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 '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 '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.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.new", "title")
  importFrom("methods", "new")
  importFrom("stats", "na.omit")
  importFrom("utils", "packageVersion", "read.delim", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').