centrality: no visible global function definition for 'vcount'
centrality: no visible global function definition for 'degree'
centrality: no visible global function definition for 'betweenness'
cepa: no visible global function definition for 'read.table'
cepa.all: no visible global function definition for 'read.table'
cepa.all.parallel.by.snow: no visible global function definition for
  'makeCluster'
cepa.all.parallel.by.snow: no visible global function definition for
  'clusterCall'
cepa.all.parallel.by.snow: no visible global function definition for
  'clusterApply'
cepa.all.parallel.by.snow: no visible global function definition for
  'stopCluster'
cepa.ora: no visible global function definition for 'read.table'
cepa.ora: no visible global function definition for 'quantile'
cepa.ora: no visible global function definition for 'rbinom'
cepa.ora.all: no visible global function definition for 'read.table'
cepa.univariate: no visible global function definition for 'prcomp'
cepa.univariate: no visible global function definition for 'predict'
cepa.univariate: no visible global function definition for 'quantile'
cepa.univariate.all: no visible global function definition for 'prcomp'
cepa.univariate.all: no visible global function definition for
  'predict'
generate.pathway: no visible global function definition for
  'graph.edgelist'
get_color: no visible global function definition for 'col2rgb'
get_color: no visible global function definition for 'rgb'
jitt: no visible global function definition for 'runif'
nodeLevelFun.tvalue: no visible global function definition for 'var'
p.heatmap: no visible binding for global variable 'p.adjust'
p.heatmap: no visible global function definition for 'plot'
p.heatmap: no visible global function definition for 'text'
p.heatmap: no visible global function definition for 'layout'
p.heatmap: no visible global function definition for 'lcm'
p.heatmap: no visible global function definition for 'par'
p.heatmap: no visible global function definition for 'rect'
p.table: no visible binding for global variable 'p.adjust'
pathway.nodes: no visible global function definition for 'vcount'
pathway.nodes: no visible global function definition for
  'get.vertex.attribute'
pathwayLevelFun.median: no visible global function definition for
  'median'
pathwayLevelFun.rank: no visible global function definition for
  'wilcox.test'
plot.cepa.all: no visible global function definition for 'plot'
plot.igraph2: no visible binding for global variable 'layout.random'
plot.igraph2: no visible global function definition for 'V'
plot.igraph2: no visible global function definition for 'E'
plot.igraph2: no visible global function definition for 'plot'
plot.igraph2: no visible global function definition for 'box'
plot.igraph2: no visible global function definition for 'points'
plot.igraph2: no visible global function definition for 'text'
plot.igraph2: no visible global function definition for 'get.edgelist'
plot.igraph2: no visible global function definition for 'par'
plot.igraph2: no visible global function definition for 'segments'
plot.igraph2: no visible global function definition for 'ecount'
plot.igraph2: no visible global function definition for 'polygon'
plot.pathway.catalogue: no visible global function definition for 'par'
plot.pathway.catalogue: no visible global function definition for
  'plot'
plot.pathway.catalogue: no visible global function definition for
  'abline'
plotGraph: no visible global function definition for 'plot'
plotGraph: no visible global function definition for 'text'
plotGraph: no visible global function definition for 'par'
plotGraph: no visible global function definition for 'rgb'
plotGraph: no visible global function definition for 'V'
plotGraph: no visible global function definition for 'V<-'
plotGraph: no visible global function definition for 'E'
plotGraph: no visible global function definition for 'E<-'
plotGraph : layout.method: no visible global function definition for
  'layout.reingold.tilford'
plotGraph: no visible global function definition for 'legend'
plotGraph: no visible global function definition for 'rect'
plotGraph: no visible global function definition for 'title'
plotNull: no visible global function definition for 'plot'
plotNull: no visible global function definition for 'text'
plotNull: no visible global function definition for 'par'
plotNull: no visible global function definition for 'rgb'
plotNull: no visible global function definition for 'matplot'
plotNull: no visible global function definition for 'points'
plotNull: no visible global function definition for 'legend'
plotNull: no visible global function definition for 'abline'
plotNull: no visible global function definition for 'hist'
plotNull: no visible global function definition for 'box'
radiality: no visible global function definition for 'shortest.paths'
radiality: no visible global function definition for 'vcount'
radiality: no visible global function definition for 'diameter'
reach: no visible global function definition for 'E'
reach: no visible global function definition for 'shortest.paths'
read.gct: no visible global function definition for 'read.table'
report: no visible global function definition for 'png'
report: no visible global function definition for 'plot'
report: no visible global function definition for 'dev.off'
report: no visible binding for global variable 'p.adjust'
report: no visible global function definition for 'write.graph'
report: no visible global function definition for 'write.table'
spread: no visible global function definition for 'E'
spread: no visible global function definition for 'shortest.paths'
table.content: no visible binding for global variable 'p.adjust'
Undefined global functions or variables:
  E E<- V V<- abline betweenness box clusterApply clusterCall col2rgb
  degree dev.off diameter ecount get.edgelist get.vertex.attribute
  graph.edgelist hist layout layout.random layout.reingold.tilford lcm
  legend makeCluster matplot median p.adjust par plot png points
  polygon prcomp predict quantile rbinom read.table rect rgb runif
  segments shortest.paths stopCluster text title var vcount wilcox.test
  write.graph write.table
Consider adding
  importFrom("grDevices", "col2rgb", "dev.off", "png", "rgb")
  importFrom("graphics", "abline", "box", "hist", "layout", "lcm",
             "legend", "matplot", "par", "plot", "points", "polygon",
             "rect", "segments", "text", "title")
  importFrom("stats", "median", "p.adjust", "prcomp", "predict",
             "quantile", "rbinom", "runif", "var", "wilcox.test")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.