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 '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
  'dev.off'
plotTimeCourseAgents: no visible global function definition for 'pdf'
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 'dev.off'
Undefined global functions or variables:
  dev.off diversity filled.contour legend lines pdf points read.csv
  xmlAttrs xmlName xmlRoot xmlSize xmlTreeParse xmlValue
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "filled.contour", "legend", "lines", "points")
  importFrom("utils", "read.csv")
to your NAMESPACE file.