CRAN Package Check Results for Package phangorn

Last updated on 2015-07-05 22:47:38.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.99-13 6.35 116.19 122.54 NOTE
r-devel-linux-x86_64-debian-gcc 1.99-13 6.36 118.51 124.87 NOTE
r-devel-linux-x86_64-fedora-clang 1.99-13 242.42 NOTE
r-devel-linux-x86_64-fedora-gcc 1.99-13 235.35 NOTE
r-devel-osx-x86_64-clang 1.99-13 216.36 OK
r-devel-windows-ix86+x86_64 1.99-13 32.00 196.00 228.00 NOTE
r-patched-linux-x86_64 1.99-13 6.40 114.90 121.30 OK
r-patched-solaris-sparc 1.99-13 997.50 OK --no-vignettes
r-patched-solaris-x86 1.99-13 332.00 OK
r-release-linux-x86_64 1.99-13 8.58 116.55 125.13 OK
r-release-osx-x86_64-mavericks 1.99-13 OK
r-release-windows-ix86+x86_64 1.99-13 31.00 208.00 239.00 OK
r-oldrel-windows-ix86+x86_64 1.99-13 35.00 231.00 266.00 OK

Check Details

Version: 1.99-13
Check: R code for possible problems
Result: NOTE
    .check.pkg: no visible global function definition for
     ‘installed.packages’
    SH.test: no visible global function definition for ‘update’
    SOWH.test: no visible global function definition for ‘update’
    anova.pml: no visible global function definition for ‘pchisq’
    bootstrap.pml : pmlPar: no visible global function definition for
     ‘update’
    compareSplits: no visible global function definition for ‘reshape’
    compareSplits: no visible binding for global variable ‘trees’
    densiTree: no visible global function definition for ‘plot.new’
    densiTree: no visible global function definition for ‘strwidth’
    densiTree: no visible global function definition for ‘plot.window’
    densiTree: no visible global function definition for ‘axis’
    densiTree: no visible global function definition for ‘text’
    densiTree: no visible global function definition for ‘adjustcolor’
    discrete.gamma: no visible global function definition for ‘qgamma’
    discrete.gamma: no visible global function definition for ‘pgamma’
    diversity: no visible global function definition for ‘model.matrix’
    diversity: no visible global function definition for ‘stack’
    getClips: no visible global function definition for ‘cophenetic’
    kSPR: no visible global function definition for ‘na.omit’
    lento: no visible global function definition for ‘plot.new’
    lento: no visible global function definition for ‘plot.window’
    lento: no visible global function definition for ‘title’
    lento: no visible global function definition for ‘segments’
    lento: no visible global function definition for ‘abline’
    lento: no visible global function definition for ‘axis’
    lento: no visible global function definition for ‘text’
    lento: no visible global function definition for ‘points’
    lento: no visible global function definition for ‘rgb’
    makePart: no visible global function definition for ‘xtabs’
    makePart: no visible global function definition for ‘update’
    mmsNew0: no visible global function definition for ‘na.omit’
    modelTest : fitPar: no visible global function definition for ‘update’
    my.supertree: no visible global function definition for ‘hasArg’
    nnls.tree: no visible global function definition for ‘lm.fit’
    optEdgeMulti: no visible global function definition for ‘update’
    optW: no visible global function definition for ‘optimize’
    optW: no visible global function definition for ‘optim’
    optWPen: no visible global function definition for ‘optimize’
    optWPen: no visible global function definition for ‘optim’
    optim.pml: no visible global function definition for ‘update’
    optimBf: no visible global function definition for ‘optim’
    optimCodon: no visible global function definition for ‘optim’
    optimGamma: no visible global function definition for ‘optimize’
    optimInv: no visible global function definition for ‘optimize’
    optimMixBf : fn: no visible global function definition for ‘update’
    optimMixBf: no visible global function definition for ‘optim’
    optimMixEdge: no visible global function definition for ‘update’
    optimMixInv : fn: no visible global function definition for ‘update’
    optimMixInv: no visible global function definition for ‘optimize’
    optimMixQ : fn: no visible global function definition for ‘update’
    optimMixQ: no visible global function definition for ‘optim’
    optimMixRate : fn: no visible global function definition for ‘update’
    optimMixRate: no visible global function definition for ‘constrOptim’
    optimPartBf : fn: no visible global function definition for ‘update’
    optimPartBf: no visible global function definition for ‘optim’
    optimPartEdge: no visible global function definition for ‘update’
    optimPartGamma : fn: no visible global function definition for ‘update’
    optimPartGamma: no visible global function definition for ‘optimize’
    optimPartInv : fn: no visible global function definition for ‘update’
    optimPartInv: no visible global function definition for ‘optimize’
    optimPartNNI: no visible global function definition for ‘update’
    optimPartQ : fn: no visible global function definition for ‘update’
    optimPartQ: no visible global function definition for ‘optim’
    optimPartQGeneral : fn: no visible global function definition for
     ‘update’
    optimPartQGeneral: no visible global function definition for ‘optim’
    optimQ: no visible global function definition for ‘optim’
    optimRate: no visible global function definition for ‘optimize’
    optimRooted : scaleEdges: no visible global function definition for
     ‘optimize’
    optimRooted: no visible global function definition for ‘optimize’
    optimW: no visible global function definition for ‘optim’
    parsimony.plot: no visible global function definition for ‘plot’
    phyDat.AA: no visible global function definition for ‘na.omit’
    phyDat.DNA: no visible global function definition for ‘na.omit’
    phyDat.codon: no visible global function definition for ‘na.omit’
    phyDat.default: no visible global function definition for ‘na.omit’
    plot.pmlCluster: no visible global function definition for ‘image’
    plot.pmlCluster: no visible global function definition for ‘matplot’
    plot2D: no visible global function definition for ‘par’
    plot2D: no visible global function definition for ‘plot.new’
    plot2D: no visible global function definition for ‘plot.window’
    plot2D: no visible global function definition for ‘text’
    plotAnc: no visible global function definition for ‘par’
    plotAnc: no visible global function definition for ‘plot’
    plotAnc: no visible global function definition for ‘rainbow’
    plotAnc: no visible global function definition for ‘legend’
    plotBS: no visible global function definition for ‘plot’
    plotRGL: no visible global function definition for ‘par’
    pmlCluster.fit: no visible global function definition for ‘update’
    pmlCluster.fit: no visible global function definition for ‘quantile’
    pmlMix: no visible global function definition for ‘update’
    pmlMixPen: no visible global function definition for ‘update’
    pmlPart: no visible global function definition for ‘update’
    print.summary.clanistics: no visible global function definition for
     ‘aggregate’
    rNNI: no visible global function definition for ‘na.omit’
    rNNI_Old: no visible global function definition for ‘na.omit’
    read.FASTA.AA: no visible global function definition for
     ‘download.file’
    read.nexus.splits: no visible global function definition for ‘na.omit’
    readAArate: no visible global function definition for ‘read.table’
    rooted.nni: no visible global function definition for ‘optim’
    summary.SOWH: no visible global function definition for ‘hist’
    summary.SOWH: no visible global function definition for ‘abline’
    upgma: no visible global function definition for ‘as.dist’
    upgma: no visible global function definition for ‘hclust’
    wpgma: no visible global function definition for ‘as.dist’
    wpgma: no visible global function definition for ‘hclust’
    write.nexus.splits: no visible global function definition for
     ‘citation’
    Undefined global functions or variables:
     abline adjustcolor aggregate as.dist axis citation constrOptim
     cophenetic download.file hasArg hclust hist image installed.packages
     legend lm.fit matplot model.matrix na.omit optim optimize par pchisq
     pgamma plot plot.new plot.window points qgamma quantile rainbow
     read.table reshape rgb segments stack strwidth text title trees
     update xtabs
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