Cline.fit: no visible global function definition for 'aggregate'
Cline.fit: no visible global function definition for 'na.omit'
Cline.fit: no visible global function definition for 'mahalanobis'
Cline.fit: no visible global function definition for 'cov'
Cline.fit: no visible global function definition for 'pchisq'
Cline.plot : Beta.p: no visible global function definition for 'pbeta'
Cline.plot: no visible global function definition for 'par'
Cline.plot: no visible global function definition for 'lines'
Cline.plot: no visible global function definition for 'qchisq'
HIest : HIproposal: no visible global function definition for
  'rmultinom'
HIest: no visible global function definition for 'optim'
HIest: no visible global function definition for 'runif'
gcline.fn: no visible global function definition for 'glm'
gcline.fn: no visible global function definition for 'logLik'
gcline.fn: no visible global function definition for 'multinom'
gcline.fn : LL.fn: no visible global function definition for 'dbinom'
gcline.fn : GR: no visible global function definition for 'rlnorm'
gcline.fn : GR: no visible global function definition for 'rnorm'
gcline.fn : LL.fn: no visible global function definition for 'pbeta'
gcline.fn: no visible global function definition for 'optim'
gcline.fn: no visible global function definition for 'runif'
longX2: no visible global function definition for 'pchisq'
spatial.AD : rbnorm: no visible global function definition for 'rnorm'
spatial.AD: no visible global function definition for 'dist'
spatial.AD: no visible global function definition for 'dnorm'
spatial.AD: no visible global function definition for 'rpois'
spatial.AD: no visible global function definition for 'runif'
spatial.AD: no visible global function definition for 'rbinom'
spatial.HZ : rbnorm: no visible global function definition for 'rnorm'
spatial.HZ: no visible global function definition for 'dist'
spatial.HZ: no visible global function definition for 'dnorm'
spatial.HZ: no visible global function definition for 'rpois'
spatial.HZ: no visible global function definition for 'rbinom'
threeway : GR: no visible global function definition for 'rmultinom'
threeway: no visible global function definition for 'runif'
threeway: no visible global function definition for 'optim'
Undefined global functions or variables:
  aggregate cov dbinom dist dnorm glm lines logLik mahalanobis multinom
  na.omit optim par pbeta pchisq qchisq rbinom rlnorm rmultinom rnorm
  rpois runif
Consider adding
  importFrom("graphics", "lines", "par")
  importFrom("stats", "aggregate", "cov", "dbinom", "dist", "dnorm",
             "glm", "logLik", "mahalanobis", "na.omit", "optim", "pbeta",
             "pchisq", "qchisq", "rbinom", "rlnorm", "rmultinom",
             "rnorm", "rpois", "runif")
to your NAMESPACE file.