CRAN Package Check Results for Package mlgt

Last updated on 2015-07-28 06:47:56.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.16 1.06 16.97 18.02 NOTE
r-devel-linux-x86_64-debian-gcc 0.16 1.02 16.44 17.46 NOTE
r-devel-linux-x86_64-fedora-clang 0.16 34.09 NOTE
r-devel-linux-x86_64-fedora-gcc 0.16 32.64 NOTE
r-devel-osx-x86_64-clang 0.16 28.62 NOTE
r-devel-windows-ix86+x86_64 0.16 4.00 43.00 47.00 NOTE
r-patched-linux-x86_64 0.16 1.02 17.29 18.30 NOTE
r-patched-solaris-sparc 0.16 216.60 NOTE
r-patched-solaris-x86 0.16 45.80 NOTE
r-release-linux-x86_64 0.16 1.02 17.44 18.46 NOTE
r-release-osx-x86_64-mavericks 0.16 NOTE
r-release-windows-ix86+x86_64 0.16 6.00 45.00 51.00 NOTE
r-oldrel-windows-ix86+x86_64 0.16 6.00 30.00 36.00 NOTE

Check Details

Version: 0.16
Check: top-level files
Result: NOTE
    Non-standard file/directory found at top level:
     ‘CHANGELOG.txt’
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-linux-x86_64, r-release-linux-x86_64

Version: 0.16
Check: dependencies in R code
Result: NOTE
    Packages in Depends field not imported from:
     ‘methods’ ‘seqinr’
     These packages need to be imported from (in the NAMESPACE file)
     for when this namespace is loaded but not attached.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-osx-x86_64-clang, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-x86_64, r-release-osx-x86_64-mavericks, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 0.16
Check: R code for possible problems
Result: NOTE
    alignReport: no visible global function definition for ‘pdf’
    alignReport: no visible global function definition for ‘as.alignment’
    alignReport: no visible global function definition for ‘consensus’
    alignReport: no visible global function definition for ‘con’
    alignReport: no visible global function definition for ‘par’
    alignReport: no visible global function definition for ‘plot.new’
    alignReport: no visible global function definition for ‘title’
    alignReport: no visible global function definition for ‘legend’
    alignReport: no visible global function definition for ‘barplot’
    alignReport: no visible global function definition for ‘hist’
    alignReport: no visible global function definition for ‘abline’
    alignReport: no visible global function definition for ‘dev.off’
    callGenotypes: no visible global function definition for ‘new’
    createKnownAlleleList: no visible global function definition for
     ‘read.alignment’
    createKnownAlleleList: no visible global function definition for
     ‘write.fasta’
    createKnownAlleleList: no visible global function definition for
     ‘read.fasta’
    createKnownAlleleList: no visible global function definition for ‘s2c’
    createKnownAlleleList: no visible binding for global variable ‘name’
    createKnownAlleleList: no visible global function definition for ‘new’
    createKnownAlleleList: no visible global function definition for
     ‘as.SeqFastadna’
    dumpVariantMap.mlgtResult: no visible global function definition for
     ‘write.fasta’
    dumpVariantMap.mlgtResult: no visible binding for global variable ‘s2c’
    dumpVariants: no visible global function definition for ‘as.alignment’
    dumpVariants: no visible global function definition for ‘write.fasta’
    dumpVariants: no visible binding for global variable ‘s2c’
    errorCorrect.alignment: no visible global function definition for
     ‘consensus’
    errorCorrect.alignment: no visible global function definition for ‘con’
    errorCorrect.alignment: no visible global function definition for
     ‘as.matrix.alignment’
    errorCorrect.alignment: no visible binding for global variable ‘c2s’
    errorCorrect.alignment: no visible global function definition for
     ‘as.alignment’
    errorCorrect.mlgtResult: no visible global function definition for
     ‘getSequence’
    errorCorrect.mlgtResult: no visible global function definition for
     ‘as.alignment’
    errorCorrect.mlgtResult: no visible global function definition for
     ‘new’
    errorCorrect.mlgtResult: no visible global function definition for
     ‘as.SeqFastadna’
    getSubSeqsTable: no visible global function definition for ‘new’
    getSubSeqsTable: no visible global function definition for ‘read.fasta’
    getSubSeqsTable: no visible global function definition for
     ‘write.fasta’
    getSubSeqsTable: no visible global function definition for
     ‘as.alignment’
    getSubSeqsTable: no visible global function definition for ‘s2c’
    getTopBlastHits: no visible global function definition for ‘read.delim’
    inspectBlastResults: no visible global function definition for ‘par’
    inspectBlastResults: no visible global function definition for ‘hist’
    makeVarAlleleBlastMap: no visible global function definition for
     ‘getName’
    makeVarAlleleBlastMap: no visible global function definition for
     ‘write.fasta’
    mergeMlgtResults.complex: no visible global function definition for
     ‘na.omit’
    mlgt.mlgtDesign: no visible global function definition for ‘read.delim’
    mlgt.mlgtDesign: no visible global function definition for
     ‘getSequence’
    mlgt.mlgtDesign: no visible global function definition for ‘new’
    mlgt.mlgtDesign: no visible global function definition for
     ‘as.SeqFastadna’
    plotGenotypeEvidence.genotypeCall: no visible global function
     definition for ‘par’
    plotGenotypeEvidence.genotypeCall: no visible global function
     definition for ‘hist’
    plotGenotypeEvidence.genotypeCall: no visible global function
     definition for ‘abline’
    plotGenotypeEvidence.genotypeCall: no visible global function
     definition for ‘plot’
    plotGenotypeEvidence.genotypeCall: no visible global function
     definition for ‘legend’
    plotGenotypeEvidence.genotypeCall.file: no visible global function
     definition for ‘pdf’
    plotGenotypeEvidence.genotypeCall.file: no visible global function
     definition for ‘dev.off’
    plotGenotypeEvidence.list: no visible global function definition for
     ‘pdf’
    plotGenotypeEvidence.list: no visible global function definition for
     ‘dev.off’
    prepareMlgtRun.listDesign: no visible global function definition for
     ‘new’
    prepareMlgtRun.mlgtDesign: no visible global function definition for
     ‘write.fasta’
    printBlastResultGraphs: no visible global function definition for ‘pdf’
    printBlastResultGraphs: no visible global function definition for
     ‘dev.off’
    stripGapColumns: no visible global function definition for ‘con’
    stripGapColumns: no visible binding for global variable ‘c2s’
    stripGapColumns: no visible global function definition for
     ‘as.alignment’
    writeGenotypeCallsToFile.genotypeCall: no visible global function
     definition for ‘packageVersion’
    writeGenotypeCallsToFile.genotypeCall: no visible global function
     definition for ‘write.table’
    writeGenotypeCallsToFile.list: no visible global function definition
     for ‘write.table’
    errorCorrect,missing-list: no visible global function definition for
     ‘consensus’
    errorCorrect,missing-list: no visible global function definition for
     ‘con’
    errorCorrect,missing-list: no visible global function definition for
     ‘as.matrix.alignment’
    errorCorrect,missing-list: no visible binding for global variable ‘c2s’
    errorCorrect,missing-list: no visible global function definition for
     ‘as.alignment’
    errorCorrect,mlgtResult-missing: no visible global function definition
     for ‘getSequence’
    errorCorrect,mlgtResult-missing: no visible global function definition
     for ‘as.alignment’
    errorCorrect,mlgtResult-missing: no visible global function definition
     for ‘new’
    errorCorrect,mlgtResult-missing: no visible global function definition
     for ‘as.SeqFastadna’
    mlgt,mlgtDesign: no visible global function definition for ‘read.delim’
    mlgt,mlgtDesign: no visible global function definition for
     ‘getSequence’
    mlgt,mlgtDesign: no visible global function definition for ‘new’
    mlgt,mlgtDesign: no visible global function definition for
     ‘as.SeqFastadna’
    plotGenotypeEvidence,genotypeCall-missing-character: no visible global
     function definition for ‘pdf’
    plotGenotypeEvidence,genotypeCall-missing-character: no visible global
     function definition for ‘dev.off’
    plotGenotypeEvidence,genotypeCall-missing-missing: no visible global
     function definition for ‘par’
    plotGenotypeEvidence,genotypeCall-missing-missing: no visible global
     function definition for ‘hist’
    plotGenotypeEvidence,genotypeCall-missing-missing: no visible global
     function definition for ‘abline’
    plotGenotypeEvidence,genotypeCall-missing-missing: no visible global
     function definition for ‘plot’
    plotGenotypeEvidence,genotypeCall-missing-missing: no visible global
     function definition for ‘legend’
    plotGenotypeEvidence,missing-list-character: no visible global function
     definition for ‘pdf’
    plotGenotypeEvidence,missing-list-character: no visible global function
     definition for ‘dev.off’
    prepareMlgtRun,missing-character-character-character-list-list-list-character-character:
     no visible global function definition for ‘new’
    prepareMlgtRun,mlgtDesign-missing-missing-missing-missing-missing-missing-missing-character:
     no visible global function definition for ‘write.fasta’
    writeGenotypeCallsToFile,list-missing: no visible global function
     definition for ‘write.table’
    writeGenotypeCallsToFile,missing-genotypeCall: no visible global
     function definition for ‘packageVersion’
    writeGenotypeCallsToFile,missing-genotypeCall: no visible global
     function definition for ‘write.table’
    Undefined global functions or variables:
     abline as.SeqFastadna as.alignment as.matrix.alignment barplot c2s
     con consensus dev.off getName getSequence hist legend na.omit name
     new packageVersion par pdf plot plot.new read.alignment read.delim
     read.fasta s2c title write.fasta write.table
    Consider adding
     importFrom("grDevices", "dev.off", "pdf")
     importFrom("graphics", "abline", "barplot", "hist", "legend", "par",
     "plot", "plot.new", "title")
     importFrom("methods", "new")
     importFrom("stats", "na.omit")
     importFrom("utils", "packageVersion", "read.delim", "write.table")
    to your NAMESPACE.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64

Version: 0.16
Check: R code for possible problems
Result: NOTE
    alignReport: no visible global function definition for ‘as.alignment’
    alignReport: no visible global function definition for ‘consensus’
    alignReport: no visible global function definition for ‘con’
    createKnownAlleleList: no visible global function definition for
     ‘read.alignment’
    createKnownAlleleList: no visible global function definition for
     ‘write.fasta’
    createKnownAlleleList: no visible global function definition for
     ‘read.fasta’
    createKnownAlleleList: no visible global function definition for ‘s2c’
    createKnownAlleleList: no visible binding for global variable ‘name’
    createKnownAlleleList: no visible global function definition for
     ‘as.SeqFastadna’
    dumpVariantMap.mlgtResult: no visible global function definition for
     ‘write.fasta’
    dumpVariantMap.mlgtResult: no visible binding for global variable ‘s2c’
    dumpVariants: no visible global function definition for ‘as.alignment’
    dumpVariants: no visible global function definition for ‘write.fasta’
    dumpVariants: no visible binding for global variable ‘s2c’
    errorCorrect.alignment: no visible global function definition for
     ‘consensus’
    errorCorrect.alignment: no visible global function definition for ‘con’
    errorCorrect.alignment: no visible global function definition for
     ‘as.matrix.alignment’
    errorCorrect.alignment: no visible binding for global variable ‘c2s’
    errorCorrect.alignment: no visible global function definition for
     ‘as.alignment’
    errorCorrect.mlgtResult: no visible global function definition for
     ‘getSequence’
    errorCorrect.mlgtResult: no visible global function definition for
     ‘as.alignment’
    errorCorrect.mlgtResult: no visible global function definition for
     ‘as.SeqFastadna’
    getSubSeqsTable: no visible global function definition for ‘read.fasta’
    getSubSeqsTable: no visible global function definition for
     ‘write.fasta’
    getSubSeqsTable: no visible global function definition for
     ‘as.alignment’
    getSubSeqsTable: no visible global function definition for ‘s2c’
    makeVarAlleleBlastMap: no visible global function definition for
     ‘getName’
    makeVarAlleleBlastMap: no visible global function definition for
     ‘write.fasta’
    mlgt.mlgtDesign: no visible global function definition for
     ‘getSequence’
    mlgt.mlgtDesign: no visible global function definition for
     ‘as.SeqFastadna’
    prepareMlgtRun.mlgtDesign: no visible global function definition for
     ‘write.fasta’
    stripGapColumns: no visible global function definition for ‘con’
    stripGapColumns: no visible binding for global variable ‘c2s’
    stripGapColumns: no visible global function definition for
     ‘as.alignment’
    errorCorrect,missing-list: no visible global function definition for
     ‘consensus’
    errorCorrect,missing-list: no visible global function definition for
     ‘con’
    errorCorrect,missing-list: no visible global function definition for
     ‘as.matrix.alignment’
    errorCorrect,missing-list: no visible binding for global variable ‘c2s’
    errorCorrect,missing-list: no visible global function definition for
     ‘as.alignment’
    errorCorrect,mlgtResult-missing: no visible global function definition
     for ‘getSequence’
    errorCorrect,mlgtResult-missing: no visible global function definition
     for ‘as.alignment’
    errorCorrect,mlgtResult-missing: no visible global function definition
     for ‘as.SeqFastadna’
    mlgt,mlgtDesign: no visible global function definition for
     ‘getSequence’
    mlgt,mlgtDesign: no visible global function definition for
     ‘as.SeqFastadna’
    prepareMlgtRun,mlgtDesign-missing-missing-missing-missing-missing-missing-missing-character:
     no visible global function definition for ‘write.fasta’
    Undefined global functions or variables:
     as.SeqFastadna as.alignment as.matrix.alignment c2s con consensus
     getName getSequence name read.alignment read.fasta s2c write.fasta
Flavor: r-devel-osx-x86_64-clang

Version: 0.16
Check: R code for possible problems
Result: NOTE
    alignReport: no visible global function definition for ‘as.alignment’
    alignReport: no visible global function definition for ‘consensus’
    alignReport: no visible global function definition for ‘con’
    createKnownAlleleList: no visible global function definition for
     ‘read.alignment’
    createKnownAlleleList: no visible global function definition for
     ‘write.fasta’
    createKnownAlleleList: no visible global function definition for
     ‘read.fasta’
    createKnownAlleleList: no visible global function definition for ‘s2c’
    createKnownAlleleList: no visible binding for global variable ‘name’
    createKnownAlleleList: no visible global function definition for
     ‘as.SeqFastadna’
    dumpVariantMap.mlgtResult: no visible global function definition for
     ‘write.fasta’
    dumpVariantMap.mlgtResult: no visible binding for global variable ‘s2c’
    dumpVariants: no visible global function definition for ‘as.alignment’
    dumpVariants: no visible global function definition for ‘write.fasta’
    dumpVariants: no visible binding for global variable ‘s2c’
    errorCorrect.alignment: no visible global function definition for
     ‘consensus’
    errorCorrect.alignment: no visible global function definition for ‘con’
    errorCorrect.alignment: no visible global function definition for
     ‘as.matrix.alignment’
    errorCorrect.alignment: no visible binding for global variable ‘c2s’
    errorCorrect.alignment: no visible global function definition for
     ‘as.alignment’
    errorCorrect.mlgtResult: no visible global function definition for
     ‘getSequence’
    errorCorrect.mlgtResult: no visible global function definition for
     ‘as.alignment’
    errorCorrect.mlgtResult: no visible global function definition for
     ‘as.SeqFastadna’
    getSubSeqsTable: no visible global function definition for ‘read.fasta’
    getSubSeqsTable: no visible global function definition for
     ‘write.fasta’
    getSubSeqsTable: no visible global function definition for
     ‘as.alignment’
    getSubSeqsTable: no visible global function definition for ‘s2c’
    makeVarAlleleBlastMap: no visible global function definition for
     ‘getName’
    makeVarAlleleBlastMap: no visible global function definition for
     ‘write.fasta’
    mlgt.mlgtDesign: no visible global function definition for
     ‘getSequence’
    mlgt.mlgtDesign: no visible global function definition for
     ‘as.SeqFastadna’
    prepareMlgtRun.mlgtDesign: no visible global function definition for
     ‘write.fasta’
    stripGapColumns: no visible global function definition for ‘con’
    stripGapColumns: no visible binding for global variable ‘c2s’
    stripGapColumns: no visible global function definition for
     ‘as.alignment’
    errorCorrect,missing-list : .local: no visible global function
     definition for ‘consensus’
    errorCorrect,missing-list : .local: no visible global function
     definition for ‘con’
    errorCorrect,missing-list : .local: no visible global function
     definition for ‘as.matrix.alignment’
    errorCorrect,missing-list : .local: no visible binding for global
     variable ‘c2s’
    errorCorrect,missing-list : .local: no visible global function
     definition for ‘as.alignment’
    errorCorrect,mlgtResult-missing : .local: no visible global function
     definition for ‘getSequence’
    errorCorrect,mlgtResult-missing : .local: no visible global function
     definition for ‘as.alignment’
    errorCorrect,mlgtResult-missing : .local: no visible global function
     definition for ‘as.SeqFastadna’
    mlgt,mlgtDesign: no visible global function definition for
     ‘getSequence’
    mlgt,mlgtDesign: no visible global function definition for
     ‘as.SeqFastadna’
    prepareMlgtRun,mlgtDesign-missing-missing-missing-missing-missing-missing-missing-character
     : .local: no visible global function definition for ‘write.fasta’
Flavors: r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-x86_64, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 0.16
Check: R code for possible problems
Result: NOTE
    alignReport: no visible global function definition for ‘as.alignment’
    alignReport: no visible global function definition for ‘consensus’
    alignReport: no visible global function definition for ‘con’
    createKnownAlleleList: no visible global function definition for
     ‘read.alignment’
    createKnownAlleleList: no visible global function definition for
     ‘write.fasta’
    createKnownAlleleList: no visible global function definition for
     ‘read.fasta’
    createKnownAlleleList: no visible global function definition for ‘s2c’
    createKnownAlleleList: no visible binding for global variable ‘name’
    createKnownAlleleList: no visible global function definition for
     ‘as.SeqFastadna’
    dumpVariantMap.mlgtResult: no visible global function definition for
     ‘write.fasta’
    dumpVariantMap.mlgtResult: no visible binding for global variable ‘s2c’
    dumpVariants: no visible global function definition for ‘as.alignment’
    dumpVariants: no visible global function definition for ‘write.fasta’
    dumpVariants: no visible binding for global variable ‘s2c’
    errorCorrect.alignment: no visible global function definition for
     ‘consensus’
    errorCorrect.alignment: no visible global function definition for ‘con’
    errorCorrect.alignment: no visible global function definition for
     ‘as.matrix.alignment’
    errorCorrect.alignment: no visible binding for global variable ‘c2s’
    errorCorrect.alignment: no visible global function definition for
     ‘as.alignment’
    errorCorrect.mlgtResult: no visible global function definition for
     ‘getSequence’
    errorCorrect.mlgtResult: no visible global function definition for
     ‘as.alignment’
    errorCorrect.mlgtResult: no visible global function definition for
     ‘as.SeqFastadna’
    getSubSeqsTable: no visible global function definition for ‘read.fasta’
    getSubSeqsTable: no visible global function definition for
     ‘write.fasta’
    getSubSeqsTable: no visible global function definition for
     ‘as.alignment’
    getSubSeqsTable: no visible global function definition for ‘s2c’
    makeVarAlleleBlastMap: no visible global function definition for
     ‘getName’
    makeVarAlleleBlastMap: no visible global function definition for
     ‘write.fasta’
    mlgt.mlgtDesign: no visible global function definition for
     ‘getSequence’
    mlgt.mlgtDesign: no visible global function definition for
     ‘as.SeqFastadna’
    prepareMlgtRun.mlgtDesign: no visible global function definition for
     ‘write.fasta’
    stripGapColumns: no visible global function definition for ‘con’
    stripGapColumns: no visible binding for global variable ‘c2s’
    stripGapColumns: no visible global function definition for
     ‘as.alignment’
    mlgt,mlgtDesign: no visible global function definition for
     ‘getSequence’
    mlgt,mlgtDesign: no visible global function definition for
     ‘as.SeqFastadna’
Flavor: r-release-osx-x86_64-mavericks