CRAN Package Check Results for Package CNVassoc

Last updated on 2015-08-02 23:47:57.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 2.1 3.34 90.65 94.00 NOTE
r-devel-linux-x86_64-debian-gcc 2.1 4.11 85.00 89.11 NOTE
r-devel-linux-x86_64-fedora-clang 2.1 181.95 NOTE
r-devel-linux-x86_64-fedora-gcc 2.1 174.23 NOTE
r-devel-osx-x86_64-clang 2.1 138.23 OK
r-devel-windows-ix86+x86_64 2.1 29.00 160.00 189.00 NOTE
r-patched-linux-x86_64 2.1 3.76 103.60 107.36 OK
r-patched-solaris-sparc 2.1 1225.60 OK
r-patched-solaris-x86 2.1 215.40 OK
r-release-linux-x86_64 2.1 3.76 87.52 91.28 OK
r-release-osx-x86_64-mavericks 2.1 WARN
r-release-windows-ix86+x86_64 2.1 40.00 166.00 206.00 OK
r-oldrel-windows-ix86+x86_64 2.1 42.00 194.00 236.00 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’
    Undefined global functions or variables:
     abline as.formula axis barplot coef contrasts cor dbinom density
     dnorm dpois dweibull glm glm.control integrate layout legend lines
     locator logLik model.matrix model.response p.adjust p.adjust.methods
     par pchisq plot pnorm points polygon printCoefmat pweibull qnorm
     rbinom rmultinom rnorm rpois rweibull sd
    Consider adding
     importFrom("graphics", "abline", "axis", "barplot", "layout", "legend",
     "lines", "locator", "par", "plot", "points", "polygon")
     importFrom("stats", "as.formula", "coef", "contrasts", "cor", "dbinom",
     "density", "dnorm", "dpois", "dweibull", "glm",
     "glm.control", "integrate", "logLik", "model.matrix",
     "model.response", "p.adjust", "p.adjust.methods", "pchisq",
     "pnorm", "printCoefmat", "pweibull", "qnorm", "rbinom",
     "rmultinom", "rnorm", "rpois", "rweibull", "sd")
    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: 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