFile,parent.frame,%
---
> path.package,path.expand,parseNamespaceFile,parse.dcf,parent.frame,%
720,778c715,774
< packageEvent,packBits,open.srcfilecopy,open.srcfilealias,open.srcfile,%
< open.connection,open,on.exit,oldClass<-,oldClass,%
< nzchar,numeric_version,normalizePath,norm,ngettext,%
< new.env,namespaceImportMethods,namespaceImportFrom,namespaceImportClasses,namespaceImport,%
< namespaceExport,names<-.POSIXlt,names<-,names.POSIXlt,mostattributes<-,%
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< memory.profile,memDecompress,memCompress,mem.limits,mean.difftime,%
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< max.col,match.fun,match.call,match.arg,mat.or.vec,%
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< 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,%
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< 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,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,format.data.frame,format.POSIXlt,format.POSIXct,%
< format.Date,format.AsIs,formals<-,force,flush.connection,%
< flush,findRestart,findPackageEnv,findInterval,find.package,%
< file.symlink,file.show,file.rename,file.remove,file.path,%
< file.link,file.info,file.exists,file.create,file.copy,%
< file.choose,file.append,file.access,fifo,factorial,%
< expm1,expand.grid,eval.parent,environmentName,environmentIsLocked,%
< environment<-,env.profile,enquote,encodeString,enc2utf8,%
< enc2native,emptyenv,eapply,dyn.unload,dyn.load,%
< duplicated.numeric_version,duplicated.matrix,duplicated.default,duplicated.data.frame,duplicated.array,%
< duplicated.POSIXlt,droplevels.factor,droplevels.data.frame,droplevels,do.call,%
< dir.create,dimnames<-.data.frame,dimnames<-,dimnames.data.frame,dim<-,%
< dim.data.frame,difftime,diff.default,diff.POSIXt,diff.Date,%
< diag<-,determinant.matrix,determinant,det,delayedAssign,%
< default.stringsAsFactors,debugonce,data.matrix,data.frame,data.class,%
< dQuote,cut.default,cut.POSIXt,cut.Date,contributors,%
< conditionMessage.condition,conditionMessage,conditionCall.condition,conditionCall,computeRestarts,%
< comment<-,colnames<-,colSums,colMeans,closeAllConnections,%
---
> packageEvent,package.description,packBits,open.srcfilecopy,open.srcfilealias,%
> open.srcfile,open.connection,open,on.exit,oldClass<-,%
> oldClass,nzchar,numeric_version,normalizePath,norm,%
> ngettext,new.env,namespaceImportMethods,namespaceImportFrom,namespaceImportClasses,%
> namespaceImport,namespaceExport,names<-.POSIXlt,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,loadURL,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,getAllConnections,%
> gctorture2,gc.time,formatDL,format.pval,format.packageInfo,%
> format.octmode,format.numeric_version,format.libraryIQR,format.info,format.hexmode,%
> format.factor,format.difftime,format.default,format.data.frame,format.char,%
> format.POSIXlt,format.POSIXct,format.Date,format.AsIs,formals<-,%
> force,flush.connection,flush,findRestart,findPackageEnv,%
> findInterval,find.package,file.symlink,file.show,file.rename,%
> file.remove,file.path,file.link,file.info,file.exists,%
> file.create,file.copy,file.choose,file.append,file.access,%
> fifo,factorial,expm1,expand.grid,eval.parent,%
> environmentName,environmentIsLocked,environment<-,env.profile,enquote,%
> encodeString,enc2utf8,enc2native,emptyenv,eapply,%
> dyn.unload,dyn.load,duplicated.numeric_version,duplicated.matrix,duplicated.default,%
> duplicated.data.frame,duplicated.array,duplicated.POSIXlt,droplevels.factor,droplevels.data.frame,%
> droplevels,do.call,dir.create,dimnames<-.data.frame,dimnames<-,%
> dimnames.data.frame,dim<-,dim.data.frame,difftime,diff.default,%
> diff.POSIXt,diff.Date,diag<-,determinant.matrix,determinant,%
> det,delayedAssign,default.stringsAsFactors,debugonce,data.matrix,%
> data.frame,data.class,dQuote,cut.default,cut.POSIXt,%
> cut.Date,contributors,conditionMessage.condition,conditionMessage,conditionCall.condition,%
> conditionCall,computeRestarts,comment<-,colnames<-,colSums,%
> colMeans,codes<-,codes.ordered,codes.factor,closeAllConnections,%
815,816c811,812
< Sys.setlocale,Sys.setenv,Sys.setFileTime,Sys.readlink,Sys.localeconv,%
< Sys.junction,Sys.info,Sys.glob,Sys.getpid,Sys.getlocale,%
---
> Sys.setlocale,Sys.setenv,Sys.setFileTime,Sys.readlink,Sys.putenv,%
> Sys.localeconv,Sys.info,Sys.glob,Sys.getpid,Sys.getlocale,%
823,825c819,822
< Math.POSIXt,Math.Date,Map,La.svd,LETTERS,%
< ISOdatetime,ISOdate,Find,Filter,F,%
< Encoding<-,Encoding,Cstack_info%
---
> Math.POSIXt,Math.Date,Map,La.svd,La.eigen,%
> La.chol2inv,La.chol,LETTERS,ISOdatetime,ISOdate,%
> Find,Filter,F,Encoding<-,Encoding,%
> Cstack_info%
1394,1402c1391,1398
< mgus1,mgus,match.ratetable,lung,logan,%
< leukemia,labels.survreg,kidney,jasa1,jasa,%
< is.ratetable,is.na.ratetable,is.na.coxph.penalty,is.na.Surv,is.Surv,%
< heart,frailty.t,frailty.gaussian,frailty.gamma,frailty,%
< format.Surv,dsurvreg,coxph.fit,coxph.detail,coxph.control,%
< coxph,cox.zph,colon,cluster,clogit,%
< cgd,cch,cancer,bladder2,bladder1,%
< bladder,basehaz,attrassign,aml,aareg,%
< Surv%
---
> mgus1,mgus,match.ratetable,lung,leukemia,%
> labels.survreg,kidney,jasa1,jasa,is.ratetable,%
> is.na.ratetable,is.na.coxph.penalty,is.na.Surv,is.Surv,heart,%
> frailty.t,frailty.gaussian,frailty.gamma,frailty,format.Surv,%
> dsurvreg,coxph.fit,coxph.detail,coxph.control,coxph,%
> cox.zph,colon,cluster,clogit,cgd,%
> cch,cancer,bladder2,bladder1,bladder,%
> basehaz,attrassign,aml,aareg,Surv%
2061c2057
< [1,] "2.3.3"
---
> [1,] "2.3.4"
OK
** running examples for arch 'x64' ... OK
** checking differences from 'SweaveListingUtils-Ex_x64.Rout' to 'SweaveListingUtils-Ex.Rout.save' ...
2c2
< :startupmsg> Utilities for start-up messages (version 0.7.2)
---
> :startupmsg> Utilities for start-up messages (version 0.7.3)
78c78,79
< ... nothing discovered so far ...>
---
> ... nothing discovered so far ...
> >
399c400
< \newcommand{\pkgversion}{{\tt 2.3.3}}
---
> \newcommand{\pkgversion}{{\tt 2.3.4}}
453,495c454,495
< 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%
---
> pacf,p.adjust.methods,p.adjust,order.dendrogram,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%
517,533c517,532
< morekeywords={[6]xyz.coords,xyTable,xy.coords,xfig,windowsFonts,%
< windowsFont,windows.options,windows,win.print,win.metafile,%
< win.graph,trans3d,topo.colors,tiff,terrain.colors,%
< svg,setPS,setGraphicsEventHandlers,setGraphicsEventEnv,setEPS,%
< savePlot,rgb2hsv,replayPlot,recordPlot,recordGraphics,%
< ps.options,postscriptFonts,postscriptFont,png,pdfFonts,%
< pdf.options,pdf,nclass.scott,nclass.Sturges,nclass.FD,%
< n2mfrow,msgWindow,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,bringToTop,boxplot.stats,bmp,blues9,%
---
> morekeywords={[6]xyz.coords,xyTable,xy.coords,xfig,trans3d,%
> 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,%
535c534,535
< Type1Font,Hershey,CIDFont%
---
> X11Fonts,X11Font,X11.options,Type1Font,Hershey,%
> CIDFont%
542,565c542,560
< morekeywords={[7]zip.unpack,zip.file.extract,wsbrowser,writeClipboard,write.table,%
< write.socket,write.csv2,write.csv,winProgressBar,winMenuNames,%
< winMenuItems,winMenuDelItem,winMenuDel,winMenuAddItem,winMenuAdd,%
< winDialogString,winDialog,win.version,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,shortPathName,setWindowTitle,%
< setWinProgressBar,setTxtProgressBar,setStatusBar,setRepositories,setInternet2,%
< setBreakpoint,sessionInfo,select.list,savehistory,rtags,%
< removeSource,remove.packages,relist,recover,readRegistry,%
< readClipboard,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,news,new.packages,modifyList,mirror2html,%
< memory.size,memory.limit,makeRweaveLatexCodeRunner,make.socket,make.packages.html,%
< maintainer,lsf.str,ls.str,localeToCharset,loadhistory,%
< loadRconsole,limitedLabels,is.relistable,installed.packages,install.packages,%
< history,help.start,help.search,help.request,head.matrix,%
< head,glob2rx,getWindowsHandles,getWindowsHandle,getWindowTitle,%
< getWinProgressBar,getTxtProgressBar,getSrcref,getSrcLocation,getSrcFilename,%
< getSrcDirectory,getS3method,getIdentification,getFromNamespace,getClipboardFormats,%
---
> 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,glob2rx,getTxtProgressBar,getSrcref,%
> getSrcLocation,getSrcFilename,getSrcDirectory,getS3method,getFromNamespace,%
571,581c566,575
< citEntry,chooseCRANmirror,chooseBioCmirror,choose.files,choose.dir,%
< 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,arrangeWindows,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,Filters,DLL.version,CRAN.packages%
---
> citEntry,chooseCRANmirror,chooseBioCmirror,checkCRAN,capture.output,%
> bug.report,browseVignettes,browseURL,browseEnv,bibentry,%
> available.packages,assignInNamespace,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%
665,709c659,704
< writeChar,writeBin,write.dcf,within.list,within.data.frame,%
< within,withVisible,withRestarts,withCallingHandlers,with.default,%
< with,which.min,which.max,weekdays.POSIXt,weekdays.Date,%
< weekdays,version,vapply,utf8ToInt,upper.tri,%
< unz,untracemem,unsplit,unserialize,unlockBinding,%
< unloadNamespace,unix.time,units<-.difftime,units<-,units.difftime,%
< units,unique.numeric_version,unique.matrix,unique.default,unique.data.frame,%
< unique.array,unique.POSIXlt,tryCatch,truncate.connection,truncate,%
< trunc.POSIXt,trunc.Date,transform.default,transform.data.frame,tracingState,%
< tracemem,toupper,topenv,tolower,toString.default,%
< toString,textConnectionValue,textConnection,testPlatformEquivalence,tempdir,%
< tcrossprod,taskCallbackManager,t.default,t.data.frame,system2,%
< system.time,system.file,sys.status,sys.source,sys.save.image,%
< sys.parents,sys.parent,sys.on.exit,sys.nframe,sys.load.image,%
< sys.function,sys.frames,sys.frame,sys.calls,sys.call,%
< suppressWarnings,suppressPackageStartupMessages,suppressMessages,summary.table,summary.srcref,%
< summary.srcfile,summary.matrix,summary.factor,summary.default,summary.data.frame,%
< summary.connection,summary.POSIXlt,summary.POSIXct,summary.Date,substring<-,%
< substr<-,subset.matrix,subset.default,subset.data.frame,strwrap,%
< strtrim,strtoi,strptime,strftime,storage.mode<-,%
< storage.mode,stopifnot,stdout,stdin,stderr,%
< standardGeneric,srcref,srcfilecopy,srcfilealias,srcfile,%
< sprintf,split<-.default,split<-.data.frame,split<-,split.default,%
< split.data.frame,split.POSIXct,split.Date,sort.list,sort.int,%
< sort.default,sort.POSIXlt,solve.qr,solve.default,socketSelect,%
< socketConnection,slice.index,sink.number,simplify2array,simpleWarning,%
< simpleMessage,simpleError,simpleCondition,signalCondition,showConnections,%
< shell.exec,shell,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,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,%
---
> writeChar,writeBin,write.table0,write.dcf,within.list,%
> within.data.frame,within,withVisible,withRestarts,withCallingHandlers,%
> with.default,with,which.min,which.max,weekdays.POSIXt,%
> weekdays.Date,weekdays,version,vapply,utf8ToInt,%
> upper.tri,unz,untracemem,unsplit,unserialize,%
> unlockBinding,unloadNamespace,unix.time,units<-.difftime,units<-,%
> units.difftime,units,unique.numeric_version,unique.matrix,unique.default,%
> unique.data.frame,unique.array,unique.POSIXlt,tryCatch,truncate.connection,%
> truncate,trunc.POSIXt,trunc.Date,transform.default,transform.data.frame,%
> tracingState,tracemem,toupper,topenv,tolower,%
> toString.default,toString,textConnectionValue,textConnection,testPlatformEquivalence,%
> tempdir,tcrossprod,taskCallbackManager,t.default,t.data.frame,%
> system2,system.time,system.file,sys.status,sys.source,%
> sys.save.image,sys.parents,sys.parent,sys.on.exit,sys.nframe,%
> sys.load.image,sys.function,sys.frames,sys.frame,sys.calls,%
> sys.call,symbol.For,symbol.C,suppressWarnings,suppressPackageStartupMessages,%
> suppressMessages,summary.table,summary.srcref,summary.srcfile,summary.matrix,%
> summary.factor,summary.default,summary.data.frame,summary.connection,summary.POSIXlt,%
> summary.POSIXct,summary.Date,substring<-,substr<-,subset.matrix,%
> subset.default,subset.data.frame,strwrap,strtrim,strtoi,%
> strptime,strftime,storage.mode<-,storage.mode,stopifnot,%
> stdout,stdin,stderr,standardGeneric,srcref,%
> srcfilecopy,srcfilealias,srcfile,sprintf,split<-.default,%
> split<-.data.frame,split<-,split.default,split.data.frame,split.POSIXct,%
> split.Date,source.url,sort.list,sort.int,sort.default,%
> sort.POSIXlt,solve.qr,solve.default,socketSelect,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,%
> scan.url,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.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.table.url,%
> 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,printNoClass,%
718c713
< path.package,path.expand,paste0,parseNamespaceFile,parent.frame,%
---
> path.package,path.expand,parseNamespaceFile,parse.dcf,parent.frame,%
720,778c715,774
< packageEvent,packBits,open.srcfilecopy,open.srcfilealias,open.srcfile,%
< open.connection,open,on.exit,oldClass<-,oldClass,%
< nzchar,numeric_version,normalizePath,norm,ngettext,%
< new.env,namespaceImportMethods,namespaceImportFrom,namespaceImportClasses,namespaceImport,%
< namespaceExport,names<-.POSIXlt,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,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,format.data.frame,format.POSIXlt,format.POSIXct,%
< format.Date,format.AsIs,formals<-,force,flush.connection,%
< flush,findRestart,findPackageEnv,findInterval,find.package,%
< file.symlink,file.show,file.rename,file.remove,file.path,%
< file.link,file.info,file.exists,file.create,file.copy,%
< file.choose,file.append,file.access,fifo,factorial,%
< expm1,expand.grid,eval.parent,environmentName,environmentIsLocked,%
< environment<-,env.profile,enquote,encodeString,enc2utf8,%
< enc2native,emptyenv,eapply,dyn.unload,dyn.load,%
< duplicated.numeric_version,duplicated.matrix,duplicated.default,duplicated.data.frame,duplicated.array,%
< duplicated.POSIXlt,droplevels.factor,droplevels.data.frame,droplevels,do.call,%
< dir.create,dimnames<-.data.frame,dimnames<-,dimnames.data.frame,dim<-,%
< dim.data.frame,difftime,diff.default,diff.POSIXt,diff.Date,%
< diag<-,determinant.matrix,determinant,det,delayedAssign,%
< default.stringsAsFactors,debugonce,data.matrix,data.frame,data.class,%
< dQuote,cut.default,cut.POSIXt,cut.Date,contributors,%
< conditionMessage.condition,conditionMessage,conditionCall.condition,conditionCall,computeRestarts,%
< comment<-,colnames<-,colSums,colMeans,closeAllConnections,%
---
> packageEvent,package.description,packBits,open.srcfilecopy,open.srcfilealias,%
> open.srcfile,open.connection,open,on.exit,oldClass<-,%
> oldClass,nzchar,numeric_version,normalizePath,norm,%
> ngettext,new.env,namespaceImportMethods,namespaceImportFrom,namespaceImportClasses,%
> namespaceImport,namespaceExport,names<-.POSIXlt,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,loadURL,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,getAllConnections,%
> gctorture2,gc.time,formatDL,format.pval,format.packageInfo,%
> format.octmode,format.numeric_version,format.libraryIQR,format.info,format.hexmode,%
> format.factor,format.difftime,format.default,format.data.frame,format.char,%
> format.POSIXlt,format.POSIXct,format.Date,format.AsIs,formals<-,%
> force,flush.connection,flush,findRestart,findPackageEnv,%
> findInterval,find.package,file.symlink,file.show,file.rename,%
> file.remove,file.path,file.link,file.info,file.exists,%
> file.create,file.copy,file.choose,file.append,file.access,%
> fifo,factorial,expm1,expand.grid,eval.parent,%
> environmentName,environmentIsLocked,environment<-,env.profile,enquote,%
> encodeString,enc2utf8,enc2native,emptyenv,eapply,%
> dyn.unload,dyn.load,duplicated.numeric_version,duplicated.matrix,duplicated.default,%
> duplicated.data.frame,duplicated.array,duplicated.POSIXlt,droplevels.factor,droplevels.data.frame,%
> droplevels,do.call,dir.create,dimnames<-.data.frame,dimnames<-,%
> dimnames.data.frame,dim<-,dim.data.frame,difftime,diff.default,%
> diff.POSIXt,diff.Date,diag<-,determinant.matrix,determinant,%
> det,delayedAssign,default.stringsAsFactors,debugonce,data.matrix,%
> data.frame,data.class,dQuote,cut.default,cut.POSIXt,%
> cut.Date,contributors,conditionMessage.condition,conditionMessage,conditionCall.condition,%
> conditionCall,computeRestarts,comment<-,colnames<-,colSums,%
> colMeans,codes<-,codes.ordered,codes.factor,closeAllConnections,%
815,816c811,812
< Sys.setlocale,Sys.setenv,Sys.setFileTime,Sys.readlink,Sys.localeconv,%
< Sys.junction,Sys.info,Sys.glob,Sys.getpid,Sys.getlocale,%
---
> Sys.setlocale,Sys.setenv,Sys.setFileTime,Sys.readlink,Sys.putenv,%
> Sys.localeconv,Sys.info,Sys.glob,Sys.getpid,Sys.getlocale,%
823,825c819,822
< Math.POSIXt,Math.Date,Map,La.svd,LETTERS,%
< ISOdatetime,ISOdate,Find,Filter,F,%
< Encoding<-,Encoding,Cstack_info%
---
> Math.POSIXt,Math.Date,Map,La.svd,La.eigen,%
> La.chol2inv,La.chol,LETTERS,ISOdatetime,ISOdate,%
> Find,Filter,F,Encoding<-,Encoding,%
> Cstack_info%
1394,1402c1391,1398
< mgus1,mgus,match.ratetable,lung,logan,%
< leukemia,labels.survreg,kidney,jasa1,jasa,%
< is.ratetable,is.na.ratetable,is.na.coxph.penalty,is.na.Surv,is.Surv,%
< heart,frailty.t,frailty.gaussian,frailty.gamma,frailty,%
< format.Surv,dsurvreg,coxph.fit,coxph.detail,coxph.control,%
< coxph,cox.zph,colon,cluster,clogit,%
< cgd,cch,cancer,bladder2,bladder1,%
< bladder,basehaz,attrassign,aml,aareg,%
< Surv%
---
> mgus1,mgus,match.ratetable,lung,leukemia,%
> labels.survreg,kidney,jasa1,jasa,is.ratetable,%
> is.na.ratetable,is.na.coxph.penalty,is.na.Surv,is.Surv,heart,%
> frailty.t,frailty.gaussian,frailty.gamma,frailty,format.Surv,%
> dsurvreg,coxph.fit,coxph.detail,coxph.control,coxph,%
> cox.zph,colon,cluster,clogit,cgd,%
> cch,cancer,bladder2,bladder1,bladder,%
> basehaz,attrassign,aml,aareg,Surv%
2061c2057
< [1,] "2.3.3"
---
> [1,] "2.3.4"
OK
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes in 'inst/doc' ... OK
- checking running R code from vignettes ... OK
- checking re-building of vignette PDFs ... OK
- checking PDF version of manual ... OK