- using R version 2.11.1 Patched (2010-07-29 r52657)
- using session charset: ISO8859-1
- checking for file 'SweaveListingUtils/DESCRIPTION' ... OK
- this is package 'SweaveListingUtils' version '0.5'
- package encoding: latin1
- checking package name space information ... OK
- checking package dependencies ... OK
- checking if this is a source package ... OK
- checking whether package 'SweaveListingUtils' can be installed ... 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 name space can be loaded with stated dependencies ... OK
- checking whether the name space 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 examples ... OK
- checking differences from 'SweaveListingUtils-Ex.Rout' to 'SweaveListingUtils-Ex.Rout.save' ...
1d0
< > options(pager = "console")
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< ... nothing discovered so far ...>
---
> ... nothing discovered so far ...
> >
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< > ### `SweaveListingUtils'
---
> > ### 'SweaveListingUtils'
399c399
< \newcommand{\pkgversion}{{\tt 2.3.2}}
---
> \newcommand{\pkgversion}{{\tt 2.3}}
502,508c502,509
< spineplot,smoothScatter,rasterImage,points.default,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%
---
> spineplot,smoothScatter,rasterImage,polypath,points.default,%
> 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%
515,519c516,520
< 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,setEPS,savePlot,rgb2hsv,replayPlot,%
< recordPlot,recordGraphics,ps.options,postscriptFonts,postscriptFont,%
---
> 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,%
521,523c522,524
< nclass.Sturges,nclass.FD,n2mfrow,msgWindow,make.rgb,%
< jpeg,is.raster,heat.colors,hcl,grey.colors,%
< gray.colors,graphics.off,getGraphicsEvent,extendrange,embedFonts,%
---
> nclass.Sturges,nclass.FD,n2mfrow,make.rgb,jpeg,%
> is.raster,heat.colors,hcl,grey.colors,gray.colors,%
> graphics.off,getGraphicsEventEnv,getGraphicsEvent,extendrange,embedFonts,%
529,530c530,532
< check.options,bringToTop,boxplot.stats,bmp,blues9,%
< bitmap,as.raster,as.graphicsAnnot,Type1Font,Hershey,%
---
> check.options,cairo_ps,cairo_pdf,boxplot.stats,bmp,%
> blues9,bitmap,as.raster,as.graphicsAnnot,adjustcolor,%
> X11Fonts,X11Font,X11.options,Type1Font,Hershey,%
538,561c540,558
< 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,%
< 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,packageStatus,packageDescription,%
< package.skeleton,package.contents,old.packages,object.size,normalizePath,%
< news,new.packages,modifyList,mirror2html,memory.size,%
< memory.limit,makeRweaveLatexCodeRunner,make.socket,make.packages.html,maintainer,%
< lsf.str,ls.str,localeToCharset,loadhistory,loadRconsole,%
< link.html.help,limitedLabels,is.relistable,installed.packages,install.packages,%
< history,help.start,help.search,help.request,head.matrix,%
< head,glob2rx,getWindowsHandles,getWindowsHandle,getWindowTitle,%
< getWinProgressBar,getTxtProgressBar,getS3method,getIdentification,getFromNamespace,%
< getClipboardFormats,getCRANmirrors,getAnywhere,formatUL,formatOL,%
---
> 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,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,normalizePath,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,getS3method,%
> getFromNamespace,getCRANmirrors,getAnywhere,formatUL,formatOL,%
566,575c563,572
< citEntry,chooseCRANmirror,chooseBioCmirror,choose.files,choose.dir,%
< checkCRAN,capture.output,bug.report,browseVignettes,browseURL,%
< browseEnv,available.packages,assignInNamespace,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,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,CRAN.packages%
614,637c611,635
< setPrimitiveMethods,setPackageName,setOldClass,setMethod,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,%
< 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,%
< insertMethod,initialize,inheritedSlotNames,implicitGeneric,hasMethods,%
< hasMethod,hasArg,getVirtual,getValidity,getSubclasses,%
< getSlots,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,emptyMethodsList,empty.dump,%
---
> setRefClass,setPrimitiveMethods,setPackageName,setOldClass,setMethod,%
> 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,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,%
656,722c654,721
< xtfrm,xpdrows.data.frame,writeLines,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,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,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,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,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,%
< rep.numeric_version,rep.int,rep.factor,rep.POSIXlt,rep.POSIXct,%
< rep.Date,removeTaskCallback,removeCConverter,registerS3methods,registerS3method,%
< reg.finalizer,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.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,pos.to.env,pmin.int,%
< pmax.int,pipe,pi,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,norm,%
< ngettext,new.env,namespaceImportMethods,namespaceImportFrom,namespaceImportClasses,%
< namespaceImport,namespaceExport,names<-,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,list.files,library.dynam.unload,%
---
> xtfrm,xpdrows.data.frame,xor.octmode,xor.hexmode,writeLines,%
> 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,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,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,%
> 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,rep.numeric_version,rep.int,rep.factor,rep.POSIXlt,%
> rep.POSIXct,rep.Date,removeTaskCallback,removeCConverter,registerS3methods,%
> registerS3method,reg.finalizer,readRenviron,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.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,norm,ngettext,%
> new.env,namespaceImportMethods,namespaceImportFrom,namespaceImportClasses,namespaceImport,%
> namespaceExport,names<-,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,library.dynam.unload,%
727,758c726,758
< isdebugged,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,%
< gregexpr,gettextf,gettext,getTaskCallbackNames,getSrcLines,%
< getRversion,getNumCConverters,getNativeSymbolInfo,getNamespaceVersion,getNamespaceUsers,%
< getNamespaceName,getNamespaceInfo,getNamespaceImports,getNamespaceExports,getNamespace,%
< getLoadedDLLs,getHook,getExportedValue,getDLLRegisteredRoutines.character,getDLLRegisteredRoutines.DLLInfo,%
< getDLLRegisteredRoutines,getConnection,getCallingDLLe,getCallingDLL,getCConverterStatus,%
< getCConverterDescriptions,getAllConnections,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,%
< file.symlink,file.show,file.rename,file.remove,file.path,%
< 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,encodeString,enc2utf8,enc2native,emptyenv,%
< eapply,dyn.unload,dyn.load,duplicated.numeric_version,duplicated.matrix,%
< duplicated.default,duplicated.data.frame,duplicated.array,duplicated.POSIXlt,do.call,%
---
> 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,gregexpr,gettextf,gettext,getTaskCallbackNames,%
> getSrcLines,getRversion,getNumCConverters,getNativeSymbolInfo,getNamespaceVersion,%
> getNamespaceUsers,getNamespaceName,getNamespaceInfo,getNamespaceImports,getNamespaceExports,%
> getNamespace,getLoadedDLLs,getHook,getExportedValue,getDLLRegisteredRoutines.character,%
> getDLLRegisteredRoutines.DLLInfo,getDLLRegisteredRoutines,getConnection,getCallingDLLe,getCallingDLL,%
> getCConverterStatus,getCConverterDescriptions,getAllConnections,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,file.symlink,file.show,file.rename,file.remove,%
> file.path,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,%
773,812c773,812
< attachNamespace,assign,asS4,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,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,%
< 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.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%
---
> 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,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.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%
1377c1377
< survfitcoxph.fit,survfit,survexp.usr,survexp.us,survexp.mn,%
---
> survfit,survexp.usr,survexp.us,survexp.mnwhite,survexp.mn,%
1379,1389c1379,1389
< stanford2,ridge,rats,ratetableDate,ratetable,%
< qsurvreg,pyears,psurvreg,pspline,pbcseq,%
< pbc,ovarian,nwtco,mgus2,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%
---
> stanford2,ridge,rats,ratetable,qsurvreg,%
> pyears,psurvreg,pspline,pbcseq,pbc,%
> ovarian,nwtco,mgus2,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%
2046a2047,2048
> Warning: closing unused connection 4 (http://r-forge.r-project.org/scm/viewvc.php/*checkout*/pkg/distr/R/BinomialDistribution.R?root=distr)
> Warning: closing unused connection 3 (http://r-forge.r-project.org/scm/viewvc.php/*checkout*/pkg/distr/man/Binom-class.Rd?root=distr)
2048c2050
< [1,] "2.3.2"
---
> [1,] "2.3"
OK
- checking package vignettes in 'inst/doc' ... OK
- checking PDF version of manual ... OK