HWE.chisq.genotype: no visible global function definition for
  ‘chisq.test’
HWE.chisq.genotype: no visible global function definition for ‘pchisq’
LD.genotype: no visible global function definition for ‘optimize’
LD.genotype: no visible global function definition for ‘pchisq’
LDplot: no visible global function definition for ‘matplot’
LDplot: no visible global function definition for ‘axis’
LDplot: no visible global function definition for ‘title’
LDtable: no visible global function definition for ‘heat.colors’
LDtable: no visible global function definition for ‘image’
LDtable: no visible global function definition for ‘abline’
LDtable: no visible global function definition for ‘axis’
LDtable: no visible global function definition for ‘par’
LDtable: no visible global function definition for ‘strwidth’
LDtable: no visible global function definition for ‘strheight’
LDtable: no visible global function definition for ‘text’
LDtable: no visible global function definition for ‘title’
diseq.ci : <anonymous>: no visible global function definition for
  ‘quantile’
groupGenotype: no visible global function definition for ‘mapLevels<-’
groupGenotype: no visible global function definition for ‘as.levelsMap’
hapenum: no visible global function definition for ‘complete.cases’
hapfreq: no visible global function definition for ‘complete.cases’
hapshuffle: no visible global function definition for ‘runif’
plot.LD.data.frame: no visible global function definition for
  ‘heat.colors’
plot.LD.data.frame: no visible global function definition for ‘par’
plot.genotype: no visible global function definition for ‘barplot’
power.casectrl.plot: no visible global function definition for
  ‘matplot’
power.casectrl.plot: no visible global function definition for ‘abline’
power.casectrl.plot: no visible global function definition for ‘legend’
power.casectrl.plot: no visible global function definition for
  ‘locator’
pw: no visible global function definition for ‘lm’
pw: no visible global function definition for ‘plot’
pw: no visible global function definition for ‘anova’
simu.genotype.conti: no visible global function definition for ‘lm’
simu.genotype.conti: no visible global function definition for ‘plot’
simu.genotype.conti: no visible global function definition for ‘anova’
write.marker.file: no visible global function definition for
  ‘write.table’
write.pedigree.file: no visible global function definition for
  ‘write.table’
write.pop.file: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  abline anova as.levelsMap axis barplot chisq.test complete.cases
  heat.colors image legend lm locator mapLevels<- matplot optimize par
  pchisq plot quantile runif strheight strwidth text title write.table
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "abline", "axis", "barplot", "image", "legend",
             "locator", "matplot", "par", "plot", "strheight",
             "strwidth", "text", "title")
  importFrom("stats", "anova", "chisq.test", "complete.cases", "lm",
             "optimize", "pchisq", "quantile", "runif")
  importFrom("utils", "write.table")
to your NAMESPACE file.