Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/AbstractMassObject-class.Rd:113: file link ‘trim,AbstractMassObject,numeric-method’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/AbstractMassObject-class.Rd:117: file link ‘transformIntensity,AbstractMassObject-method’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/AbstractMassObject-class.Rd:127: file link ‘plot,AbstractMassObject,missing-method’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/AbstractMassObject-class.Rd:128: file link ‘transformIntensity,AbstractMassObject-method’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/AbstractMassObject-class.Rd:129: file link ‘trim,AbstractMassObject,numeric-method’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/MALDIquant-defunct.Rd:9: file link ‘plotMsiSlice’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/MALDIquant-defunct.Rd:14: file link ‘calibrateIntensity’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/MALDIquant-defunct.Rd:16: file link ‘calibrateIntensity’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/MALDIquant-defunct.Rd:18: file link ‘calibrateIntensity’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/MALDIquant-defunct.Rd:21: file link ‘trim’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/MALDIquant-defunct.Rd:23: file link ‘trim’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/MALDIquant-defunct.Rd:24: file link ‘averageMassSpectra’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/MALDIquant-defunct.Rd:26: file link ‘smoothIntensity’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/MALDIquant-defunct.Rd:28: file link ‘smoothIntensity’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/MALDIquant-parallel.Rd:6: file link ‘mcmapply’ in package ‘parallel’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/MALDIquant-parallel.Rd:15: file link ‘removeBaseline’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/MALDIquant-parallel.Rd:16: file link ‘detectPeaks’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/MALDIquant-parallel.Rd:27: file link ‘trim,list,numeric-method’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/MALDIquant-parallel.Rd:28: file link ‘transformIntensity,list-method’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/MALDIquant-parallel.Rd:29: file link ‘smoothIntensity,list-method’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/MALDIquant-parallel.Rd:30: file link ‘removeBaseline,list-method’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/MALDIquant-parallel.Rd:31: file link ‘calibrateIntensity,list-method’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/MALDIquant-parallel.Rd:32: file link ‘detectPeaks,list-method’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/MALDIquant-parallel.Rd:33: file link ‘alignSpectra’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/MALDIquant-parallel.Rd:34: file link ‘averageMassSpectra’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/MALDIquant-parallel.Rd:35: file link ‘mergeMassPeaks’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/MALDIquant-parallel.Rd:41: file link ‘mcmapply’ in package ‘parallel’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/MassPeaks-class.Rd:15: file link ‘createMassPeaks’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/MassPeaks-class.Rd:43: file link ‘createMassPeaks’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/MassPeaks-class.Rd:44: file link ‘detectPeaks,MassSpectrum-method’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/MassPeaks-class.Rd:45: file link ‘labelPeaks,MassPeaks-method’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/MassSpectrum-class.Rd:19: file link ‘createMassSpectrum’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/MassSpectrum-class.Rd:30: file link ‘calibrateIntensity,MassSpectrum-method’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/MassSpectrum-class.Rd:35: file link ‘detectPeaks,MassSpectrum-method’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/MassSpectrum-class.Rd:40: file link ‘estimateBaseline,MassSpectrum-method’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/MassSpectrum-class.Rd:45: file link ‘estimateNoise,MassSpectrum-method’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/MassSpectrum-class.Rd:55: file link ‘removeBaseline,MassSpectrum-method’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/MassSpectrum-class.Rd:59: file link ‘smoothIntensity,MassSpectrum-method’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/MassSpectrum-class.Rd:69: file link ‘createMassSpectrum’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/MassSpectrum-class.Rd:70: file link ‘calibrateIntensity,MassSpectrum-method’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/MassSpectrum-class.Rd:71: file link ‘detectPeaks,MassSpectrum-method’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/MassSpectrum-class.Rd:72: file link ‘estimateBaseline,MassSpectrum-method’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/MassSpectrum-class.Rd:73: file link ‘estimateNoise,MassSpectrum-method’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/MassSpectrum-class.Rd:74: file link ‘removeBaseline,MassSpectrum-method’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/MassSpectrum-class.Rd:75: file link ‘smoothIntensity,MassSpectrum-method’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/alignSpectra-functions.Rd:20: file link ‘detectPeaks’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/alignSpectra-functions.Rd:23: file link ‘detectPeaks’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/alignSpectra-functions.Rd:27: file link ‘detectPeaks’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/alignSpectra-functions.Rd:32: file link ‘referencePeaks’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/alignSpectra-functions.Rd:33: file link ‘determineWarpingFunctions’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/alignSpectra-functions.Rd:39: file link ‘determineWarpingFunctions’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/alignSpectra-functions.Rd:43: file link ‘determineWarpingFunctions’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/alignSpectra-functions.Rd:48: file link ‘determineWarpingFunctions’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/alignSpectra-functions.Rd:56: file link ‘warpMassSpectra’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/alignSpectra-functions.Rd:59: file link ‘detectPeaks,MassSpectrum-method’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/alignSpectra-functions.Rd:63: file link ‘detectPeaks’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/alignSpectra-functions.Rd:64: file link ‘determineWarpingFunctions’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/alignSpectra-functions.Rd:65: file link ‘warpMassSpectra’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/alignSpectra-functions.Rd:75: file link ‘detectPeaks’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/alignSpectra-functions.Rd:76: file link ‘determineWarpingFunctions’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/alignSpectra-functions.Rd:77: file link ‘referencePeaks’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/alignSpectra-functions.Rd:78: file link ‘warpMassSpectra’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/averageMassSpectra-functions.Rd:38: file link ‘mergeMassPeaks’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/binPeaks-functions.Rd:58: file link ‘intensityMatrix’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/createMassPeaks-functions.Rd:9: file link ‘detectPeaks,MassSpectrum-method’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/createMassPeaks-functions.Rd:36: file link ‘detectPeaks,MassSpectrum-method’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/detectPeaks-methods.Rd:26: file link ‘estimateNoise,MassSpectrum-method’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/detectPeaks-methods.Rd:32: file link ‘estimateNoise,MassSpectrum-method’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/detectPeaks-methods.Rd:44: file link ‘estimateNoise,MassSpectrum-method’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/determineWarpingFunctions-functions.Rd:24: file link ‘referencePeaks’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/determineWarpingFunctions-functions.Rd:80: file link ‘referencePeaks’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/determineWarpingFunctions-functions.Rd:81: file link ‘warpMassPeaks’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/determineWarpingFunctions-functions.Rd:82: file link ‘warpMassSpectra’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/estimateBaseline-methods.Rd:106: file link ‘removeBaseline,MassSpectrum-method’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/estimateNoise-methods.Rd:45: file link ‘detectPeaks,MassSpectrum-method’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/filterPeaks-functions.Rd:57: file link ‘intensityMatrix’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/findEmptyMassObjects-functions.Rd:33: file link ‘isEmpty,AbstractMassObject-method’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/intensityMatrix-functions.Rd:24: file link ‘binPeaks’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/intensityMatrix-functions.Rd:25: file link ‘intensityMatrix’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/intensityMatrix-functions.Rd:40: file link ‘binPeaks’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/labelPeaks-methods.Rd:7: file link ‘labelPeaks’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/labelPeaks-methods.Rd:53: file link ‘plot,AbstractMassObject,missing-method’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/mergeMassPeaks-functions.Rd:37: file link ‘averageMassSpectra’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/monoisotopicPeaks-methods.Rd:38: file link ‘monoisotopicPeaks,MassPeaks-method’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/monoisotopicPeaks-methods.Rd:60: file link ‘detectPeaks,MassSpectrum-method’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/msiSlices-functions.Rd:8: file link ‘intensityMatrix’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/msiSlices-functions.Rd:50: file link ‘coordinates,AbstractMassObject-method’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/msiSlices-functions.Rd:51: file link ‘plotMsiSlice,list-method’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/plot-methods.Rd:25: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/plot-methods.Rd:34: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/plotMsiSlice-methods.Rd:29: file link ‘msiSlices’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/plotMsiSlice-methods.Rd:34: file link ‘msiSlices’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/plotMsiSlice-methods.Rd:37: file link ‘msiSlices’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/plotMsiSlice-methods.Rd:64: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/plotMsiSlice-methods.Rd:84: file link ‘coordinates,AbstractMassObject-method’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/plotMsiSlice-methods.Rd:85: file link ‘msiSlices’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/plotMsiSlice-methods.Rd:86: file link ‘plot,MassSpectrum,missing-method’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/referencePeaks-functions.Rd:10: file link ‘binPeaks’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/referencePeaks-functions.Rd:11: file link ‘filterPeaks’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/referencePeaks-functions.Rd:22: file link ‘binPeaks’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/referencePeaks-functions.Rd:37: file link ‘intensity’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/referencePeaks-functions.Rd:45: file link ‘binPeaks’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/referencePeaks-functions.Rd:46: file link ‘filterPeaks’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/removeBaseline-methods.Rd:25: file link ‘estimateBaseline,MassSpectrum-method’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/removeBaseline-methods.Rd:28: file link ‘estimateBaseline,MassSpectrum-method’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/removeBaseline-methods.Rd:40: file link ‘estimateBaseline,MassSpectrum-method’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/warp-functions.Rd:24: file link ‘determineWarpingFunctions’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpruiJ4v/R.INSTALL16707ddedec3/MALDIquant/man/warp-functions.Rd:47: file link ‘determineWarpingFunctions’ in package ‘MALDIquant’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/MALDIquant.Rcheck/00install.out’ for details.