* using log directory 'd:/Rcompile/CRANpkg/local/3.3/mlgt.Rcheck'
* using R version 3.3.2 (2016-10-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* checking for file 'mlgt/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'mlgt' version '0.16'
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'mlgt' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over 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 loading without being on the library search path ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... 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.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... 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 file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [1s] OK
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs