cluster.strains: no visible global function definition for 'hclust'
cluster.strains: no visible global function definition for 'as.dist'
convert.genes.to.GRanges: no visible global function definition for
  'GRanges'
convert.genes.to.GRanges: no visible global function definition for
  'IRanges'
convert.genes.to.GRanges: no visible global function definition for
  'metadata<-'
convert.pos.to.GRanges: no visible global function definition for
  'GRanges'
convert.pos.to.GRanges: no visible global function definition for
  'IRanges'
convert.variants.to.GRanges: no visible global function definition for
  'GRanges'
convert.variants.to.GRanges: no visible global function definition for
  'IRanges'
convert.variants.to.GRanges: no visible global function definition for
  'metadata<-'
find.overlapping.genes: no visible global function definition for
  'findOverlaps'
find.overlapping.genes: no visible global function definition for
  'subjectHits'
gene.plot: no visible global function definition for 'par'
gene.plot: no visible global function definition for 'plot'
gene.plot: no visible global function definition for 'strwidth'
gene.plot: no visible global function definition for 'strheight'
gene.plot: no visible global function definition for 'rect'
gene.plot: no visible global function definition for 'text'
get.mgi.features: no visible global function definition for 'TabixFile'
get.mgi.features: no visible global function definition for
  'headerTabix'
get.mgi.features: no visible global function definition for 'scanTabix'
get.strains: no visible global function definition for 'TabixFile'
get.strains: no visible global function definition for 'headerTabix'
get.variants: no visible global function definition for 'TabixFile'
get.variants: no visible global function definition for 'headerTabix'
get.variants: no visible global function definition for 'scanTabix'
snp.plot: no visible global function definition for 'par'
snp.plot: no visible global function definition for 'layout'
snp.plot: no visible global function definition for 'image'
snp.plot: no visible global function definition for 'mtext'
snp.plot: no visible global function definition for 'abline'
snp.plot: no visible global function definition for 'axis'
snp.plot: no visible global function definition for 'rect'
snp.plot: no visible global function definition for 'rgb'
snp.plot: no visible global function definition for 'lines'
snp.plot: no visible global function definition for 'text'
snp.plot: no visible global function definition for 'approx'
snp.plot: no visible global function definition for 'quantile'
snp.plot: no visible global function definition for 'colorRampPalette'
Undefined global functions or variables:
  GRanges IRanges TabixFile abline approx as.dist axis colorRampPalette
  findOverlaps hclust headerTabix image layout lines metadata<- mtext
  par plot quantile rect rgb scanTabix strheight strwidth subjectHits
  text
Consider adding
  importFrom("grDevices", "colorRampPalette", "rgb")
  importFrom("graphics", "abline", "axis", "image", "layout", "lines",
             "mtext", "par", "plot", "rect", "strheight", "strwidth",
             "text")
  importFrom("stats", "approx", "as.dist", "hclust", "quantile")
to your NAMESPACE file.