* using log directory 'd:/Rcompile/CRANpkg/local/3.3/pathClass.Rcheck'
* using R version 3.3.2 (2016-10-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* checking for file 'pathClass/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'pathClass' version '0.9.4'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'svmpath' 'kernlab' 'affy' 'Biobase' 'ROCR' 'igraph' 'lpSolve'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'pathClass' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to 'ROCR' which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'Biobase' 'ROCR' 'affy' 'igraph' 'kernlab' 'lpSolve' 'svmpath'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
':::' call which should be '::': 'parallel:::detectCores'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
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.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... [3s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking re-building of vignette outputs ... [22s] OK
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs