col.group: no visible global function definition for 'read.table'
dif: no visible global function definition for 'complete.cases'
dis: no visible global function definition for 'data'
dis: no visible binding for global variable 'sub.mat'
dis : Sij: no visible global function definition for 'na.omit'
dis : Tij: no visible global function definition for 'na.omit'
dis: no visible global function definition for 'complete.cases'
mat.dis: no visible global function definition for 'data'
mat.dis: no visible binding for global variable 'sub.mat'
mmds.2D.multi: no visible global function definition for 'dev.new'
mmds.2D.multi: no visible global function definition for 'pdf'
mmds.2D.multi: no visible global function definition for 'png'
mmds.2D.multi: no visible global function definition for 'tiff'
mmds.2D.multi: no visible global function definition for 'postscript'
mmds.2D.multi : <anonymous>: no visible global function definition for
  'points'
mmds.2D.multi : <anonymous>: no visible global function definition for
  'lines'
mmds.2D.multi: no visible global function definition for 'abline'
mmds.2D.multi: no visible global function definition for 'box'
mmds.2D.multi: no visible global function definition for 'dev.off'
mmds.2D.plot: no visible global function definition for 'dev.new'
mmds.2D.plot: no visible global function definition for 'pdf'
mmds.2D.plot: no visible global function definition for 'png'
mmds.2D.plot: no visible global function definition for 'tiff'
mmds.2D.plot: no visible global function definition for 'postscript'
mmds.2D.plot: no visible global function definition for 'text'
mmds.2D.plot: no visible global function definition for 'points'
mmds.2D.plot: no visible global function definition for 'abline'
mmds.2D.plot: no visible global function definition for 'box'
mmds.2D.plot: no visible global function definition for 'dev.off'
mmds.3D.plot: no visible global function definition for 'box3d'
mmds.3D.plot: no visible global function definition for 'axes3d'
mmds.plot: no visible global function definition for 'dev.new'
mmds.plot: no visible global function definition for 'pdf'
mmds.plot: no visible global function definition for 'layout'
mmds.plot: no visible global function definition for 'dev.off'
scree.plot: no visible global function definition for 'dev.new'
scree.plot: no visible global function definition for 'pdf'
scree.plot: no visible global function definition for 'barplot'
scree.plot: no visible global function definition for 'text'
scree.plot: no visible global function definition for 'dev.off'
sil.score: no visible global function definition for 'dist'
write.mmds.pdb: no visible global function definition for 'col2rgb'
Undefined global functions or variables:
  abline axes3d barplot box box3d col2rgb complete.cases data dev.new
  dev.off dist layout lines na.omit pdf png points postscript
  read.table sub.mat text tiff
Consider adding
  importFrom("grDevices", "col2rgb", "dev.new", "dev.off", "pdf", "png",
             "postscript", "tiff")
  importFrom("graphics", "abline", "barplot", "box", "layout", "lines",
             "points", "text")
  importFrom("stats", "complete.cases", "dist", "na.omit")
  importFrom("utils", "data", "read.table")
to your NAMESPACE file.