agent_returnGridResolution: no visible global function definition for
  'xmlAttrs'
agent_returnIVoxels: no visible global function definition for
  'xmlAttrs'
agent_returnJVoxels: no visible global function definition for
  'xmlAttrs'
agent_returnKVoxels: no visible global function definition for
  'xmlAttrs'
agent_returnSimIteration: no visible global function definition for
  'xmlAttrs'
agent_returnSimTime: no visible global function definition for
  'xmlAttrs'
agent_returnSpeciesResultData: no visible global function definition
  for 'xmlSize'
agent_returnSpeciesResultData: no visible global function definition
  for 'xmlAttrs'
agent_returnSpeciesResultData: no visible global function definition
  for 'read.csv'
env_returnConcentrationAndRateChange: no visible global function
  definition for 'xmlSize'
env_returnConcentrationAndRateChange: no visible global function
  definition for 'xmlName'
env_returnConcentrationAndRateChange: no visible global function
  definition for 'xmlAttrs'
env_returnGlobalProductionRates: no visible global function definition
  for 'xmlSize'
env_returnGlobalProductionRates: no visible global function definition
  for 'xmlAttrs'
env_returnSimIteration: no visible global function definition for
  'xmlAttrs'
env_returnSimTime: no visible global function definition for 'xmlAttrs'
env_returnSoluteGridIVoxels: no visible global function definition for
  'xmlAttrs'
env_returnSoluteGridJVoxels: no visible global function definition for
  'xmlAttrs'
env_returnSoluteGridKVoxels: no visible global function definition for
  'xmlAttrs'
env_returnSoluteGridRes: no visible global function definition for
  'xmlAttrs'
env_returnSpecifiedSoluteData: no visible global function definition
  for 'xmlSize'
env_soluteProductionRateOverTime: no visible global function definition
  for 'xmlValue'
plotAgents: no visible global function definition for 'pdf'
plotAgents: no visible global function definition for 'plot'
plotAgents: no visible global function definition for 'points'
plotAgents: no visible global function definition for 'legend'
plotAgents: no visible global function definition for 'dev.off'
plotContour: no visible global function definition for 'pdf'
plotContour: no visible global function definition for 'filled.contour'
plotContour: no visible global function definition for 'dev.off'
plotTimeCourseAbund: no visible global function definition for 'pdf'
plotTimeCourseAbund: no visible global function definition for 'plot'
plotTimeCourseAbund: no visible global function definition for
  'dev.off'
plotTimeCourseAgents: no visible global function definition for 'pdf'
plotTimeCourseAgents: no visible global function definition for 'plot'
plotTimeCourseAgents: no visible global function definition for 'lines'
plotTimeCourseAgents: no visible global function definition for
  'legend'
plotTimeCourseAgents: no visible global function definition for
  'dev.off'
readSimResultFile: no visible global function definition for
  'xmlTreeParse'
readSimResultFile: no visible global function definition for 'xmlRoot'
simpsonIndex: no visible global function definition for 'pdf'
simpsonIndex: no visible global function definition for 'diversity'
simpsonIndex: no visible global function definition for 'plot'
simpsonIndex: no visible global function definition for 'dev.off'
Undefined global functions or variables:
  dev.off diversity filled.contour legend lines pdf plot points
  read.csv xmlAttrs xmlName xmlRoot xmlSize xmlTreeParse xmlValue
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "filled.contour", "legend", "lines", "plot",
             "points")
  importFrom("utils", "read.csv")
to your NAMESPACE file.