CRAN Package Check Results for Package pathClass

Last updated on 2016-09-27 10:47:41.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.9.4 4.70 47.23 51.92 NOTE
r-devel-linux-x86_64-debian-gcc 0.9.4 4.54 49.80 54.34 NOTE
r-devel-linux-x86_64-fedora-clang 0.9.4 74.48 NOTE
r-devel-linux-x86_64-fedora-gcc 0.9.4 69.98 NOTE
r-devel-macos-x86_64-clang 0.9.4 57.50 NOTE
r-devel-windows-ix86+x86_64 0.9.4 15.00 80.00 95.00 NOTE
r-patched-linux-x86_64 0.9.4 3.82 49.26 53.08 NOTE
r-patched-solaris-sparc 0.9.4 443.30 NOTE
r-patched-solaris-x86 0.9.4 94.30 NOTE
r-release-linux-x86_64 0.9.4 4.56 51.33 55.89 NOTE
r-release-osx-x86_64-mavericks 0.9.4 WARN
r-release-windows-ix86+x86_64 0.9.4 14.00 125.00 139.00 NOTE
r-oldrel-windows-ix86+x86_64 0.9.4 15.00 140.00 155.00 WARN

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-macos-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-macos-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

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-macos-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 file.
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-macos-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

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’
     ...
    
     union
    
    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:
     ...
    
     lowess
    
    Loading required package: igraph
    
    Attaching package: ‘igraph’
    
    The following objects are masked from ‘package:BiocGenerics’:
    
     normalize, union
    
    The following objects are masked from ‘package:stats’:
    
     decompose, spectrum
    
    The following object is masked from ‘package:base’:
    
     union
    
    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

Version: 0.9.4
Check: dependencies in R code
Result: NOTE
    Loading required package: ROCR
    Loading required package: gplots
    
    Attaching package: 'gplots'
    
    The following object is masked from 'package:stats':
    
     lowess
    
    Loading required package: igraph
    
    Attaching package: 'igraph'
    
    The following objects are masked from 'package:BiocGenerics':
    
     normalize, union
    
    The following objects are masked from 'package:stats':
    
     decompose, spectrum
    
    The following object is masked from 'package:base':
    
     union
    
    Loading required package: lpSolve
    '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.
Flavor: r-oldrel-windows-ix86+x86_64

Version: 0.9.4
Check: S3 generic/method consistency
Result: WARN
    Loading required package: ROCR
    Loading required package: gplots
    
    Attaching package: 'gplots'
    
    The following object is masked from 'package:stats':
    
     lowess
    
    Loading required package: igraph
    
    Attaching package: 'igraph'
    
    The following objects are masked from 'package:BiocGenerics':
    
     normalize, union
    
    The following objects are masked from 'package:stats':
    
     decompose, spectrum
    
    The following object is masked from 'package:base':
    
     union
    
    Loading required package: lpSolve
    See section 'Generic functions and methods' in the 'Writing R
    Extensions' manual.
Flavor: r-oldrel-windows-ix86+x86_64

Version: 0.9.4
Check: replacement functions
Result: WARN
    Loading required package: ROCR
    Loading required package: gplots
    
    Attaching package: 'gplots'
    
    The following object is masked from 'package:stats':
    
     lowess
    
    Loading required package: igraph
    
    Attaching package: 'igraph'
    
    The following objects are masked from 'package:BiocGenerics':
    
     normalize, union
    
    The following objects are masked from 'package:stats':
    
     decompose, spectrum
    
    The following object is masked from 'package:base':
    
     union
    
    Loading required package: lpSolve
    The argument of a replacement function which corresponds to the right
    hand side must be named 'value'.
Flavor: r-oldrel-windows-ix86+x86_64

Version: 0.9.4
Check: foreign function calls
Result: NOTE
    Loading required package: ROCR
    Loading required package: gplots
    
    Attaching package: 'gplots'
    
    The following object is masked from 'package:stats':
    
     lowess
    
    Loading required package: igraph
    
    Attaching package: 'igraph'
    
    The following objects are masked from 'package:BiocGenerics':
    
     normalize, union
    
    The following objects are masked from 'package:stats':
    
     decompose, spectrum
    
    The following object is masked from 'package:base':
    
     union
    
    Loading required package: lpSolve
    See chapter 'System and foreign language interfaces' in the 'Writing R
    Extensions' manual.
Flavor: r-oldrel-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'
Flavor: r-oldrel-windows-ix86+x86_64

Version: 0.9.4
Check: for missing documentation entries
Result: WARN
    
    Attaching package: 'gplots'
    
    The following object is masked from 'package:stats':
    
     lowess
    
    
    Attaching package: 'igraph'
    
    The following objects are masked from 'package:BiocGenerics':
    
     normalize, union
    
    The following objects are masked from 'package:stats':
    
     decompose, spectrum
    
    The following object is masked from 'package:base':
    
     union
    
    All user-level objects in a package should have documentation entries.
    See chapter 'Writing R documentation files' in the 'Writing R
    Extensions' manual.
Flavor: r-oldrel-windows-ix86+x86_64

Version: 0.9.4
Check: for code/documentation mismatches
Result: WARN
    Loading required package: ROCR
    Loading required package: gplots
    
    Attaching package: 'gplots'
    
    The following object is masked from 'package:stats':
    
     lowess
    
    Loading required package: igraph
    
    Attaching package: 'igraph'
    
    The following objects are masked from 'package:BiocGenerics':
    
     normalize, union
    
    The following objects are masked from 'package:stats':
    
     decompose, spectrum
    
    The following object is masked from 'package:base':
    
     union
    
    Loading required package: lpSolve
    Loading required package: ROCR
    Loading required package: gplots
    
    Attaching package: 'gplots'
    
    The following object is masked from 'package:stats':
    
     lowess
    
    Loading required package: igraph
    
    Attaching package: 'igraph'
    
    The following objects are masked from 'package:BiocGenerics':
    
     normalize, union
    
    The following objects are masked from 'package:stats':
    
     decompose, spectrum
    
    The following object is masked from 'package:base':
    
     union
    
    Loading required package: lpSolve
    Loading required package: ROCR
    Loading required package: gplots
    
    Attaching package: 'gplots'
    
    The following object is masked from 'package:stats':
    
     lowess
    
    Loading required package: igraph
    
    Attaching package: 'igraph'
    
    The following objects are masked from 'package:BiocGenerics':
    
     normalize, union
    
    The following objects are masked from 'package:stats':
    
     decompose, spectrum
    
    The following object is masked from 'package:base':
    
     union
    
    Loading required package: lpSolve
Flavor: r-oldrel-windows-ix86+x86_64

Version: 0.9.4
Check: Rd \usage sections
Result: NOTE
    Loading required package: ROCR
    Loading required package: gplots
    
    Attaching package: 'gplots'
    
    The following object is masked from 'package:stats':
    
     lowess
    
    Loading required package: igraph
    
    Attaching package: 'igraph'
    
    The following objects are masked from 'package:BiocGenerics':
    
     normalize, union
    
    The following objects are masked from 'package:stats':
    
     decompose, spectrum
    
    The following object is masked from 'package:base':
    
     union
    
    Loading required package: lpSolve
    The \usage entries for S3 methods should use the \method markup and not
    their full name.
    See chapter 'Writing R documentation files' in the 'Writing R
    Extensions' manual.
Flavor: r-oldrel-windows-ix86+x86_64