BFD_Processor: no visible global function definition for ‘read.table’
BFD_Processor: no visible global function definition for ‘write.table’
BFD_Processor: no visible global function definition for ‘png’
BFD_Processor: no visible global function definition for ‘plot’
BFD_Processor: no visible global function definition for ‘dev.off’
BFD_Processor: no visible global function definition for ‘read.delim’
BFD_Processor: no visible global function definition for ‘pdf’
BFD_Processor: no visible global function definition for ‘levelplot’
BFD_Processor: no visible global function definition for ‘heatmap’
BFD_Processor: no visible global function definition for ‘cor’
BFD_Processor: no visible global function definition for ‘corrplot’
DEGREE_MEASURE: no visible global function definition for ‘write.table’
Exhaustive_double_deletion: no visible global function definition for
  ‘combn’
Exhaustive_double_deletion: no visible global function definition for
  ‘write.table’
Exhaustive_single_deletion: no visible global function definition for
  ‘write.table’
Exhaustive_single_deletion: no visible global function definition for
  ‘hist’
Exhaustive_single_deletion: no visible global function definition for
  ‘pdf’
Exhaustive_single_deletion: no visible global function definition for
  ‘barplot’
Exhaustive_single_deletion: no visible global function definition for
  ‘dev.off’
FBA_solve: no visible global function definition for ‘Rglpk_solve_LP’
FLUX_VAR_ANALYSIS: no visible global function definition for
  ‘write.table’
PERTURBATION_analysis: no visible global function definition for ‘plot’
PERTURBATION_analysis: no visible global function definition for ‘png’
PERTURBATION_analysis: no visible global function definition for
  ‘dev.off’
PERTURBATION_analysis: no visible global function definition for
  ‘write.table’
PHPP: no visible global function definition for ‘levelplot’
PHPP: no visible global function definition for ‘persp3d’
PHPP: no visible global function definition for ‘play3d’
PHPP: no visible global function definition for ‘spin3d’
PLOT_FVA_SPAN: no visible global function definition for ‘pdf’
PLOT_FVA_SPAN: no visible global function definition for ‘barplot’
PLOT_FVA_SPAN: no visible global function definition for ‘par’
PLOT_FVA_SPAN: no visible global function definition for ‘dev.off’
SINGLE_DEL_FLUXOME: no visible global function definition for ‘pdf’
SINGLE_DEL_FLUXOME: no visible global function definition for ‘barplot’
SINGLE_DEL_FLUXOME: no visible global function definition for ‘par’
SINGLE_DEL_FLUXOME: no visible global function definition for ‘dev.off’
flux_difference_plotter: no visible global function definition for
  ‘pdf’
flux_difference_plotter: no visible global function definition for
  ‘barplot’
flux_difference_plotter: no visible global function definition for
  ‘par’
flux_difference_plotter: no visible global function definition for
  ‘dev.off’
Undefined global functions or variables:
  Rglpk_solve_LP barplot combn cor corrplot dev.off heatmap hist
  levelplot par pdf persp3d play3d plot png read.delim read.table
  spin3d write.table
Consider adding
  importFrom("grDevices", "dev.off", "pdf", "png")
  importFrom("graphics", "barplot", "hist", "par", "plot")
  importFrom("stats", "cor", "heatmap")
  importFrom("utils", "combn", "read.delim", "read.table", "write.table")
to your NAMESPACE file.