BayeScanR: no visible global function definition for 'rnorm'
MK: no visible global function definition for 'combn'
MS: no visible global function definition for 'var'
MS: no visible binding for global variable 'var'
PopGplot: no visible global function definition for 'rainbow'
PopGplot: no visible global function definition for 'loess'
PopGplot: no visible global function definition for 'plot'
PopGplot: no visible global function definition for 'predict'
PopGplot: no visible global function definition for 'lines'
Whop_readVCF: no visible global function definition for 'read.table'
calc_average_nuc_diversity_between_per_site: no visible global function
  definition for 'combn'
calc_diversities: no visible global function definition for 'combn'
calc_hwhafsth: no visible global function definition for 'combn'
calc_hwhafsth_FAST: no visible global function definition for 'combn'
calc_pi: no visible global function definition for 'combn'
calc_quantile: no visible global function definition for 'quantile'
coalsim: no visible global function definition for 'var'
coalsim: no visible binding for global variable 'var'
fstcalc: no visible global function definition for 'combn'
get.feature.names: no visible global function definition for
  'read.table'
get_gff_info: no visible global function definition for 'read.table'
get_ref_alleles: no visible global function definition for 'read.table'
gffRead: no visible global function definition for 'read.table'
gtest: no visible global function definition for 'pchisq'
hudsonkaplan85rm: no visible global function definition for 'combn'
intern.calc.R2 : <anonymous>: no visible global function definition for
  'fisher.test'
jump_model_codominant: no visible global function definition for
  'rnorm'
jump_model_codominant: no visible global function definition for
  'runif'
linkdisequ: no visible global function definition for 'combn'
mismatch: no visible global function definition for 'combn'
my_rdirichlet: no visible global function definition for 'rgamma'
pair_linkdisequ_FAST : <anonymous>: no visible global function
  definition for 'fisher.test'
permute: no visible global function definition for 'combn'
plot_avg_cs: no visible global function definition for 'plot'
plot_avg_cs: no visible global function definition for 'density'
plot_avg_cs: no visible global function definition for 'abline'
readData: no visible global function definition for 'combn'
readSNP: no visible global function definition for 'read.table'
readVCF: no visible global function definition for 'read.table'
readVCFchunk: no visible global function definition for 'read.table'
readVCFchunkHap: no visible global function definition for 'read.table'
readVCFchunk_tet: no visible global function definition for
  'read.table'
readVCFchunk_tri: no visible global function definition for
  'read.table'
set_gff_info: no visible global function definition for 'read.table'
snn: no visible global function definition for 'combn'
split_data_into_GFF_attributes: no visible global function definition
  for 'read.table'
update_d_alphaco_i: no visible global function definition for 'rnorm'
update_d_alphaco_i: no visible global function definition for 'runif'
update_d_betaco: no visible global function definition for 'rnorm'
update_d_betaco: no visible global function definition for 'runif'
update_freq_codominant: no visible global function definition for
  'runif'
F_ST.stats.2,GENOME: no visible global function definition for 'combn'
F_ST.stats,GENOME: no visible global function definition for 'combn'
MKT,GENOME: no visible global function definition for 'combn'
MKT,GENOME : <anonymous>: no visible global function definition for
  'fisher.test'
PG_plot.biallelic.matrix,GENOME: no visible global function definition
  for 'colors'
PG_plot.biallelic.matrix,GENOME: no visible global function definition
  for 'plot'
PG_plot.biallelic.matrix,GENOME: no visible global function definition
  for 'axis'
PG_plot.biallelic.matrix,GENOME: no visible global function definition
  for 'abline'
PG_plot.biallelic.matrix,GENOME: no visible global function definition
  for 'points'
SNPFST,GENOME: no visible global function definition for 'combn'
diversity.stats,GENOME: no visible global function definition for
  'combn'
mult.linkage.stats,GENOME: no visible global function definition for
  'combn'
popFSTN,GENOME: no visible global function definition for 'combn'
Undefined global functions or variables:
  abline axis colors combn density fisher.test lines loess pchisq plot
  points predict quantile rainbow read.table rgamma rnorm runif var
Consider adding
  importFrom("grDevices", "colors", "rainbow")
  importFrom("graphics", "abline", "axis", "lines", "plot", "points")
  importFrom("stats", "density", "fisher.test", "loess", "pchisq",
             "predict", "quantile", "rgamma", "rnorm", "runif", "var")
  importFrom("utils", "combn", "read.table")
to your NAMESPACE file.