* using log directory 'd:/Rcompile/CRANpkg/local/2.13/SweaveListingUtils.Rcheck'
* using R version 2.13.2 (2011-09-30)
* using platform: i386-pc-mingw32 (32-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 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
* 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 examples ... OK
* checking differences from 'SweaveListingUtils-Ex.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}}
401c402
< Warning in kws[idxRec] <- rep(getSweaveListingOption("Recomd.Keywordstyle"),  :
---
> Warning in setBaseOrRecommended(pkgs = pkgs) :
470,494c471,495
< get_all_vars,getInitial,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%
---
> 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%
503,509c504,510
< plot.xy,plot.window,plot.new,plot.design,plot.default,%
< pie,panel.smooth,pairs.default,lines.default,layout.show,%
< image.default,hist.default,grconvertY,grconvertX,fourfoldplot,%
< filled.contour,erase.screen,dotchart,contour.default,co.intervals,%
< close.screen,clip,cdplot,boxplot.matrix,boxplot.default,%
< barplot.default,axis.POSIXct,axis.Date,axTicks,assocplot,%
< Axis%
---
> plot.xy,plot.window,plot.new,plot.function,plot.design,%
> plot.default,pie,panel.smooth,pairs.default,lines.default,%
> layout.show,image.default,hist.default,grconvertY,grconvertX,%
> fourfoldplot,filled.contour,erase.screen,dotchart,contour.default,%
> co.intervals,close.screen,clip,cdplot,boxplot.matrix,%
> boxplot.default,barplot.default,axis.POSIXct,axis.Date,axTicks,%
> assocplot,Axis%
516,532c517,535
< 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,%
< 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.cur,%
< dev.copy2pdf,dev.copy2eps,dev.copy,dev.control,densCols,%
< convertColor,contourLines,colorspaces,colorRampPalette,colorRamp,%
< colorConverter,col2rgb,cm.colors,check.options,bringToTop,%
< boxplot.stats,bmp,blues9,bitmap,as.raster,%
< as.graphicsAnnot,adjustcolor,Type1Font,Hershey,CIDFont%
---
> 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,%
> bitmap,axisTicks,as.raster,as.graphicsAnnot,adjustcolor,%
> X11Fonts,X11Font,X11.options,Type1Font,Hershey,%
> CIDFont%
539,562c542,560
< 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,%
568,578c566,575
< citEntry,chooseCRANmirror,chooseBioCmirror,choose.files,choose.dir,%
< 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,arrangeWindows,argsAnywhere,alarm,%
< 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%
625,651c622,649
< newBasic,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,initialize,initFieldArgs,%
< inheritedSlotNames,implicitGeneric,hasMethods,hasMethod,hasArg,%
< getVirtual,getValidity,getSubclasses,getSlots,getRefClass,%
< getPrototype,getProperties,getPackageName,getMethodsMetaData,getMethodsForDispatch,%
< getMethods,getMethod,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,evalSource,emptyMethodsList,empty.dump,%
< elNamed<-,elNamed,el<-,el,dumpMethods,%
< dumpMethod,doPrimitiveMethod,defaultPrototype,defaultDumpName,conformMethod,%
< completeSubclasses,completeExtends,completeClassDefinition,coerce<-,coerce,%
< classesToAM,classMetaName,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%
---
> 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,initialize,%
> initRefFields,initFieldArgs,inheritedSlotNames,implicitGeneric,hasMethods,%
> hasMethod,hasArg,getVirtual,getValidity,getSubclasses,%
> getSlots,getRefClass,getPrototype,getProperties,getPackageName,%
> getMethodsMetaData,getMethodsForDispatch,getMethods,getMethod,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,evalSource,%
> 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%
683,696c681,694
< srcfilecopy,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,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,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,replicate,%
---
> 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,%
698,753c696,752
< rep.Date,removeTaskCallback,removeCConverter,registerS3methods,registerS3method,%
< 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,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,print.function,%
< print.factor,print.difftime,print.default,print.data.frame,print.connection,%
< print.condition,print.by,print.POSIXlt,print.POSIXct,print.NativeRoutineList,%
< print.Date,print.DLLRegisteredRoutines,print.DLLInfoList,print.DLLInfo,print.AsIs,%
< prettyNum,pretty.default,pos.to.env,pmin.int,pmax.int,%
< pipe,pi,path.package,path.expand,parseNamespaceFile,%
< parse.dcf,parent.frame,parent.env<-,parent.env,package_version,%
< packageStartupMessage,packageHasNamespace,packageEvent,package.description,packBits,%
< open.srcfilecopy,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,getDLLRegisteredRoutines.character,getDLLRegisteredRoutines.DLLInfo,getDLLRegisteredRoutines,getConnection,%
---
> 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,%
> 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,print.function,print.factor,print.difftime,%
> print.default,print.data.frame,print.connection,print.condition,print.by,%
> print.POSIXlt,print.POSIXct,print.NativeRoutineList,print.Date,print.DLLRegisteredRoutines,%
> print.DLLInfoList,print.DLLInfo,print.AsIs,prettyNum,pretty.default,%
> pos.to.env,pmin.int,pmax.int,pipe,pi,%
> path.package,path.expand,parseNamespaceFile,parse.dcf,parent.frame,%
> parent.env<-,parent.env,package_version,packageStartupMessage,packageHasNamespace,%
> 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,%
755,822c754,822
< gctorture2,gc.time,formatDL,format.pval,format.octmode,%
< format.numeric_version,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,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,asNamespace,%
< as.vector.factor,as.vector,as.table.default,as.table,as.symbol,%
< as.single.default,as.single,as.real,as.raw,as.qr,%
< as.pairlist,as.package_version,as.ordered,as.octmode,as.numeric_version,%
< as.numeric,as.null.default,as.null,as.name,as.matrix.noquote,%
< as.matrix.default,as.matrix.data.frame,as.matrix.POSIXlt,as.matrix,as.logical.factor,%
< as.logical,as.list.numeric_version,as.list.function,as.list.factor,as.list.environment,%
< as.list.default,as.list.data.frame,as.list.POSIXct,as.list.Date,as.list,%
< as.integer,as.hexmode,as.function.default,as.function,as.factor,%
< as.expression.default,as.expression,as.environment,as.double.difftime,as.double.POSIXlt,%
< as.double,as.difftime,as.data.frame.vector,as.data.frame.ts,as.data.frame.table,%
< as.data.frame.raw,as.data.frame.ordered,as.data.frame.numeric_version,as.data.frame.numeric,as.data.frame.model.matrix,%
< as.data.frame.matrix,as.data.frame.logical,as.data.frame.list,as.data.frame.integer,as.data.frame.factor,%
< as.data.frame.difftime,as.data.frame.default,as.data.frame.data.frame,as.data.frame.complex,as.data.frame.character,%
< as.data.frame.array,as.data.frame.POSIXlt,as.data.frame.POSIXct,as.data.frame.Date,as.data.frame.AsIs,%
< as.data.frame,as.complex,as.character.srcref,as.character.octmode,as.character.numeric_version,%
< as.character.hexmode,as.character.factor,as.character.error,as.character.default,as.character.condition,%
< as.character.POSIXt,as.character.Date,as.character,as.call,as.array.default,%
< as.array,as.POSIXlt.numeric,as.POSIXlt.factor,as.POSIXlt.default,as.POSIXlt.dates,%
< as.POSIXlt.date,as.POSIXlt.character,as.POSIXlt.POSIXct,as.POSIXlt.Date,as.POSIXlt,%
< as.POSIXct.numeric,as.POSIXct.default,as.POSIXct.dates,as.POSIXct.date,as.POSIXct.POSIXlt,%
< as.POSIXct.Date,as.POSIXct,as.Date.numeric,as.Date.factor,as.Date.default,%
< as.Date.dates,as.Date.date,as.Date.character,as.Date.POSIXlt,as.Date.POSIXct,%
< as.Date,arrayInd,aperm.table,aperm.default,anyDuplicated.matrix,%
< anyDuplicated.default,anyDuplicated.data.frame,anyDuplicated.array,anyDuplicated,all.vars,%
< all.names,all.equal.raw,all.equal.numeric,all.equal.list,all.equal.language,%
< all.equal.formula,all.equal.factor,all.equal.default,all.equal.character,all.equal.POSIXct,%
< all.equal,agrep,addTaskCallback,addNA,Vectorize,%
< T,Sys.which,Sys.unsetenv,Sys.umask,Sys.timezone,%
< Sys.time,Sys.sleep,Sys.setlocale,Sys.setenv,Sys.readlink,%
< Sys.putenv,Sys.localeconv,Sys.info,Sys.glob,Sys.getpid,%
< Sys.getlocale,Sys.getenv,Sys.chmod,Sys.Date,Summary.ordered,%
< Summary.numeric_version,Summary.factor,Summary.difftime,Summary.data.frame,Summary.POSIXlt,%
< Summary.POSIXct,Summary.Date,Reduce,R_system_version,RNGversion,%
< R.version.string,R.version,R.home,R.Version,Position,%
< Ops.ordered,Ops.numeric_version,Ops.factor,Ops.difftime,Ops.data.frame,%
< Ops.POSIXt,Ops.Date,Negate,Math.factor,Math.difftime,%
< Math.data.frame,Math.POSIXt,Math.Date,Map,La.svd,%
< La.eigen,La.chol2inv,La.chol,LETTERS,ISOdatetime,%
< ISOdate,Find,Filter,F,Encoding<-,%
< Encoding,Cstack_info%
---
> 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,%
> 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,asNamespace,as.vector.factor,as.vector,%
> as.table.default,as.table,as.symbol,as.single.default,as.single,%
> as.real,as.raw,as.qr,as.pairlist,as.package_version,%
> as.ordered,as.octmode,as.numeric_version,as.numeric,as.null.default,%
> as.null,as.name,as.matrix.noquote,as.matrix.default,as.matrix.data.frame,%
> as.matrix.POSIXlt,as.matrix,as.logical.factor,as.logical,as.list.numeric_version,%
> as.list.function,as.list.factor,as.list.environment,as.list.default,as.list.data.frame,%
> as.list.POSIXct,as.list.Date,as.list,as.integer,as.hexmode,%
> as.function.default,as.function,as.factor,as.expression.default,as.expression,%
> as.environment,as.double.difftime,as.double.POSIXlt,as.double,as.difftime,%
> as.data.frame.vector,as.data.frame.ts,as.data.frame.table,as.data.frame.raw,as.data.frame.ordered,%
> as.data.frame.numeric_version,as.data.frame.numeric,as.data.frame.model.matrix,as.data.frame.matrix,as.data.frame.logical,%
> as.data.frame.list,as.data.frame.integer,as.data.frame.factor,as.data.frame.difftime,as.data.frame.default,%
> as.data.frame.data.frame,as.data.frame.complex,as.data.frame.character,as.data.frame.array,as.data.frame.POSIXlt,%
> as.data.frame.POSIXct,as.data.frame.Date,as.data.frame.AsIs,as.data.frame,as.complex,%
> as.character.srcref,as.character.octmode,as.character.numeric_version,as.character.hexmode,as.character.factor,%
> as.character.error,as.character.default,as.character.condition,as.character.POSIXt,as.character.Date,%
> as.character,as.call,as.array.default,as.array,as.POSIXlt.numeric,%
> as.POSIXlt.factor,as.POSIXlt.default,as.POSIXlt.dates,as.POSIXlt.date,as.POSIXlt.character,%
> as.POSIXlt.POSIXct,as.POSIXlt.Date,as.POSIXlt,as.POSIXct.numeric,as.POSIXct.default,%
> as.POSIXct.dates,as.POSIXct.date,as.POSIXct.POSIXlt,as.POSIXct.Date,as.POSIXct,%
> as.Date.numeric,as.Date.factor,as.Date.default,as.Date.dates,as.Date.date,%
> as.Date.character,as.Date.POSIXlt,as.Date.POSIXct,as.Date,arrayInd,%
> aperm.table,aperm.default,anyDuplicated.matrix,anyDuplicated.default,anyDuplicated.data.frame,%
> anyDuplicated.array,anyDuplicated,all.vars,all.names,all.equal.raw,%
> all.equal.numeric,all.equal.list,all.equal.language,all.equal.formula,all.equal.factor,%
> all.equal.default,all.equal.character,all.equal.POSIXct,all.equal,agrep,%
> addTaskCallback,addNA,Vectorize,T,Sys.which,%
> Sys.unsetenv,Sys.umask,Sys.timezone,Sys.time,Sys.sleep,%
> Sys.setlocale,Sys.setenv,Sys.setFileTime,Sys.readlink,Sys.putenv,%
> Sys.localeconv,Sys.info,Sys.glob,Sys.getpid,Sys.getlocale,%
> Sys.getenv,Sys.chmod,Sys.Date,Summary.ordered,Summary.numeric_version,%
> Summary.factor,Summary.difftime,Summary.data.frame,Summary.POSIXlt,Summary.POSIXct,%
> Summary.Date,Reduce,R_system_version,RNGversion,R.version.string,%
> R.version,R.home,R.Version,Position,Ops.ordered,%
> Ops.numeric_version,Ops.factor,Ops.difftime,Ops.data.frame,Ops.POSIXt,%
> Ops.Date,Negate,Math.factor,Math.difftime,Math.data.frame,%
> Math.POSIXt,Math.Date,Map,La.svd,La.eigen,%
> La.chol2inv,La.chol,LETTERS,ISOdatetime,ISOdate,%
> Find,Filter,F,Encoding<-,Encoding,%
> Cstack_info%
1391,1399c1391,1398
< 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%
2058c2057
< [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 vignettes ... NOTE
Error in re-building vignettes:
  ...


Attaching package: 'SweaveListingUtils'

The following object(s) are masked from 'package:base':

    library, require

Warning in print.taglist(taglist, LineLength = LineLength, offset.start = nchar(startS),  :
  Some elements of taglist are too long
Warning in kws[idxRec] <- rep(getSweaveListingOption("Recomd.Keywordstyle"),  :
  number of items to replace is not a multiple of replacement length
Warning in function (object)  :
  arithmetics on distributions are understood as operations on r.v.'s
see 'distrARITH()'; for switching off this warning see '?distroptions'
Warning: running command '"d:\compiler\texmf\miktex\bin\texi2dvi.exe" --quiet --pdf "ExampleSweaveListingUtils.tex"  -I "d:/Rcompile/recent/R-2.13.2/share/texmf/tex/latex" -I "d:/Rcompile/recent/R-2.13.2/share/texmf/bibtex/bst"' had status 1
Error: running 'texi2dvi' on 'ExampleSweaveListingUtils.tex' failed

LaTeX errors:
! Package Listings Error: File `preamble(.tex)' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: tex)

Execution halted

* checking PDF version of manual ... OK