CRAN Package Check Results for Package mlgt

Last updated on 2015-07-06 06:46:48.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.16 1.02 16.91 17.93 NOTE
r-devel-linux-x86_64-debian-gcc 0.16 1.08 16.28 17.37 NOTE
r-devel-linux-x86_64-fedora-clang 0.16 33.52 NOTE
r-devel-linux-x86_64-fedora-gcc 0.16 31.24 NOTE
r-devel-osx-x86_64-clang 0.16 30.43 NOTE
r-devel-windows-ix86+x86_64 0.16 6.00 26.00 32.00 NOTE
r-patched-linux-x86_64 0.16 1.04 16.28 17.32 NOTE
r-patched-solaris-sparc 0.16 208.70 NOTE
r-patched-solaris-x86 0.16 44.60 NOTE
r-release-linux-x86_64 0.16 1.03 16.47 17.50 NOTE
r-release-osx-x86_64-mavericks 0.16 NOTE
r-release-windows-ix86+x86_64 0.16 5.00 45.00 50.00 NOTE
r-oldrel-windows-ix86+x86_64 0.16 7.00 31.00 38.00 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
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’
    mlgt,mlgtDesign: no visible global function definition for
     ‘getSequence’
    mlgt,mlgtDesign: no visible global function definition for
     ‘as.SeqFastadna’
Flavors: 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