CRAN Package Check Results for Package CNVassoc

Last updated on 2015-07-01 21:46:26.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 2.1 3.32 86.85 90.17 NOTE
r-devel-linux-x86_64-debian-gcc 2.1 3.60 90.89 94.49 NOTE
r-devel-linux-x86_64-fedora-clang 2.1 181.58 NOTE
r-devel-linux-x86_64-fedora-gcc 2.1 172.35 NOTE
r-devel-osx-x86_64-clang 2.1 148.64 OK
r-devel-windows-ix86+x86_64 2.1 29.00 146.00 175.00 NOTE
r-patched-linux-x86_64 2.1 3.74 85.76 89.50 OK
r-patched-solaris-sparc 2.1 1230.50 OK
r-patched-solaris-x86 2.1 216.20 OK
r-release-linux-x86_64 2.1 3.59 90.41 94.00 OK
r-release-osx-x86_64-mavericks 2.1 WARN
r-release-windows-ix86+x86_64 2.1 28.00 154.00 182.00 OK
r-oldrel-windows-ix86+x86_64 2.1 48.00 170.00 218.00 OK

Check Details

Version: 2.1
Check: R code for possible problems
Result: NOTE
    CNVassoc: no visible global function definition for ‘model.matrix’
    CNVassoc: no visible binding for global variable ‘contrasts’
    CNVassoc: no visible global function definition for ‘sd’
    CNVtest: no visible global function definition for ‘glm’
    CNVtest: no visible global function definition for ‘logLik’
    CNVtest: no visible global function definition for ‘pchisq’
    EMWeibull: no visible global function definition for ‘model.matrix’
    EMWeibull : <anonymous>: no visible global function definition for
     ‘dweibull’
    EMWeibull : <anonymous>: no visible global function definition for
     ‘pweibull’
    EMlogistic: no visible global function definition for ‘model.matrix’
    EMlogistic : <anonymous>: no visible global function definition for
     ‘dbinom’
    EMmixt : <anonymous>: no visible global function definition for ‘dnorm’
    EMnorm: no visible global function definition for ‘model.matrix’
    EMnorm : <anonymous>: no visible global function definition for ‘dnorm’
    EMpoisson: no visible global function definition for ‘model.matrix’
    EMpoisson : <anonymous>: no visible global function definition for
     ‘dpois’
    anova.CNVassoc: no visible global function definition for ‘logLik’
    anova.CNVassoc: no visible global function definition for ‘pchisq’
    assocCNV.i: no visible global function definition for ‘as.formula’
    checkCNV: no visible global function definition for ‘cor’
    classCNV: no visible global function definition for ‘dnorm’
    cnvBatches : <anonymous>: no visible global function definition for
     ‘dnorm’
    cnvDefault: no visible global function definition for ‘plot’
    fastCNVassoc: no visible global function definition for ‘model.matrix’
    fastCNVassoc: no visible binding for global variable ‘contrasts’
    fastCNVassoc: no visible global function definition for
     ‘model.response’
    fastCNVassoc: no visible global function definition for ‘glm’
    fastCNVassoc: no visible global function definition for ‘coef’
    fastCNVassoc: no visible global function definition for ‘pnorm’
    fastCNVinter: no visible global function definition for ‘model.matrix’
    fastCNVinter: no visible binding for global variable ‘contrasts’
    fastCNVinter: no visible global function definition for
     ‘model.response’
    fastCNVinter: no visible global function definition for ‘glm’
    fastCNVinter: no visible global function definition for ‘coef’
    fastCNVinter: no visible global function definition for ‘pnorm’
    getPvalBH: no visible binding for global variable ‘p.adjust.methods’
    getPvalBH : <anonymous>: no visible global function definition for
     ‘p.adjust’
    getQualityScore.default: no visible global function definition for
     ‘rnorm’
    getQualityScore.default : <anonymous>: no visible global function
     definition for ‘dnorm’
    getQualityScore.default : f : <anonymous>: no visible global function
     definition for ‘dnorm’
    getQualityScore.default: no visible global function definition for
     ‘integrate’
    linear.fit: no visible global function definition for ‘glm.control’
    logLike.logistic : <anonymous>: no visible global function definition
     for ‘dbinom’
    logLike.norm : <anonymous>: no visible global function definition for
     ‘dnorm’
    logLike.poisson : <anonymous>: no visible global function definition
     for ‘dpois’
    logLike.weibull : <anonymous>: no visible global function definition
     for ‘dweibull’
    logLike.weibull : <anonymous>: no visible global function definition
     for ‘pweibull’
    logistic.fit: no visible global function definition for ‘glm.control’
    plot.cnv.intensities: no visible global function definition for ‘par’
    plot.cnv.intensities: no visible global function definition for
     ‘layout’
    plot.cnv.intensities: no visible global function definition for
     ‘density’
    plot.cnv.intensities: no visible global function definition for ‘plot’
    plot.cnv.intensities: no visible global function definition for
     ‘polygon’
    plot.cnv.intensities: no visible global function definition for
     ‘points’
    plot.cnv.intensities: no visible global function definition for ‘lines’
    plot.cnv.intensities: no visible global function definition for
     ‘legend’
    plot.cnv.intensities: no visible global function definition for
     ‘abline’
    plot.cnv.probabilities: no visible global function definition for
     ‘barplot’
    plot.cnv.probabilities: no visible global function definition for
     ‘axis’
    plot.cnv.probabilities: no visible global function definition for ‘par’
    plot.cnv.probabilities: no visible global function definition for
     ‘legend’
    plotSignal : foo: no visible global function definition for ‘par’
    plotSignal : foo: no visible global function definition for ‘layout’
    plotSignal : foo: no visible global function definition for ‘density’
    plotSignal : foo: no visible global function definition for ‘plot’
    plotSignal : foo: no visible global function definition for ‘polygon’
    plotSignal : foo: no visible global function definition for ‘points’
    plotSignal : foo: no visible global function definition for ‘legend’
    plotSignal : foo: no visible global function definition for ‘abline’
    plotSignal: no visible global function definition for ‘locator’
    poisson.fit: no visible global function definition for ‘glm.control’
    print.CNVassoc: no visible global function definition for ‘logLik’
    print.summary.CNVassoc: no visible global function definition for
     ‘printCoefmat’
    simCNVdataBinary: no visible global function definition for ‘rmultinom’
    simCNVdataBinary : <anonymous>: no visible global function definition
     for ‘rnorm’
    simCNVdataBinary : <anonymous>: no visible global function definition
     for ‘rbinom’
    simCNVdataCaseCon: no visible global function definition for
     ‘rmultinom’
    simCNVdataCaseCon : <anonymous>: no visible global function definition
     for ‘rnorm’
    simCNVdataNorm: no visible global function definition for ‘rmultinom’
    simCNVdataNorm : <anonymous>: no visible global function definition for
     ‘rnorm’
    simCNVdataPois: no visible global function definition for ‘rmultinom’
    simCNVdataPois : <anonymous>: no visible global function definition for
     ‘rnorm’
    simCNVdataPois : <anonymous>: no visible global function definition for
     ‘rpois’
    simCNVdataWeibull: no visible global function definition for
     ‘rmultinom’
    simCNVdataWeibull : <anonymous>: no visible global function definition
     for ‘rnorm’
    simCNVdataWeibull : <anonymous>: no visible global function definition
     for ‘rweibull’
    simNormMixt: no visible global function definition for ‘rmultinom’
    simNormMixt : <anonymous>: no visible global function definition for
     ‘rnorm’
    summary.CNVassoc: no visible global function definition for ‘qnorm’
    summary.CNVassoc: no visible global function definition for ‘pnorm’
    summary.CNVassoc: no visible global function definition for ‘logLik’
    translate: no visible global function definition for ‘coef’
    weibull.fit: no visible global function definition for ‘coef’
    weibull.fit: no visible global function definition for ‘model.matrix’
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: 2.1
Check: package dependencies
Result: NOTE
    Packages suggested but not available for checking:
     ‘CGHcall’ ‘CGHregions’ ‘CNVtools’ ‘CGHbase’
Flavor: r-release-osx-x86_64-mavericks

Version: 2.1
Check: Rd cross-references
Result: NOTE
    Package unavailable to check Rd xrefs: ‘CGHcall’
Flavor: r-release-osx-x86_64-mavericks

Version: 2.1
Check: running R code from vignettes
Result: WARN
    Errors in running code in vignettes:
    when running code in ‘CNVassoc_vignette.Rnw’
     ...
    > data(NeveCalled)
    
    > probs <- getProbs(NeveCalled)
    Loading required package: CGHbase
    Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
     there is no package called ‘CGHbase’
    
     When sourcing ‘CNVassoc_vignette.R’:
    Error: unable to find required package ‘CGHbase’
    Execution halted
Flavor: r-release-osx-x86_64-mavericks

Version: 2.1
Check: re-building of vignette outputs
Result: NOTE
    Error in re-building vignettes:
     ...
    Loading required package: CNVassocData
    Loading required package: mixdist
    Loading required package: mclust
    Package 'mclust' version 5.0.0
    Type 'citation("mclust")' for citing this R package in publications.
    Loading required package: survival
    Loading required package: CGHbase
    Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
     there is no package called ‘CGHbase’
    
    Error: processing vignette 'CNVassoc_vignette.Rnw' failed with diagnostics:
     chunk 40
    Error in .requirePackage(package) :
     unable to find required package ‘CGHbase’
    Execution halted
Flavor: r-release-osx-x86_64-mavericks