• using R version 2.14.2 (2012-02-29)
• 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 if there is a namespace ... OK
• checking whether package 'SweaveListingUtils' can be installed ... OK
• checking installed package size ... OK
• checking package directory ... OK
• checking for portable file names ... OK
• checking DESCRIPTION meta-information ... OK
• checking top-level files ... OK
• checking index information ... OK
• checking package subdirectories ... OK
• checking R files for non-ASCII characters ... OK
• checking R files for syntax errors ... OK
• 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}}
  516,532c517,532
  < morekeywords={[6]xyz.coords,xyTable,xy.coords,xfig,windowsFonts,%
  < windowsFont,windows.options,windows,win.print,win.metafile,%
  < win.graph,trans3d,topo.colors,tiff,terrain.colors,%
  < svg,setPS,setGraphicsEventHandlers,setGraphicsEventEnv,setEPS,%
  < savePlot,rgb2hsv,replayPlot,recordPlot,recordGraphics,%
  < ps.options,postscriptFonts,postscriptFont,png,pdfFonts,%
  < pdf.options,pdf,nclass.scott,nclass.Sturges,nclass.FD,%
  < n2mfrow,msgWindow,make.rgb,jpeg,is.raster,%
  < heat.colors,hcl,grey.colors,gray.colors,graphics.off,%
  < getGraphicsEventEnv,getGraphicsEvent,extendrange,embedFonts,deviceIsInteractive,%
  < devAskNewPage,dev.size,dev.set,dev.print,dev.prev,%
  < dev.off,dev.next,dev.new,dev.list,dev.interactive,%
  < dev.hold,dev.flush,dev.cur,dev.copy2pdf,dev.copy2eps,%
  < dev.copy,dev.control,dev.capture,dev.capabilities,densCols,%
  < convertColor,contourLines,colorspaces,colorRampPalette,colorRamp,%
  < colorConverter,col2rgb,cm.colors,check.options,cairo_ps,%
  < cairo_pdf,bringToTop,boxplot.stats,bmp,blues9,%
  ---
  > morekeywords={[6]xyz.coords,xyTable,xy.coords,xfig,trans3d,%
  > topo.colors,tiff,terrain.colors,svg,setPS,%
  > setGraphicsEventHandlers,setGraphicsEventEnv,setEPS,savePlot,rgb2hsv,%
  > replayPlot,recordPlot,recordGraphics,quartzFonts,quartzFont,%
  > quartz.options,quartz,ps.options,postscriptFonts,postscriptFont,%
  > png,pdfFonts,pdf.options,pdf,nclass.scott,%
  > nclass.Sturges,nclass.FD,n2mfrow,make.rgb,jpeg,%
  > is.raster,heat.colors,hcl,grey.colors,gray.colors,%
  > graphics.off,getGraphicsEventEnv,getGraphicsEvent,extendrange,embedFonts,%
  > deviceIsInteractive,devAskNewPage,dev.size,dev.set,dev.print,%
  > dev.prev,dev.off,dev.next,dev.new,dev.list,%
  > dev.interactive,dev.hold,dev.flush,dev.cur,dev.copy2pdf,%
  > dev.copy2eps,dev.copy,dev.control,dev.capture,dev.capabilities,%
  > densCols,convertColor,contourLines,colorspaces,colorRampPalette,%
  > colorRamp,colorConverter,col2rgb,cm.colors,check.options,%
  > cairo_ps,cairo_pdf,boxplot.stats,bmp,blues9,%
  534c534,535
  < Type1Font,Hershey,CIDFont%
  ---
  > X11Fonts,X11Font,X11.options,Type1Font,Hershey,%
  > CIDFont%
  541,564c542,560
  < 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,%
  570,580c566,575
  < 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,aregexec,%
  < alarm,adist,View,URLencode,URLdecode,%
  < SweaveSyntaxNoweb,SweaveSyntaxLatex,SweaveSyntConv,SweaveHooks,Sweave,%
  < Stangle,RweaveTryStop,RweaveLatexWritedoc,RweaveLatexSetup,RweaveLatexOptions,%
  < RweaveLatexFinish,RweaveLatex,RweaveEvalWithOpt,RweaveChunkPrefix,RtangleWritedoc,%
  < RtangleSetup,Rtangle,Rprofmem,Rprof,RSiteSearch,%
  < RShowDoc,Filters,DLL.version,CRAN.packages%
  ---
  > citEntry,chooseCRANmirror,chooseBioCmirror,checkCRAN,capture.output,%
  > bug.report,browseVignettes,browseURL,browseEnv,bibentry,%
  > available.packages,assignInNamespace,aspell_write_personal_dictionary_file,aspell_package_vignettes,aspell_package_Rd_files,%
  > aspell,as.roman,as.relistable,as.personList,as.person,%
  > argsAnywhere,aregexec,alarm,adist,View,%
  > URLencode,URLdecode,SweaveSyntaxNoweb,SweaveSyntaxLatex,SweaveSyntConv,%
  > SweaveHooks,Sweave,Stangle,RweaveTryStop,RweaveLatexWritedoc,%
  > RweaveLatexSetup,RweaveLatexOptions,RweaveLatexFinish,RweaveLatex,RweaveEvalWithOpt,%
  > RweaveChunkPrefix,RtangleWritedoc,RtangleSetup,Rtangle,Rprofmem,%
  > Rprof,RSiteSearch,RShowDoc,CRAN.packages%
  691,827c686,822
  < 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,%
  < requireNamespace,replicate,rep.numeric_version,rep.int,rep.factor,%
  < rep.POSIXlt,rep.POSIXct,rep.Date,removeTaskCallback,removeCConverter,%
  < regmatches<-,regmatches,registerS3methods,registerS3method,regexec,%
  < reg.finalizer,readRenviron,readRDS,readLines,readChar,%
  < readBin,read.table.url,read.dcf,rcond,rbind.data.frame,%
  < rawToChar,rawToBits,rawShift,rawConnectionValue,rawConnection,%
  < raw,rapply,range.default,quarters.POSIXt,quarters.Date,%
  < quarters,qr.solve,qr.resid,qr.qy,qr.qty,%
  < qr.fitted,qr.default,qr.coef,qr.X,qr.R,%
  < qr.Q,pushBackLength,pushBack,psigamma,prop.table,%
  < proc.time,printNoClass,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%
  ---
  > simpleError,simpleCondition,signalCondition,showConnections,shQuote,%
  > setTimeLimit,setSessionTimeLimit,setNamespaceInfo,setHook,setCConverterStatus,%
  > set.seed,serialize,seq_len,seq_along,seq.int,%
  > seq.default,seq.POSIXt,seq.Date,seek.connection,seek,%
  > scan.url,scale.default,saveRDS,save.image,sample.int,%
  > sQuote,rowsum.default,rowsum.data.frame,rownames<-,rowSums,%
  > rowMeans,row.names<-.default,row.names<-.data.frame,row.names<-,row.names.default,%
  > row.names.data.frame,row.names,round.POSIXt,round.Date,rev.default,%
  > retracemem,restartFormals,restartDescription,requireNamespace,replicate,%
  > rep.numeric_version,rep.int,rep.factor,rep.POSIXlt,rep.POSIXct,%
  > rep.Date,removeTaskCallback,removeCConverter,regmatches<-,regmatches,%
  > registerS3methods,registerS3method,regexec,reg.finalizer,readRenviron,%
  > readRDS,readLines,readChar,readBin,read.table.url,%
  > read.dcf,rcond,rbind.data.frame,rawToChar,rawToBits,%
  > rawShift,rawConnectionValue,rawConnection,raw,rapply,%
  > range.default,quarters.POSIXt,quarters.Date,quarters,qr.solve,%
  > qr.resid,qr.qy,qr.qty,qr.fitted,qr.default,%
  > qr.coef,qr.X,qr.R,qr.Q,pushBackLength,%
  > pushBack,psigamma,prop.table,proc.time,printNoClass,%
  > 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%
  1396,1404c1391,1398
  < 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%
  2063c2057
  < [1,] "2.3.3"
  ---
  > [1,] "2.3.4"
  OK
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes in 'inst/doc' ... OK
• checking running R code from vignettes ... OK
• checking re-building of vignette PDFs ... OK
• checking PDF version of manual ... OK