CRAN Package Check Results for Package pathClass

Last updated on 2015-08-04 09:47:28.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.9.4 2.90 39.08 41.98 NOTE
r-devel-linux-x86_64-debian-gcc 0.9.4 2.80 38.70 41.50 NOTE
r-devel-linux-x86_64-fedora-clang 0.9.4 86.08 NOTE
r-devel-linux-x86_64-fedora-gcc 0.9.4 81.73 NOTE
r-devel-osx-x86_64-clang 0.9.4 78.54 NOTE
r-devel-windows-ix86+x86_64 0.9.4 15.00 67.00 82.00 NOTE
r-patched-linux-x86_64 0.9.4 2.92 39.46 42.38 NOTE
r-patched-solaris-sparc 0.9.4 535.50 NOTE
r-patched-solaris-x86 0.9.4 126.20 NOTE
r-release-linux-x86_64 0.9.4 3.20 39.41 42.62 NOTE
r-release-osx-x86_64-mavericks 0.9.4 WARN
r-release-windows-ix86+x86_64 0.9.4 14.00 70.00 84.00 NOTE
r-oldrel-windows-ix86+x86_64 0.9.4 17.00 147.00 164.00 NOTE

Check Details

Version: 0.9.4
Check: package dependencies
Result: 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.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-osx-x86_64-clang, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-x86_64, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 0.9.4
Check: dependencies in R code
Result: 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.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-osx-x86_64-clang, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-x86_64, r-release-osx-x86_64-mavericks, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 0.9.4
Check: S3 generic/method consistency
Result: NOTE
    Found the following apparent S3 methods exported but not registered:
     plot.pathClassResult predict.graphSVM predict.networkBasedSVM
     predict.rfe predict.rrfe
    See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
    manual.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-osx-x86_64-clang, r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-x86_64

Version: 0.9.4
Check: R code for possible problems
Result: 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.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64

Version: 0.9.4
Check: R code for possible problems
Result: 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 : <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.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’
    Undefined global functions or variables:
     alphaindex as.kernelMatrix b error get.adjacency graph.adjacency
     graph.laplacian igraph.from.graphNEL kernelMatrix kernelf ksvm lp
     mclapply param performance prediction rbfdot rowMedians vanilladot
Flavor: r-devel-osx-x86_64-clang

Version: 0.9.4
Check: R code for possible problems
Result: 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 : <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.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’
Flavors: r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-x86_64, r-release-osx-x86_64-mavericks, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 0.9.4
Check: package dependencies
Result: NOTE
    Packages suggested but not available for checking: ‘hu6800.db’ ‘golubEsets’
    
    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.
Flavor: r-release-osx-x86_64-mavericks

Version: 0.9.4
Check: running R code from vignettes
Result: WARN
    Errors in running code in vignettes:
    when running code in ‘pathClass.rnw’
     ...
     lowess
    
    Loading required package: igraph
    Loading required package: lpSolve
    
    > library(golubEsets)
    
     When sourcing ‘pathClass.R’:
    Error: there is no package called ‘golubEsets’
    Execution halted
Flavor: r-release-osx-x86_64-mavericks

Version: 0.9.4
Check: re-building of vignette outputs
Result: NOTE
    Error in re-building vignettes:
     ...
     unique, unlist, unsplit
    
    Loading required package: Biobase
    Welcome to Bioconductor
    
     Vignettes contain introductory material; view with
     'browseVignettes()'. To cite Bioconductor, see
     'citation("Biobase")', and for packages 'citation("pkgname")'.
    
    Loading required package: ROCR
    Loading required package: gplots
    
    Attaching package: ‘gplots’
    
    The following object is masked from ‘package:stats’:
    
     lowess
    
    Loading required package: igraph
    Loading required package: lpSolve
    
    Error: processing vignette 'pathClass.rnw' failed with diagnostics:
     chunk 2 (label = loadALLpackage)
    Error in library(golubEsets) : there is no package called ‘golubEsets’
    Execution halted
Flavor: r-release-osx-x86_64-mavericks