GenomicControl : WGchisq: no visible global function definition for
  ‘qchisq’
GenomicControl: no visible binding for global variable ‘median’
GenomicControl: no visible global function definition for ‘pchisq’
LD.snp: no visible global function definition for ‘optimize’
LD.snp: 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’
Table.mean.se : <anonymous>: no visible global function definition for
  ‘sd’
WGassociation: no visible global function definition for ‘as.formula’
WGassociation: no visible global function definition for ‘terms’
WGassociation : association.i: no visible global function definition
  for ‘as.formula’
WGassociation: no visible global function definition for ‘mclapply’
assoc : lrt: no visible global function definition for ‘pchisq’
assoc : G: no visible global function definition for ‘pchisq’
assoc: no visible global function definition for ‘glm’
association: no visible global function definition for ‘terms’
association.fit: no visible global function definition for ‘glm’
association.fit: no visible binding for global variable ‘binomial’
association.fit: no visible global function definition for ‘AIC’
association.fit: no visible global function definition for
  ‘fisher.test’
association.fit: no visible binding for global variable ‘gaussian’
crea.lab: no visible global function definition for ‘text’
haplo.inter.fit: no visible global function definition for ‘pchisq’
haplo.interaction: no visible global function definition for ‘terms’
interactionPval: no visible global function definition for ‘as.formula’
interactionPval: no visible global function definition for ‘glm’
interactionPval: no visible global function definition for ‘anova’
interleave: no visible global function definition for ‘mclapply’
intervals.dif: no visible global function definition for ‘qnorm’
intervals.dif: no visible global function definition for ‘anova’
intervals.haplo.glm: no visible global function definition for ‘qnorm’
intervals.or: no visible global function definition for ‘qnorm’
intervals.or: no visible global function definition for ‘anova’
maxstat.default: no visible global function definition for
  ‘complete.cases’
maxstat.matrix: no visible global function definition for ‘pchisq’
maxstat.matrix: no visible global function definition for ‘runif’
permTest : llhd2: no visible global function definition for ‘dbeta’
permTest: no visible global function definition for ‘nlm’
permTest: no visible global function definition for ‘qbeta’
plot.SNPinteraction: no visible global function definition for ‘par’
plot.SNPinteraction: no visible global function definition for ‘layout’
plot.SNPinteraction: no visible global function definition for ‘image’
plot.SNPinteraction: no visible global function definition for ‘axis’
plot.SNPinteraction: no visible global function definition for ‘title’
plot.SNPinteraction: no visible global function definition for
  ‘segments’
plot.SNPinteraction: no visible global function definition for ‘abline’
plot.SNPinteraction: no visible global function definition for ‘text’
plot.WGassociation: no visible global function definition for ‘par’
plot.WGassociation: no visible global function definition for ‘layout’
plot.WGassociation: no visible global function definition for ‘plot’
plot.WGassociation: no visible global function definition for ‘text’
plot.WGassociation: no visible global function definition for ‘legend’
plot.WGassociation: no visible global function definition for ‘axis’
plot.WGassociation: no visible global function definition for
  ‘segments’
plot.WGassociation: no visible global function definition for ‘runif’
plot.permTest: no visible global function definition for ‘density’
plot.permTest: no visible global function definition for ‘plot’
plot.permTest: no visible global function definition for ‘dbeta’
plot.permTest: no visible global function definition for ‘hist’
plot.permTest: no visible global function definition for ‘lines’
plot.permTest: no visible global function definition for ‘segments’
plot.permTest: no visible global function definition for ‘legend’
plot.setupSNP: no visible global function definition for ‘plot’
plot.snp: no visible binding for global variable ‘barplot’
plot.snp: no visible global function definition for ‘par’
plot.snp: no visible global function definition for ‘layout’
plot.snp: no visible global function definition for ‘plot’
plot.snp: no visible global function definition for ‘text’
plotMissing: no visible global function definition for ‘par’
plotMissing: no visible global function definition for ‘image’
plotMissing: no visible global function definition for ‘axis’
plotMissing: no visible global function definition for ‘title’
plotMissing: no visible global function definition for ‘segments’
plotMissing: no visible global function definition for ‘abline’
plotMissing: no visible global function definition for ‘text’
print.maxstat: no visible global function definition for ‘printCoefmat’
qqpval: no visible global function definition for ‘plot’
qqpval: no visible global function definition for ‘abline’
reorder.snp: no visible global function definition for ‘relevel’
setupSNP: no visible global function definition for ‘mclapply’
snp: no visible global function definition for ‘na.omit’
summary.haplo.glm: no visible global function definition for ‘pnorm’
summary.setupSNP: no visible global function definition for ‘mclapply’
table.corner : glm2: no visible binding for global variable ‘gaussian’
table.corner : glm2: no visible global function definition for
  ‘glm.control’
table.corner : glm2: no visible global function definition for
  ‘model.response’
table.corner : glm2: no visible global function definition for
  ‘is.empty.model’
table.corner : glm2: no visible global function definition for
  ‘model.matrix’
table.corner : glm2: no visible global function definition for
  ‘model.weights’
table.corner : glm2: no visible global function definition for
  ‘model.offset’
table.corner : glm2: no visible global function definition for
  ‘model.extract’
table.corner : glm2: no visible global function definition for
  ‘glm.fit’
table.corner : glm2: no visible global function definition for
  ‘.getXlevels’
table.corner: no visible binding for global variable ‘binomial’
table.corner: no visible binding for global variable ‘gaussian’
table.interaction: no visible global function definition for ‘glm’
table.interaction: no visible binding for global variable ‘binomial’
table.interaction: no visible global function definition for ‘anova’
table.interaction: no visible binding for global variable ‘gaussian’
tableHWE: no visible global function definition for ‘mclapply’
Undefined global functions or variables:
  .getXlevels AIC abline anova as.formula axis barplot binomial
  complete.cases dbeta density fisher.test gaussian glm glm.control
  glm.fit heat.colors hist image is.empty.model layout legend lines
  matplot mclapply median model.extract model.matrix model.offset
  model.response model.weights na.omit nlm optimize par pchisq plot
  pnorm printCoefmat qbeta qchisq qnorm relevel runif sd segments
  strheight strwidth terms text title
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "abline", "axis", "barplot", "hist", "image",
             "layout", "legend", "lines", "matplot", "par", "plot",
             "segments", "strheight", "strwidth", "text", "title")
  importFrom("stats", ".getXlevels", "AIC", "anova", "as.formula",
             "binomial", "complete.cases", "dbeta", "density",
             "fisher.test", "gaussian", "glm", "glm.control", "glm.fit",
             "is.empty.model", "median", "model.extract", "model.matrix",
             "model.offset", "model.response", "model.weights",
             "na.omit", "nlm", "optimize", "pchisq", "pnorm",
             "printCoefmat", "qbeta", "qchisq", "qnorm", "relevel",
             "runif", "sd", "terms")
to your NAMESPACE file.