CRAN Package Check Results for Package phylosim

Last updated on 2015-07-01 23:47:05.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-gcc 2.1.1 7.95 191.29 199.24 NOTE --no-vignettes
r-patched-linux-x86_64 2.1.1 8.32 207.21 215.52 NOTE --no-vignettes
r-release-linux-x86_64 2.1.1 7.80 191.06 198.85 NOTE --no-vignettes
r-release-osx-x86_64-mavericks 2.1.1 OK
r-release-windows-ix86+x86_64 2.1.1 29.00 243.00 272.00 OK --no-vignettes
r-oldrel-windows-ix86+x86_64 2.1.1 29.00 302.00 331.00 OK --no-vignettes

Check Details

Version: 2.1.1
Flags: --no-vignettes
Check: S3 generic/method consistency
Result: NOTE
    Found the following apparent S3 methods exported but not registered:
     !=.Alphabet !=.Process ==.Alphabet ==.Process
     BrownianPath.BrownianInsertor Debug.PhyloSim Log.PhyloSim
     Perform.Event Scale.QMatrix Simulate.PhyloSim Translate.CodonSequence
     Undocumented.PhyloSim areSynonymous.CodonAlphabet
     as.character.Alphabet as.character.Event
     as.character.GeneralSubstitution as.character.PhyloSim
     as.character.Process as.character.QMatrix as.character.Sequence
     as.character.Site attachHookToNode.PhyloSim attachProcess.Sequence
     attachProcess.Site attachSeqToNode.PhyloSim
     buildFromPAML.AminoAcidSubst buildFromPAML.CodonSubst
     checkConsistency.Alphabet checkConsistency.AminoAcidSubst
     checkConsistency.BinarySubst checkConsistency.BrownianInsertor
     checkConsistency.CodonAlphabet checkConsistency.CodonSequence
     checkConsistency.CodonSubst checkConsistency.CodonUNREST
     checkConsistency.ContinuousDeletor
     checkConsistency.ContinuousInsertor checkConsistency.DiscreteDeletor
     checkConsistency.DiscreteInsertor checkConsistency.Event
     checkConsistency.F81 checkConsistency.F84
     checkConsistency.FastFieldDeletor checkConsistency.GTR
     checkConsistency.GY94 checkConsistency.GeneralDeletor
     checkConsistency.GeneralInDel checkConsistency.GeneralInsertor
     checkConsistency.GeneralSubstitution checkConsistency.HKY
     checkConsistency.JC69 checkConsistency.K80 checkConsistency.K81
     checkConsistency.PSRoot checkConsistency.PSRootSummary
     checkConsistency.PhyloSim checkConsistency.Process
     checkConsistency.QMatrix checkConsistency.Sequence
     checkConsistency.Site checkConsistency.T92 checkConsistency.TN93
     checkConsistency.UNREST clearStates.Sequence
     clone.GeneralSubstitution clone.Process clone.Sequence
     copySubSequence.Sequence deleteSubSequence.Sequence
     detachHookFromNode.PhyloSim detachProcess.Sequence detachProcess.Site
     detachSeqFromNode.PhyloSim enableVirtual.PSRoot
     exportStatTree.PhyloSim flagTotalRate.Site
     generateInsert.GeneralInsertor getAcceptBy.GeneralInDel
     getAcceptWin.GeneralInsertor getAlignment.PhyloSim
     getAlignmentLength.PhyloSim getAlphabet.GeneralSubstitution
     getAlphabet.Process getAlphabet.QMatrix getAlphabet.Site
     getAlphabets.Sequence getAncestral.Sequence getAncestral.Site
     getBaseFreqs.F81 getBaseFreqs.F84 getBaseFreqs.GTR getBaseFreqs.HKY
     getBaseFreqs.K80 getBaseFreqs.K81 getBaseFreqs.TN93
     getBigRate.Sequence getBranchEvents.PhyloSim getCodonFreqs.GY94
     getComments.PSRoot getCumulativeRates.Sequence
     getCumulativeRatesFromRange.Sequence getDeletionTolerance.Sequence
     getDist.ContinuousDeletor getDist.ContinuousInsertor getEdge.PhyloSim
     getEdges.PhyloSim getEquDist.GeneralSubstitution
     getEventRate.GeneralSubstitution getEventRate.QMatrix
     getEventRateAtSite.GeneralSubstitution getEvents.Sequence
     getEvents.Site getEventsAtSite.FastFieldDeletor getEventsAtSite.GY94
     getEventsAtSite.GeneralDeletor getEventsAtSite.GeneralInsertor
     getEventsAtSite.GeneralSubstitution getEventsAtSite.Process
     getGenerateBy.GeneralInsertor getHandler.Event getId.PhyloSim
     getId.Process getId.QMatrix getId.Sequence
     getInsertHook.GeneralInsertor getInsertionTolerance.Sequence
     getKappa.F84 getKappa.GY94 getLength.Sequence
     getLengthParam1.FastFieldDeletor getLengthParam2.FastFieldDeletor
     getLogFile.PhyloSim getLogLevel.PhyloSim getMatrix.QMatrix
     getMaxLength.ContinuousDeletor getMaxLength.ContinuousInsertor
     getMethodsList.PSRoot getName.Event getName.PhyloSim getName.Process
     getName.QMatrix getName.Sequence getNedges.PhyloSim getNodes.PhyloSim
     getNtips.PhyloSim getOmegaScalingFactor.GY94 getOmegas.CodonSequence
     getOmegas.Sequence getParameterAtSite.Process
     getParameterAtSites.Sequence getPhylo.PhyloSim getPosition.Event
     getProbs.DiscreteDeletor getProbs.DiscreteInsertor getProcess.Event
     getProcess.QMatrix getProcesses.Sequence getProcesses.Site
     getProposeBy.GeneralInDel getQMatrix.GeneralSubstitution
     getRate.Event getRate.GeneralInDel getRate.GeneralSubstitution
     getRate.QMatrix getRateList.GeneralSubstitution getRateList.QMatrix
     getRateMultipliers.Sequence getRateParam.F81 getRateParam.F84
     getRateParam.GTR getRateParam.HKY getRateParam.K80 getRateParam.K81
     getRateParam.T92 getRateParam.TN93 getRateParamList.F81
     getRateParamList.F84 getRateParamList.GTR getRateParamList.HKY
     getRateParamList.K80 getRateParamList.K81 getRateParamList.T92
     getRateParamList.TN93 getRootNode.PhyloSim getRootSeq.PhyloSim
     getScale.BrownianInsertor getScaledMatrix.QMatrix
     getSeqFromNode.PhyloSim getSequence.Site getSequences.PhyloSim
     getSite.Event getSiteSpecificParamIds.Process
     getSiteSpecificParamList.Process getSites.Sequence getSize.Alphabet
     getSizes.DiscreteDeletor getSizes.DiscreteInsertor getState.Site
     getStates.Sequence getString.Sequence getSymbolFreqs.Sequence
     getSymbolLength.Alphabet getSymbols.Alphabet getTableId.CodonAlphabet
     getTemplateSeq.GeneralInsertor getTheta.T92 getTipLabels.PhyloSim
     getTips.PhyloSim getToleranceMargin.FastFieldDeletor
     getTotalRate.Site getTotalRates.Sequence
     getTotalRatesFromRange.Sequence getTransTable.CodonAlphabet
     getTreeLength.PhyloSim getType.Alphabet getType.BrownianInsertor
     getType.FastFieldDeletor getUniqueAlphabets.Sequence
     getUniqueProcesses.Sequence getWriteProtected.Alphabet
     getWriteProtected.Event getWriteProtected.Process
     getWriteProtected.QMatrix getWriteProtected.Sequence
     globalConsistencyCheck.PSRoot hasSiteSpecificParameter.Process
     hasSymbols.Alphabet hasUndefinedRate.GeneralInDel
     hasUndefinedRate.GeneralSubstitution hasUndefinedRate.Process
     insertSequence.Sequence intersect.list.PSRoot is.Alphabet.default
     is.CodonAlphabet.default is.CodonUNREST.default is.Event.default
     is.GY94.default is.GeneralDeletor.default is.GeneralInDel.default
     is.GeneralInsertor.default is.GeneralSubstitution.default
     is.PSRoot.default is.Process.default is.QMatrix.default
     is.Sequence.default is.Site.default is.na.PSRoot is.phylo.default
     is.tip.PhyloSim isAttached.Site isEmpty.Alphabet
     isStartCodon.CodonAlphabet isStopCodon.CodonAlphabet ll.PSRoot
     my.all.equal.PSRoot newAAMatrix.AminoAcidSubst newMatrix.CodonSubst
     omegaHist.CodonSequence omegaVarM0.CodonSequence
     omegaVarM1.CodonSequence omegaVarM2.CodonSequence
     omegaVarM3.CodonSequence omegaVarM4.CodonSequence
     plot.ContinuousDeletor plot.ContinuousInsertor plot.DiscreteDeletor
     plot.DiscreteInsertor plot.GeneralSubstitution plot.PSRoot
     plot.PhyloSim plot.Sequence plotParametersAtSites.Sequence
     plusGamma.Sequence plusInvGamma.Sequence print.PSRootSummary
     print.QMatrix proposeLength.GeneralInDel readAlignment.PhyloSim
     readTree.PhyloSim rescaleQMatrix.GeneralSubstitution
     revComp.NucleotideSequence sampleState.GeneralSubstitution
     sampleStates.Sequence saveAlignment.PhyloSim scaleTree.PhyloSim
     setAcceptBy.GeneralInDel setAcceptWin.GeneralInsertor
     setAlignment.PhyloSim setAlphabet.GeneralSubstitution
     setAlphabet.Process setAlphabet.QMatrix setAlphabet.Site
     setAlphabets.Sequence setAncestral.Sequence setAncestral.Site
     setBaseFreqs.F81 setBaseFreqs.F84 setBaseFreqs.GTR setBaseFreqs.HKY
     setBaseFreqs.K80 setBaseFreqs.K81 setBaseFreqs.TN93
     setBigRate.Sequence setBranchEvents.PhyloSim setCodonFreqs.GY94
     setComments.PSRoot setCumulativeRates.Sequence
     setDeletionTolerance.Sequence setDist.ContinuousDeletor
     setDist.ContinuousInsertor setEdges.PhyloSim
     setEquDist.AminoAcidSubst setEquDist.CodonSubst
     setEquDist.GeneralSubstitution setEvents.Site
     setGenerateBy.GeneralInsertor setHandler.Event setId.PhyloSim
     setId.Process setId.QMatrix setId.Sequence
     setInsertHook.GeneralInsertor setInsertionTolerance.Sequence
     setKappa.F84 setKappa.GY94 setLength.Sequence
     setLengthParam1.FastFieldDeletor setLengthParam2.FastFieldDeletor
     setLogFile.PhyloSim setLogLevel.PhyloSim setMatrix.QMatrix
     setMaxLength.ContinuousDeletor setMaxLength.ContinuousInsertor
     setMethodsList.PSRoot setName.Event setName.PhyloSim setName.Process
     setName.QMatrix setName.Sequence setNedges.PhyloSim setNodes.PhyloSim
     setNtips.PhyloSim setOmegas.CodonSequence setOmegas.Sequence
     setParameterAtSite.FastFieldDeletor setParameterAtSite.Process
     setParameterAtSites.Sequence setPhylo.PhyloSim setPosition.Event
     setProbs.DiscreteDeletor setProbs.DiscreteInsertor setProcess.Event
     setProcess.QMatrix setProcesses.Sequence setProcesses.Site
     setProposeBy.GeneralInDel setQMatrix.GeneralSubstitution
     setRate.Event setRate.GY94 setRate.GeneralInDel
     setRate.GeneralSubstitution setRate.QMatrix
     setRateList.GeneralSubstitution setRateList.QMatrix
     setRateMultipliers.Sequence setRateParam.F81 setRateParam.F84
     setRateParam.GTR setRateParam.HKY setRateParam.K80 setRateParam.K81
     setRateParam.T92 setRateParam.TN93 setRateParamList.F81
     setRateParamList.F84 setRateParamList.GTR setRateParamList.HKY
     setRateParamList.K80 setRateParamList.K81 setRateParamList.T92
     setRateParamList.TN93 setRootNode.PhyloSim setRootSeq.PhyloSim
     setScale.BrownianInsertor setScaledMatrix.QMatrix setSequence.Site
     setSequences.PhyloSim setSite.Event setSiteSpecificParamIds.Process
     setSiteSpecificParamList.Process setSize.Alphabet
     setSizes.DiscreteDeletor setSizes.DiscreteInsertor setState.Site
     setStates.Sequence setString.Sequence setSymbolLength.Alphabet
     setSymbols.Alphabet setTableId.CodonAlphabet
     setTemplateSeq.GeneralInsertor setTheta.T92 setTipLabels.PhyloSim
     setTips.PhyloSim setToleranceMargin.FastFieldDeletor
     setTotalRate.Site setTotalRates.Sequence setTransTable.CodonAlphabet
     setTreeLength.PhyloSim setType.Alphabet setType.BrownianInsertor
     setType.FastFieldDeletor setUniqueAlphabets.Sequence
     setUniqueProcesses.Sequence setWriteProtected.Alphabet
     setWriteProtected.Event setWriteProtected.Process
     setWriteProtected.QMatrix setWriteProtected.Sequence
     stringLength.default stringLengthVector.default summary.Alphabet
     summary.AminoAcidSubst summary.BinarySubst summary.BrownianInsertor
     summary.CodonAlphabet summary.CodonSubst summary.ContinuousDeletor
     summary.ContinuousInsertor summary.DiscreteDeletor
     summary.DiscreteInsertor summary.Event summary.F81 summary.F84
     summary.FastFieldDeletor summary.GTR summary.GY94
     summary.GeneralDeletor summary.GeneralInDel summary.GeneralInsertor
     summary.GeneralSubstitution summary.HKY summary.JC69 summary.K80
     summary.K81 summary.PSRoot summary.PhyloSim summary.Process
     summary.QMatrix summary.Sequence summary.Site summary.T92
     summary.TN93 summary.UNREST translateCodon.CodonAlphabet
     virtualAssignmentForbidden.PSRoot
    See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
    manual.
Flavors: r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-release-linux-x86_64

Version: 2.1.1
Flags: --no-vignettes
Check: R code for possible problems
Result: NOTE
    .GillespieDirect.PhyloSim: no visible global function definition for
     ‘rexp’
    .GillespieDirect.PhyloSim: no visible global function definition for
     ‘runif’
    .discretizeGamma.Sequence : <anonymous>: no visible global function
     definition for ‘qgamma’
    .discretizeGamma.Sequence : Igamma: no visible global function
     definition for ‘pgamma’
    .omegaVarM10Cont.CodonSequence: no visible global function definition
     for ‘rbeta’
    .omegaVarM10Cont.CodonSequence: no visible global function definition
     for ‘rgamma’
    .omegaVarM11Cont.CodonSequence : rnorm.gt.1: no visible global function
     definition for ‘rnorm’
    .omegaVarM11Cont.CodonSequence: no visible global function definition
     for ‘rbeta’
    .omegaVarM12Cont.CodonSequence : rnorm.gt.0: no visible global function
     definition for ‘rnorm’
    .omegaVarM13Cont.CodonSequence : rnorm.gt.0: no visible global function
     definition for ‘rnorm’
    .omegaVarM5Cont.CodonSequence: no visible global function definition
     for ‘rgamma’
    .omegaVarM6Cont.CodonSequence: no visible global function definition
     for ‘rgamma’
    .omegaVarM7.CodonSequence: no visible global function definition for
     ‘rbeta’
    .omegaVarM8Cont.CodonSequence: no visible global function definition
     for ‘rbeta’
    .omegaVarM9Cont.CodonSequence: no visible global function definition
     for ‘rbeta’
    .omegaVarM9Cont.CodonSequence: no visible global function definition
     for ‘rgamma’
    .plotWithAlignment.PhyloSim : alignment.colors: no visible global
     function definition for ‘colorRampPalette’
    .plotWithAlignment.PhyloSim : darker: no visible global function
     definition for ‘col2rgb’
    .plotWithAlignment.PhyloSim : darker: no visible global function
     definition for ‘rgb’
    .plotWithAlignment.PhyloSim : lighter: no visible global function
     definition for ‘col2rgb’
    .plotWithAlignment.PhyloSim : lighter: no visible global function
     definition for ‘rgb’
    .plotWithAlignment.PhyloSim: no visible global function definition for
     ‘reorder’
    .plotWithAlignment.PhyloSim: no visible binding for global variable
     ‘page’
    .plotWithAlignment.PhyloSim: no visible binding for global variable
     ‘colors’
    .plotWithAlignment.PhyloSim: no visible global function definition for
     ‘colorRamp’
    .plotWithAlignment.PhyloSim: no visible global function definition for
     ‘rgb’
    BrownianPath.BrownianInsertor : generate_brownian: no visible global
     function definition for ‘rnorm’
    omegaHist.CodonSequence: no visible global function definition for
     ‘hist’
    plot.ContinuousDeletor: no visible global function definition for
     ‘plot.default’
    plot.ContinuousDeletor: no visible global function definition for
     ‘density’
    plot.ContinuousDeletor: no visible global function definition for
     ‘axis’
    plot.ContinuousInsertor: no visible global function definition for
     ‘plot.default’
    plot.ContinuousInsertor: no visible global function definition for
     ‘density’
    plot.ContinuousInsertor: no visible global function definition for
     ‘axis’
    plot.DiscreteDeletor: no visible global function definition for
     ‘plot.default’
    plot.DiscreteDeletor: no visible global function definition for ‘axis’
    plot.DiscreteInsertor: no visible global function definition for
     ‘plot.default’
    plot.DiscreteInsertor: no visible global function definition for ‘axis’
    plot.PhyloSim: no visible global function definition for ‘plot’
    plot.Sequence: no visible global function definition for ‘plot’
    plot.Sequence: no visible global function definition for ‘axis’
    plotParametersAtSites.Sequence: no visible global function definition
     for ‘plot’
    plotParametersAtSites.Sequence: no visible global function definition
     for ‘axis’
    plusGamma.Sequence: no visible global function definition for ‘rgamma’
    plusInvGamma.Sequence: no visible global function definition for
     ‘rgamma’
    setPhylo.PhyloSim: no visible global function definition for ‘reorder’
    summary.AminoAcidSubst: no visible global function definition for
     ‘capture.output’
    summary.CodonSubst: no visible global function definition for
     ‘capture.output’
    summary.DiscreteDeletor: no visible global function definition for
     ‘weighted.mean’
    summary.DiscreteInsertor: no visible global function definition for
     ‘weighted.mean’
    summary.GeneralSubstitution: no visible global function definition for
     ‘capture.output’
    summary.PhyloSim: no visible global function definition for
     ‘capture.output’
    summary.QMatrix: no visible global function definition for
     ‘capture.output’
Flavor: r-devel-linux-x86_64-debian-gcc