GC.adj.pvalues: no visible global function definition for ‘pnorm’
GC.adj.pvalues: no visible global function definition for ‘pchisq’
LOR.flip: no visible global function definition for ‘write.table’
OR.plot.main: no visible global function definition for ‘plot’
OR.plot.main: no visible global function definition for ‘polygon’
OR.plot.main: no visible global function definition for ‘lines’
OR.plot.main: no visible global function definition for ‘axis’
OR.plot.main: no visible global function definition for ‘box’
QQ.plot: no visible global function definition for ‘plot’
QQ.plot: no visible global function definition for ‘axis’
QQ.plot: no visible global function definition for ‘box’
QQ.plot: no visible global function definition for ‘title’
QQ.plot: no visible global function definition for ‘abline’
QQ.plot: no visible global function definition for ‘points’
QQ.plot2: no visible global function definition for ‘qchisq’
QQ.plot2: no visible global function definition for ‘plot’
QQ.plot2: no visible global function definition for ‘axis’
QQ.plot2: no visible global function definition for ‘box’
QQ.plot2: no visible global function definition for ‘title’
QQ.plot2: no visible global function definition for ‘abline’
addLineSegments: no visible global function definition for ‘segments’
allele.flip: no visible global function definition for ‘write.table’
applyFormulas: no visible global function definition for ‘model.matrix’
callGLM: no visible global function definition for ‘glm’
chrm.plot.main: no visible global function definition for ‘plot’
chrm.plot.main: no visible global function definition for ‘axis’
chrm.plot.main: no visible global function definition for ‘box’
chrm.plot.main: no visible global function definition for ‘points’
chrm.plot.main: no visible global function definition for ‘abline’
chromosome.plot: no visible global function definition for
  ‘split.screen’
chromosome.plot: no visible global function definition for ‘screen’
combineByPathway_Kai: no visible global function definition for
  ‘write.table’
convert.obsfile: no visible global function definition for ‘qnorm’
crossTab: no visible binding for global variable ‘data’
dsgnMat: no visible global function definition for ‘as.formula’
dsgnMat: no visible global function definition for ‘model.matrix’
gene.plot: no visible global function definition for ‘split.screen’
gene.plot: no visible global function definition for ‘screen’
gene.plot.main: no visible global function definition for ‘plot’
gene.plot.main: no visible global function definition for ‘axis’
gene.plot.main: no visible global function definition for ‘box’
gene.plot.main: no visible global function definition for ‘points’
gene.plot.main: no visible global function definition for ‘abline’
gene.plot.main: no visible global function definition for ‘mtext’
getCI: no visible global function definition for ‘qnorm’
getColors: no visible global function definition for ‘colors’
getColors: no visible global function definition for ‘pie’
getDesignMatrix: no visible global function definition for
  ‘model.matrix’
getMAF.control: no visible global function definition for ‘read.table’
getOR.CI: no visible global function definition for ‘qnorm’
getPermutation: no visible global function definition for ‘rbinom’
getSummary: no visible global function definition for ‘pnorm’
getSummary.main: no visible global function definition for ‘pnorm’
globalAlleles: no visible global function definition for ‘write.table’
glu.create_ped: no visible global function definition for ‘write.table’
glu.ldMatrix: no visible global function definition for ‘read.table’
glu.nBins: no visible global function definition for ‘read.table’
glu.r2: no visible global function definition for ‘read.table’
heterTest: no visible global function definition for ‘glm’
inflationFactor: no visible global function definition for ‘qchisq’
inflationFactor: no visible global function definition for ‘median’
likelihoodRatio.main: no visible global function definition for
  ‘pchisq’
meta.analysis: no visible global function definition for ‘pnorm’
meta.analysis: no visible global function definition for ‘write.table’
meta.mima.scan: no visible global function definition for ‘read.table’
meta.setup: no visible global function definition for ‘qnorm’
meta.setup: no visible global function definition for ‘pnorm’
meta.update: no visible global function definition for ‘qnorm’
mima: no visible global function definition for ‘var’
mima: no visible global function definition for ‘pchisq’
mima: no visible global function definition for ‘pnorm’
mima: no visible global function definition for ‘qnorm’
myrmvnorm: no visible global function definition for ‘rnorm’
perm.glm: no visible global function definition for ‘glm.fit’
permReg : corrMatrix0: no visible global function definition for
  ‘qnorm’
permReg : corrMatrix0: no visible global function definition for ‘cor’
permReg : mvn_pval: no visible global function definition for ‘pnorm’
permReg: no visible global function definition for ‘glm’
permReg: no visible global function definition for ‘glm.control’
permReg: no visible global function definition for ‘write.table’
pvalue.normal: no visible global function definition for ‘pnorm’
readTable: no visible global function definition for ‘read.table’
runPermutations: no visible global function definition for ‘binomial’
runPermutations: no visible global function definition for ‘gaussian’
score.logReg: no visible global function definition for ‘pchisq’
set.plot: no visible global function definition for ‘bitmap’
setDevice: no visible global function definition for ‘postscript’
setDevice: no visible global function definition for ‘pdf’
setDevice: no visible global function definition for ‘jpeg’
setDevice: no visible global function definition for ‘graphics.off’
single.marker.test: no visible global function definition for ‘lm’
single.marker.test: no visible global function definition for
  ‘binomial’
single.marker.test: no visible global function definition for
  ‘fisher.test’
snp.effects.plot: no visible global function definition for
  ‘split.screen’
snp.effects.plot: no visible global function definition for ‘screen’
snp.effects.plot: no visible global function definition for
  ‘close.screen’
standardize.z: no visible global function definition for ‘var’
unadjustedGLM.counts: no visible global function definition for ‘glm’
unadjustedGLM.counts: no visible binding for global variable ‘binomial’
unadjustedGLM.counts: no visible global function definition for
  ‘write.table’
waldTest.main: no visible global function definition for ‘pnorm’
waldTest.main: no visible global function definition for ‘pchisq’
writeTable: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  abline as.formula axis binomial bitmap box close.screen colors cor
  data fisher.test gaussian glm glm.control glm.fit graphics.off jpeg
  lines lm median model.matrix mtext pchisq pdf pie plot pnorm points
  polygon postscript qchisq qnorm rbinom read.table rnorm screen
  segments split.screen title var write.table
Consider adding
  importFrom("grDevices", "bitmap", "colors", "graphics.off", "jpeg",
             "pdf", "postscript")
  importFrom("graphics", "abline", "axis", "box", "close.screen",
             "lines", "mtext", "pie", "plot", "points", "polygon",
             "screen", "segments", "split.screen", "title")
  importFrom("stats", "as.formula", "binomial", "cor", "fisher.test",
             "gaussian", "glm", "glm.control", "glm.fit", "lm", "median",
             "model.matrix", "pchisq", "pnorm", "qchisq", "qnorm",
             "rbinom", "rnorm", "var")
  importFrom("utils", "data", "read.table", "write.table")
to your NAMESPACE file.