CRAN Package Check Results for Package pathClass

Last updated on 2014-11-24 23:47:10.

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-ix86, r-release-linux-x86_64, r-release-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.
    See the information on DESCRIPTION files in the chapter ‘Creating R
    packages’ of 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-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-ix86, r-release-linux-x86_64, r-release-osx-x86_64-mavericks, r-release-osx-x86_64-snowleopard, r-release-windows-ix86+x86_64, 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’
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-ix86, r-release-linux-x86_64, 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.
Flavors: r-release-osx-x86_64-mavericks, r-release-osx-x86_64-snowleopard

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
Flavors: r-release-osx-x86_64-mavericks, r-release-osx-x86_64-snowleopard

Version: 0.9.4
Check: re-building of vignette outputs
Result: NOTE
    Error in re-building vignettes:
     ...
    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
    KernSmooth 2.23 loaded
    Copyright M. P. Wand 1997-2009
    
    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
Flavors: r-release-osx-x86_64-mavericks, r-release-osx-x86_64-snowleopard

Version: 0.9.4
Check: R code for possible problems
Result: NOTE
    Error : .onLoad failed in loadNamespace() for 'org.Hs.eg.db', details:
     call: match.arg(synchronous, c("off", "normal", "full"))
     error: 'arg' must be NULL or a character vector
Flavor: r-oldrel-windows-ix86+x86_64

Version: 0.9.4
Check: running R code from vignettes
Result: ERROR
    Errors in running code in vignettes:
    when running code in 'pathClass.rnw'
     ...
    Loading required package: AnnotationDbi
    Loading required package: org.Hs.eg.db
    Loading required package: DBI
    Error : .onLoad failed in loadNamespace() for 'org.Hs.eg.db', details:
     call: match.arg(synchronous, c("off", "normal", "full"))
     error: 'arg' must be NULL or a character vector
    
     When sourcing 'pathClass.R':
    Error: package 'org.Hs.eg.db' could not be loaded
    Execution halted
Flavor: r-oldrel-windows-ix86+x86_64