QC_GWAS: no visible global function definition for 'read.table'
QC_GWAS: no visible global function definition for 'flush.console'
QC_GWAS: no visible global function definition for 'write.table'
QC_GWAS: no visible global function definition for 'png'
QC_GWAS: no visible global function definition for 'par'
QC_GWAS: no visible global function definition for 'hist'
QC_GWAS: no visible global function definition for 'text'
QC_GWAS: no visible global function definition for 'mtext'
QC_GWAS: no visible global function definition for 'title'
QC_GWAS: no visible global function definition for 'dev.off'
QC_GWAS: no visible global function definition for 'pchisq'
QC_GWAS: no visible global function definition for 'median'
QC_GWAS : stat_save: no visible global function definition for
  'quantile'
QC_GWAS : stat_select_save: no visible global function definition for
  'quantile'
QC_GWAS: no visible global function definition for 'quantile'
QC_histogram: no visible global function definition for 'png'
QC_histogram: no visible global function definition for 'par'
QC_histogram: no visible global function definition for 'hist'
QC_histogram: no visible global function definition for 'qnorm'
QC_histogram: no visible global function definition for 'ppoints'
QC_histogram: no visible global function definition for 'sd'
QC_histogram: no visible global function definition for 'text'
QC_histogram: no visible global function definition for 'dev.off'
QC_histogram: no visible global function definition for 'write.table'
QC_plots: no visible global function definition for 'flush.console'
QC_plots: no visible global function definition for 'median'
QC_plots: no visible global function definition for 'qchisq'
QC_plots : calculateQQ: no visible global function definition for
  'ppoints'
QC_plots : addQQplot: no visible global function definition for
  'points'
QC_plots: no visible global function definition for 'qbeta'
QC_plots: no visible global function definition for 'png'
QC_plots: no visible global function definition for 'par'
QC_plots: no visible global function definition for 'mtext'
QC_plots: no visible global function definition for 'polygon'
QC_plots: no visible global function definition for 'points'
QC_plots: no visible global function definition for 'legend'
QC_plots: no visible global function definition for 'abline'
QC_plots: no visible global function definition for 'text'
QC_plots: no visible global function definition for 'title'
QC_plots: no visible global function definition for 'dev.off'
QC_plots: no visible global function definition for 'palette'
QC_plots: no visible global function definition for 'axis'
QC_series: no visible global function definition for 'flush.console'
QC_series: no visible global function definition for 'read.table'
QC_series: no visible global function definition for 'write.table'
QQ_plot: no visible global function definition for 'ppoints'
QQ_plot: no visible global function definition for 'qbeta'
QQ_plot: no visible global function definition for 'png'
QQ_plot: no visible global function definition for 'polygon'
QQ_plot: no visible global function definition for 'lines'
QQ_plot: no visible global function definition for 'points'
QQ_plot: no visible global function definition for 'dev.off'
calc_kurtosis: no visible global function definition for 'sd'
calc_skewness: no visible global function definition for 'sd'
check_P: no visible global function definition for 'pchisq'
check_P: no visible global function definition for 'cor'
check_P: no visible global function definition for 'png'
check_P: no visible global function definition for 'lines'
check_P: no visible global function definition for 'points'
check_P: no visible global function definition for 'legend'
check_P: no visible global function definition for 'text'
check_P: no visible global function definition for 'dev.off'
create_hapmap_reference: no visible global function definition for
  'flush.console'
create_hapmap_reference: no visible global function definition for
  'download.file'
create_hapmap_reference: no visible global function definition for
  'read.table'
create_hapmap_reference: no visible global function definition for
  'write.table'
filter_GWAS: no visible global function definition for 'read.table'
filter_GWAS: no visible global function definition for 'flush.console'
filter_GWAS: no visible global function definition for 'write.table'
intensity_plot: no visible global function definition for 'points'
load_GWAS: no visible global function definition for 'read.table'
load_test: no visible global function definition for 'read.table'
match_alleles: no visible global function definition for 'write.table'
match_alleles : plot_allele_cor: no visible global function definition
  for 'cor'
match_alleles : plot_allele_cor: no visible global function definition
  for 'png'
match_alleles : plot_allele_cor: no visible global function definition
  for 'legend'
match_alleles : plot_allele_cor: no visible global function definition
  for 'points'
match_alleles : plot_allele_cor: no visible global function definition
  for 'text'
match_alleles : plot_allele_cor: no visible global function definition
  for 'mtext'
match_alleles : plot_allele_cor: no visible global function definition
  for 'dev.off'
plot_distribution: no visible global function definition for 'quantile'
plot_distribution: no visible global function definition for 'png'
plot_distribution: no visible global function definition for 'boxplot'
plot_distribution: no visible global function definition for 'abline'
plot_distribution: no visible global function definition for 'median'
plot_distribution: no visible global function definition for 'dev.off'
plot_precision: no visible global function definition for 'png'
plot_precision: no visible global function definition for 'text'
plot_precision: no visible global function definition for 'dev.off'
plot_regional: no visible global function definition for 'png'
plot_regional: no visible global function definition for 'par'
plot_regional: no visible global function definition for 'abline'
plot_regional: no visible global function definition for 'text'
plot_regional: no visible global function definition for 'dev.off'
plot_skewness: no visible global function definition for 'png'
plot_skewness: no visible global function definition for 'abline'
plot_skewness: no visible global function definition for 'text'
plot_skewness: no visible global function definition for 'dev.off'
save_log: no visible global function definition for 'write.table'
Undefined global functions or variables:
  abline axis boxplot cor dev.off download.file flush.console hist
  legend lines median mtext palette par pchisq png points polygon
  ppoints qbeta qchisq qnorm quantile read.table sd text title
  write.table
Consider adding
  importFrom("grDevices", "dev.off", "palette", "png")
  importFrom("graphics", "abline", "axis", "boxplot", "hist", "legend",
             "lines", "mtext", "par", "points", "polygon", "text",
             "title")
  importFrom("stats", "cor", "median", "pchisq", "ppoints", "qbeta",
             "qchisq", "qnorm", "quantile", "sd")
  importFrom("utils", "download.file", "flush.console", "read.table",
             "write.table")
to your NAMESPACE file.