- using R version 2.15.0 Patched (2012-05-26 r59446)
- using platform: i386-pc-solaris2.10 (32-bit)
- using session charset: UTF-8
- 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 for .dll and .exe files ... 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 for sufficient/correct file permissions ... 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 installed files from ‘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)
400c400
< \newcommand{\pkgversion}{{\tt 2.3.3}}
---
> \newcommand{\pkgversion}{{\tt 2.3.4}}
443,496c443,495
< reorder,rect.hclust,read.ftable,rWishart,r2dtable,%
< quasipoisson,quasibinomial,quantile.default,quade.test,qqnorm.default,%
< qbirthday,prop.trend.test,prop.test,promax,printCoefmat,%
< print.ts,print.terms,print.logLik,print.lm,print.integrate,%
< print.infl,print.glm,print.ftable,print.formula,print.family,%
< print.density,print.coefmat,print.anova,princomp,predict.poly,%
< predict.mlm,predict.lm,predict.glm,prcomp,ppr,%
< power.t.test,power.prop.test,power.anova.test,polym,poisson.test,%
< plot.ts,plot.stepfun,plot.spec.phase,plot.spec.coherency,plot.spec,%
< plot.mlm,plot.lm,plot.ecdf,plot.density,plot.TukeyHSD,%
< plclust,pbirthday,pairwise.wilcox.test,pairwise.table,pairwise.t.test,%
< pairwise.prop.test,pacf,p.adjust.methods,p.adjust,order.dendrogram,%
< optimHess,oneway.test,numericDeriv,nobs,nls.control,%
< nls,nlminb,naresid,naprint,napredict,%
< na.pass,na.omit,na.fail,na.exclude,na.contiguous,%
< na.action,mood.test,monthplot,model.weights,model.tables,%
< model.response,model.offset,model.matrix.lm,model.matrix.default,model.matrix,%
< model.frame.lm,model.frame.glm,model.frame.default,model.frame.aovlist,model.frame,%
< model.extract,medpolish,median.default,mcnemar.test,mauchly.test,%
< mauchley.test,mantelhaen.test,manova,makepredictcall,makeARIMA,%
< make.link,ls.print,ls.diag,logLik,loess.smooth,%
< loess.control,loess,loadings,lm.wfit.null,lm.wfit,%
< lm.influence,lm.fit.null,lm.fit,lines.ts,line,%
< lag.plot,lag,ksmooth,ks.test,kruskal.test,%
< knots,kmeans,kernel,kernapply,isoreg,%
< is.tskernel,is.ts,is.stepfun,is.mts,is.leaf,%
< is.empty.model,inverse.gaussian,interaction.plot,integrate,influence.measures,%
< heatmap,hclust,hatvalues.lm,hatvalues,glm.fit.null,%
< glm.fit,glm.control,get_all_vars,getInitial,getCall,%
< friedman.test,fligner.test,fitted.values,fisher.test,filter,%
< factor.scope,factanal,expand.model.frame,estVar,embed,%
< eff.aovlist,ecdf,dummy.coef,drop.terms,drop.scope,%
< dmultinom,dist,diffinv,diff.ts,dfbeta,%
< df.residual,df.kernel,deriv3.formula,deriv3.default,deriv3,%
< deriv.formula,deriv.default,density.default,dendrapply,delete.response,%
< decompose,cutree,cpgram,cov2cor,cov.wt,%
< cor.test,cophenetic,cooks.distance,contrasts<-,contr.treatment,%
< contr.sum,contr.poly,contr.helmert,contr.SAS,constrOptim,%
< confint.default,confint,complete.cases,cmdscale,clearNames,%
< chisq.test,ccf,case.names,cancor,bw.ucv,%
< bw.nrd0,bw.nrd,bw.bcv,bw.SJ,biplot,%
< binom.test,bartlett.test,bandwidth.kernel,asOneSidedFormula,as.ts,%
< as.stepfun,as.hclust,as.formula,as.dist,as.dendrogram,%
< arima0.diag,arima0,arima.sim,arima,ar.yw,%
< ar.ols,ar.mle,ar.burg,ar,ansari.test,%
< anovalist.lm,anova.mlm,anova.lmlist,anova.lm,anova.glmlist,%
< anova.glm,aggregate.ts,aggregate.default,aggregate.data.frame,addmargins,%
< add.scope,acf2AR,acf,TukeyHSD.aov,TukeyHSD,%
< StructTS,SSweibull,SSmicmen,SSlogis,SSgompertz,%
< SSfpl,SSfol,SSbiexp,SSasympOrig,SSasympOff,%
< SSasymp,SSD,PP.test,NLSstRtAsymptote,NLSstLfAsymptote,%
< NLSstClosestX,NLSstAsymptotic,KalmanSmooth,KalmanRun,KalmanLike,%
< KalmanForecast,HoltWinters,Box.test,BIC,ARMAtoMA,%
< ARMAacf,AIC%
---
> reorder,rect.hclust,read.ftable,r2dtable,quasipoisson,%
> quasibinomial,quantile.default,quade.test,qqnorm.default,qbirthday,%
> prop.trend.test,prop.test,promax,printCoefmat,print.ts,%
> print.terms,print.logLik,print.lm,print.integrate,print.infl,%
> print.glm,print.ftable,print.formula,print.family,print.density,%
> print.coefmat,print.anova,princomp,predict.poly,predict.mlm,%
> predict.lm,predict.glm,prcomp,ppr,power.t.test,%
> power.prop.test,power.anova.test,polym,poisson.test,plot.ts,%
> plot.stepfun,plot.spec.phase,plot.spec.coherency,plot.spec,plot.mlm,%
> plot.lm,plot.ecdf,plot.density,plot.TukeyHSD,plclust,%
> pbirthday,pairwise.wilcox.test,pairwise.table,pairwise.t.test,pairwise.prop.test,%
> pacf,p.adjust.methods,p.adjust,order.dendrogram,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%
560,577c559,575
< head.matrix,head,globalVariables,glob2rx,getTxtProgressBar,%
< getSrcref,getSrcLocation,getSrcFilename,getSrcDirectory,getS3method,%
< getFromNamespace,getCRANmirrors,getAnywhere,formatUL,formatOL,%
< flush.console,fixInNamespace,findLineNum,file_test,file.edit,%
< dump.frames,download.packages,download.file,de.setup,de.restore,%
< de.ncols,data.entry,create.post,count.fields,contrib.url,%
< compareVersion,combn,close.socket,citation,citHeader,%
< citFooter,citEntry,chooseCRANmirror,chooseBioCmirror,checkCRAN,%
< capture.output,bug.report,browseVignettes,browseURL,browseEnv,%
< bibentry,available.packages,assignInNamespace,assignInMyNamespace,aspell_write_personal_dictionary_file,%
< aspell_package_vignettes,aspell_package_Rd_files,aspell,as.roman,as.relistable,%
< as.personList,as.person,argsAnywhere,aregexec,alarm,%
< adist,View,URLencode,URLdecode,SweaveSyntaxNoweb,%
< SweaveSyntaxLatex,SweaveSyntConv,SweaveHooks,Sweave,Stangle,%
< RweaveTryStop,RweaveLatexWritedoc,RweaveLatexSetup,RweaveLatexOptions,RweaveLatexFinish,%
< RweaveLatex,RweaveEvalWithOpt,RweaveChunkPrefix,RtangleWritedoc,RtangleSetup,%
< Rtangle,Rprofmem,Rprof,RSiteSearch,RShowDoc,%
< CRAN.packages%
---
> head.matrix,head,glob2rx,getTxtProgressBar,getSrcref,%
> getSrcLocation,getSrcFilename,getSrcDirectory,getS3method,getFromNamespace,%
> getCRANmirrors,getAnywhere,formatUL,formatOL,flush.console,%
> fixInNamespace,findLineNum,file_test,file.edit,dump.frames,%
> download.packages,download.file,de.setup,de.restore,de.ncols,%
> data.entry,create.post,count.fields,contrib.url,compareVersion,%
> combn,close.socket,citation,citHeader,citFooter,%
> citEntry,chooseCRANmirror,chooseBioCmirror,checkCRAN,capture.output,%
> bug.report,browseVignettes,browseURL,browseEnv,bibentry,%
> available.packages,assignInNamespace,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%
617,652c615,649
< setLoadActions,setLoadAction,setIs,setGroupGeneric,setGenericImplicit,%
< setGeneric,setDataPart,setClassUnion,setClass,setAs,%
< sessionData,selectSuperClasses,selectMethod,seemsS4Object,sealClass,%
< resetGeneric,resetClass,requireMethods,representation,removeMethodsObject,%
< removeMethods,removeMethod,removeGeneric,removeClass,rematchDefinition,%
< registerImplicitGenerics,reconcilePropertiesAndPrototype,rbind2,prototype,promptMethods,%
< promptClass,prohibitGeneric,possibleExtends,packageSlot<-,packageSlot,%
< newEmptyObject,newClassRepresentation,newBasic,multipleClasses,mlistMetaName,%
< missingArg,methodsPackageMetaName,methodSignatureMatrix,method.skeleton,metaNameUndo,%
< mergeMethods,matchSignature,makeStandardGeneric,makePrototypeFromClassDef,makeMethodsList,%
< makeGeneric,makeExtends,makeClassRepresentation,loadMethod,listFromMlist,%
< listFromMethods,linearizeMlist,languageEl<-,languageEl,isXS3Class,%
< isVirtualClass,isSealedMethod,isSealedClass,isGroup,isGrammarSymbol,%
< isGeneric,isClassUnion,isClassDef,isClass,insertSource,%
< insertMethod,initialize,initRefFields,initFieldArgs,inheritedSlotNames,%
< implicitGeneric,hasMethods,hasMethod,hasLoadAction,hasArg,%
< getVirtual,getValidity,getSubclasses,getSlots,getRefClass,%
< getPrototype,getProperties,getPackageName,getMethodsMetaData,getMethodsForDispatch,%
< getMethods,getMethod,getLoadActions,getGroupMembers,getGroup,%
< getGenerics,getGeneric,getFunction,getExtends,getDataPart,%
< getClasses,getClassPackage,getClassName,getClassDef,getClass,%
< getAllSuperClasses,getAllMethods,getAccess,generic.skeleton,functionBody<-,%
< functionBody,formalArgs,fixPre1.8,findUnique,findMethods,%
< findMethodSignatures,findMethod,findFunction,findClass,finalDefaultMethod,%
< extends,existsMethod,existsFunction,evalqOnLoad,evalSource,%
< evalOnLoad,emptyMethodsList,empty.dump,elNamed<-,elNamed,%
< el<-,el,dumpMethods,dumpMethod,doPrimitiveMethod,%
< defaultPrototype,defaultDumpName,conformMethod,completeSubclasses,completeExtends,%
< completeClassDefinition,coerce<-,coerce,classesToAM,className,%
< classMetaName,classLabel,checkSlotAssignment,cbind2,canCoerce,%
< callNextMethod,callGeneric,cacheMethod,cacheMetaData,cacheGenericsMetaData,%
< body<-,balanceMethodsList,assignMethodsMetaData,assignClassDef,asMethodDefinition,%
< as<-,allNames,allGenerics,addNextMethod,Summary,%
< SignatureMethod,S3Part<-,S3Part,S3Class<-,S3Class,%
< Quote,MethodsListSelect,MethodsList,MethodAddCoerce,Math2,%
< Logic,Complex,Compare,Arith%
---
> setIs,setGroupGeneric,setGenericImplicit,setGeneric,setDataPart,%
> setClassUnion,setClass,setAs,sessionData,selectSuperClasses,%
> selectMethod,seemsS4Object,sealClass,resetGeneric,resetClass,%
> requireMethods,representation,removeMethodsObject,removeMethods,removeMethod,%
> removeGeneric,removeClass,rematchDefinition,registerImplicitGenerics,reconcilePropertiesAndPrototype,%
> rbind2,prototype,promptMethods,promptClass,prohibitGeneric,%
> possibleExtends,packageSlot<-,packageSlot,newEmptyObject,newClassRepresentation,%
> newBasic,multipleClasses,mlistMetaName,missingArg,methodsPackageMetaName,%
> methodSignatureMatrix,method.skeleton,metaNameUndo,mergeMethods,matchSignature,%
> makeStandardGeneric,makePrototypeFromClassDef,makeMethodsList,makeGeneric,makeExtends,%
> makeClassRepresentation,loadMethod,listFromMlist,listFromMethods,linearizeMlist,%
> languageEl<-,languageEl,isXS3Class,isVirtualClass,isSealedMethod,%
> isSealedClass,isGroup,isGrammarSymbol,isGeneric,isClassUnion,%
> isClassDef,isClass,insertSource,insertMethod,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%
662,692c659,690
< 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,%
< 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,%
---
> 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,%
700,821c698,822
< readRDS,readLines,readChar,readBin,read.dcf,%
< rcond,rbind.data.frame,rawToChar,rawToBits,rawShift,%
< rawConnectionValue,rawConnection,raw,rapply,range.default,%
< quarters.POSIXt,quarters.Date,quarters,qr.solve,qr.resid,%
< qr.qy,qr.qty,qr.fitted,qr.default,qr.coef,%
< qr.X,qr.R,qr.Q,pushBackLength,pushBack,%
< psigamma,prop.table,proc.time,print.warnings,print.table,%
< 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,%
< paste0,parseNamespaceFile,parent.frame,parent.env<-,parent.env,%
< package_version,packageStartupMessage,packageHasNamespace,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,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.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,LETTERS,ISOdatetime,ISOdate,Find,%
< Filter,F,Encoding<-,Encoding,Cstack_info%
---
> 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,%
> 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,%
> 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%
1390,1398c1391,1398
< 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%
2057c2057
< [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 ... [12s/26s] OK
- checking PDF version of manual ... OK