Armitage: no visible global function definition for ‘pchisq’
Armitage.MCPerm: no visible global function definition for ‘pchisq’
Armitage.MCPerm: no visible global function definition for ‘rhyper’
Armitage.TradPerm: no visible global function definition for ‘pchisq’
HW.test: no visible global function definition for ‘pchisq’
I2.MCPerm: no visible global function definition for ‘rma’
I2.MCPerm: no visible global function definition for ‘rma.mh’
I2.MCPerm: no visible global function definition for ‘rma.peto’
I2.MCPerm: no visible global function definition for ‘rhyper’
I2.TradPerm: no visible global function definition for ‘rma’
I2.TradPerm: no visible global function definition for ‘rma.mh’
I2.TradPerm: no visible global function definition for ‘rma.peto’
OR.MCPerm: no visible global function definition for ‘rhyper’
PermMeta.Hist: no visible global function definition for ‘hist’
PermMeta.Hist: no visible global function definition for ‘points’
PermMeta.Hist: no visible global function definition for ‘arrows’
PermMeta.Hist: no visible global function definition for ‘legend’
PermMeta.LnOR.CDC: no visible binding for global variable ‘var’
PermMeta.LnOR.CDC: no visible global function definition for ‘par’
PermMeta.LnOR.CDC: no visible global function definition for ‘plot’
PermMeta.LnOR.CDC: no visible global function definition for ‘ecdf’
PermMeta.LnOR.CDC: no visible global function definition for ‘rnorm’
PermMeta.LnOR.CDC: no visible global function definition for ‘legend’
PermMeta.LnOR.CDC: no visible global function definition for ‘mtext’
PermMeta.LnOR.CDC: no visible global function definition for ‘x11’
PermMeta.LnOR.Hist: no visible binding for global variable ‘var’
PermMeta.LnOR.Hist: no visible global function definition for ‘par’
PermMeta.LnOR.Hist: no visible global function definition for ‘hist’
PermMeta.LnOR.Hist: no visible global function definition for ‘points’
PermMeta.LnOR.Hist: no visible global function definition for ‘arrows’
PermMeta.LnOR.Hist: no visible global function definition for ‘legend’
PermMeta.LnOR.Hist: no visible global function definition for ‘mtext’
PermMeta.LnOR.Hist: no visible global function definition for ‘x11’
PermMeta.LnOR.boxplot: no visible binding for global variable ‘var’
PermMeta.LnOR.boxplot: no visible global function definition for
  ‘boxplot’
PermMeta.LnOR.boxplot: no visible global function definition for
  ‘legend’
PermMeta.LnOR.boxplot: no visible global function definition for
  ‘points’
PermMeta.LnOR.boxplot: no visible global function definition for ‘text’
PermMeta.LnOR.qqnorm: no visible global function definition for ‘par’
PermMeta.LnOR.qqnorm: no visible global function definition for
  ‘qqnorm’
PermMeta.LnOR.qqnorm: no visible global function definition for
  ‘qqline’
PermMeta.LnOR.qqnorm: no visible binding for global variable ‘qnorm’
PermMeta.LnOR.qqnorm: no visible global function definition for ‘mtext’
PermMeta.LnOR.qqnorm: no visible global function definition for ‘x11’
PermMeta.boxplot: no visible global function definition for ‘par’
PermMeta.boxplot: no visible global function definition for ‘boxplot’
PermMeta.boxplot: no visible global function definition for ‘points’
PermMeta.boxplot: no visible global function definition for ‘mtext’
PermMeta.boxplot: no visible global function definition for ‘legend’
Q.MCPerm: no visible global function definition for ‘rma’
Q.MCPerm: no visible global function definition for ‘rma.mh’
Q.MCPerm: no visible global function definition for ‘rma.peto’
Q.MCPerm: no visible global function definition for ‘rhyper’
Q.TradPerm: no visible global function definition for ‘rma’
Q.TradPerm: no visible global function definition for ‘rma.mh’
Q.TradPerm: no visible global function definition for ‘rma.peto’
VS.Allele.CDC: no visible global function definition for ‘par’
VS.Allele.CDC: no visible global function definition for ‘plot’
VS.Allele.CDC: no visible global function definition for ‘ecdf’
VS.Allele.CDC: no visible global function definition for ‘legend’
VS.Allele.CDC: no visible global function definition for ‘mtext’
VS.Allele.Hist: no visible global function definition for ‘par’
VS.Allele.Hist: no visible global function definition for ‘hist’
VS.Allele.Hist: no visible global function definition for ‘legend’
VS.Allele.Hist: no visible global function definition for ‘mtext’
VS.Allele.QQ: no visible global function definition for ‘par’
VS.Allele.QQ: no visible global function definition for ‘qqplot’
VS.Allele.QQ: no visible global function definition for ‘abline’
VS.Allele.QQ: no visible global function definition for ‘mtext’
VS.CDC: no visible global function definition for ‘plot’
VS.CDC: no visible global function definition for ‘ecdf’
VS.CDC: no visible global function definition for ‘par’
VS.CDC: no visible global function definition for ‘legend’
VS.Genotype.CDC: no visible global function definition for ‘par’
VS.Genotype.CDC: no visible global function definition for ‘plot’
VS.Genotype.CDC: no visible global function definition for ‘ecdf’
VS.Genotype.CDC: no visible global function definition for ‘legend’
VS.Genotype.CDC: no visible global function definition for ‘mtext’
VS.Genotype.Hist: no visible global function definition for ‘par’
VS.Genotype.Hist: no visible global function definition for ‘hist’
VS.Genotype.Hist: no visible global function definition for ‘legend’
VS.Genotype.Hist: no visible global function definition for ‘mtext’
VS.Genotype.QQ: no visible global function definition for ‘par’
VS.Genotype.QQ: no visible global function definition for ‘qqplot’
VS.Genotype.QQ: no visible global function definition for ‘abline’
VS.Genotype.QQ: no visible global function definition for ‘mtext’
VS.Hist: no visible global function definition for ‘hist’
VS.Hist: no visible global function definition for ‘par’
VS.Hist: no visible global function definition for ‘legend’
VS.KS: no visible global function definition for ‘ks.test’
VS.KS: no visible global function definition for ‘plot’
VS.KS: no visible global function definition for ‘abline’
VS.QQ: no visible global function definition for ‘qqplot’
VS.QQ: no visible global function definition for ‘abline’
chisq.MCPerm: no visible global function definition for ‘chisq.test’
chisq.MCPerm: no visible global function definition for ‘rhyper’
chisq.TradPerm: no visible global function definition for ‘chisq.test’
fisher.MCPerm: no visible global function definition for ‘fisher.test’
fisher.MCPerm: no visible global function definition for ‘rhyper’
fisher.TradPerm: no visible global function definition for
  ‘fisher.test’
meta: no visible global function definition for ‘rma’
meta: no visible global function definition for ‘rma.mh’
meta: no visible global function definition for ‘rma.peto’
meta.MCPerm: no visible global function definition for ‘rma’
meta.MCPerm: no visible global function definition for ‘rma.mh’
meta.MCPerm: no visible global function definition for ‘rma.peto’
meta.MCPerm: no visible global function definition for ‘rhyper’
meta.TradPerm: no visible global function definition for ‘rma’
meta.TradPerm: no visible global function definition for ‘rma.mh’
meta.TradPerm: no visible global function definition for ‘rma.peto’
pearson_scatter: no visible global function definition for ‘cor.test’
pearson_scatter: no visible global function definition for ‘plot’
pearson_scatter: no visible global function definition for ‘legend’
pearson_scatter: no visible global function definition for ‘abline’
permuteGenotypeCount: no visible global function definition for
  ‘rhyper’
Undefined global functions or variables:
  abline arrows boxplot chisq.test cor.test ecdf fisher.test hist
  ks.test legend mtext par pchisq plot points qnorm qqline qqnorm
  qqplot rhyper rma rma.mh rma.peto rnorm text var x11
Consider adding
  importFrom("grDevices", "x11")
  importFrom("graphics", "abline", "arrows", "boxplot", "hist", "legend",
             "mtext", "par", "plot", "points", "text")
  importFrom("stats", "chisq.test", "cor.test", "ecdf", "fisher.test",
             "ks.test", "pchisq", "qnorm", "qqline", "qqnorm", "qqplot",
             "rhyper", "rnorm", "var")
to your NAMESPACE file.