* using log directory 'd:/Rcompile/CRANpkg/local/3.1/pathClass.Rcheck' * using R version 3.1.3 (2015-03-09) * 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 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.networkBasedSVM: no visible global function definition for 'lp' compare.auc: no visible global function definition for 'prediction' compare.auc: no visible global function definition for 'performance' crossval: no visible global function definition for 'mclapply' 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 'prediction' plot.pathClassResult: no visible global function definition for 'performance' predict.graphSVM: no visible global function definition for 'b' spanbound: no visible global function definition for 'alphaindex' 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 : : 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.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 'b' * 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 running R code from vignettes ... [8s] OK * checking re-building of vignette outputs ... [17s] OK * checking PDF version of manual ... OK * DONE NOTE: There were 3 notes.