calc.auc: no visible global function definition for ‘prediction’
calc.auc: no visible global function definition for ‘performance’
calc.diffusionKernel: no visible global function definition for
  ‘graph.adjacency’
calc.diffusionKernel: no visible global function definition for
  ‘graph.laplacian’
calc.graph.svm: no visible global function definition for
  ‘as.kernelMatrix’
calc.graph.svm: no visible global function definition for ‘ksvm’
calc.graph.svm: no visible global function definition for ‘alphaindex’
calc.graph.svm: no visible global function definition for ‘coef’
calc.networkBasedSVM: no visible global function definition for ‘lp’
classify: no visible global function definition for ‘predict’
classify: no visible global function definition for ‘setTxtProgressBar’
classify: no visible global function definition for ‘getTxtProgressBar’
compare.auc: no visible global function definition for ‘prediction’
compare.auc: no visible global function definition for ‘performance’
compare.auc: no visible global function definition for ‘wilcox.test’
compare.auc: no visible global function definition for ‘pdf’
compare.auc: no visible global function definition for ‘par’
compare.auc: no visible global function definition for ‘plot’
compare.auc: no visible global function definition for ‘boxplot’
compare.auc: no visible global function definition for ‘dev.off’
crossval: no visible global function definition for ‘txtProgressBar’
crossval: no visible global function definition for ‘mclapply’
extractFeatures: no visible global function definition for ‘write.csv’
fit.networkBasedSVM: no visible binding for global variable ‘sd’
getRanking: no visible global function definition for
  ‘igraph.from.graphNEL’
getRanking: no visible global function definition for ‘get.adjacency’
plot.pathClassResult: no visible global function definition for ‘pdf’
plot.pathClassResult: no visible global function definition for
  ‘boxplot’
plot.pathClassResult: no visible global function definition for
  ‘stripchart’
plot.pathClassResult: no visible global function definition for
  ‘dev.new’
plot.pathClassResult: no visible global function definition for
  ‘prediction’
plot.pathClassResult: no visible global function definition for
  ‘performance’
plot.pathClassResult: no visible global function definition for ‘plot’
plot.pathClassResult: no visible global function definition for
  ‘dev.off’
predict.graphSVM: no visible global function definition for ‘coef’
predict.graphSVM: no visible global function definition for ‘b’
read.hprd: no visible global function definition for ‘read.delim’
spanbound: no visible global function definition for ‘alphaindex’
spanbound: no visible global function definition for ‘coef’
spanbound: no visible global function definition for ‘predict’
spanbound: no visible global function definition for ‘param’
spanbound: no visible global function definition for ‘error’
spanbound: no visible global function definition for ‘kernelMatrix’
spanbound: no visible global function definition for ‘kernelf’
spanbound: no visible global function definition for ‘b’
summarizeProbes : <anonymous>: no visible global function definition
  for ‘median’
summarizeProbes : <anonymous>: no visible global function definition
  for ‘rowMedians’
svm.fit: no visible global function definition for ‘kernelMatrix’
svm.fit: no visible global function definition for ‘vanilladot’
svm.fit: no visible global function definition for ‘as.kernelMatrix’
svm.fit: no visible global function definition for ‘ksvm’
svm.fit: no visible global function definition for ‘alphaindex’
svm.fit: no visible global function definition for ‘coef’
svm.predict: no visible global function definition for ‘kernelMatrix’
svm.predict: no visible global function definition for ‘vanilladot’
svm.predict: no visible global function definition for ‘rbfdot’
svm.predict: no visible global function definition for ‘coef’
svm.predict: no visible global function definition for ‘b’
Undefined global functions or variables:
  alphaindex as.kernelMatrix b boxplot coef dev.new dev.off error
  get.adjacency getTxtProgressBar graph.adjacency graph.laplacian
  igraph.from.graphNEL kernelMatrix kernelf ksvm lp mclapply median par
  param pdf performance plot predict prediction rbfdot read.delim
  rowMedians sd setTxtProgressBar stripchart txtProgressBar vanilladot
  wilcox.test write.csv
Consider adding
  importFrom("grDevices", "dev.new", "dev.off", "pdf")
  importFrom("graphics", "boxplot", "par", "plot", "stripchart")
  importFrom("stats", "coef", "median", "predict", "sd", "wilcox.test")
  importFrom("utils", "getTxtProgressBar", "read.delim",
             "setTxtProgressBar", "txtProgressBar", "write.csv")
to your NAMESPACE file.