.file_path_as_absolute: no visible global function definition for
  'file_test'
.plot.text: no visible global function definition for 'par'
.plot.text: no visible global function definition for 'plot'
.plot.text: no visible global function definition for 'rect'
.plot.text: no visible global function definition for 'text'
bedgraph.to.depth: no visible global function definition for
  'read.table'
ghist: no visible global function definition for 'hist'
heatmap.3: no visible global function definition for 'par'
heatmap.3: no visible global function definition for 'flush.console'
heatmap.3: no visible global function definition for 'layout'
heatmap.3: no visible global function definition for 'image'
heatmap.3: no visible global function definition for 'axis'
heatmap.3: no visible global function definition for 'text'
heatmap.3: no visible global function definition for 'mtext'
heatmap.3: no visible global function definition for 'rect'
heatmap.3: no visible global function definition for 'abline'
heatmap.3: no visible global function definition for 'lines'
heatmap.3: no visible global function definition for 'plot'
heatmap.3: no visible global function definition for 'title'
heatmap.3: no visible global function definition for 'hist'
legend: no visible global function definition for 'par'
legend : rect2: no visible global function definition for 'rect'
legend : segments2: no visible global function definition for
  'segments'
legend : points2: no visible global function definition for 'points'
legend : text2: no visible global function definition for 'text'
legend: no visible global function definition for 'strwidth'
legend: no visible global function definition for 'xinch'
legend: no visible global function definition for 'yinch'
legend: no visible global function definition for 'strheight'
plot.elbow: no visible global function definition for 'par'
plot.elbow: no visible global function definition for 'plot'
plot.elbow: no visible global function definition for 'abline'
plot.elbow: no visible global function definition for 'mtext'
plot.elbow: no visible global function definition for 'text'
plot.elbow: no visible global function definition for 'title'
plot.gmdm: no visible global function definition for 'par'
plot.gmdm: no visible global function definition for 'plot'
plot.gmdm: no visible global function definition for 'text'
plot.gmdm: no visible global function definition for 'rect'
plot.gmdm: no visible global function definition for 'mtext'
plot.mhist: no visible global function definition for 'plot'
plot.mhist: no visible global function definition for 'abline'
plot.mhist: no visible global function definition for 'mtext'
plot.mhist: no visible global function definition for 'axis'
plot.mhist: no visible global function definition for 'rect'
plot.mhist: no visible global function definition for 'lines'
plot.mhist: no visible global function definition for 'par'
plot.mhist.summary: no visible global function definition for 'par'
ts2df: no visible global function definition for 'is'
Undefined global functions or variables:
  abline axis file_test flush.console hist image is layout lines mtext
  par plot points read.table rect segments strheight strwidth text
  title xinch yinch
Consider adding
  importFrom("graphics", "abline", "axis", "hist", "image", "layout",
             "lines", "mtext", "par", "plot", "points", "rect",
             "segments", "strheight", "strwidth", "text", "title",
             "xinch", "yinch")
  importFrom("methods", "is")
  importFrom("utils", "file_test", "flush.console", "read.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').