CRAN Package Check Results for Package ape

Last updated on 2015-07-31 10:47:16.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 3.3 7.86 74.34 82.19 NOTE
r-devel-linux-x86_64-debian-gcc 3.3 14.32 79.90 94.22 NOTE
r-devel-linux-x86_64-fedora-clang 3.3 168.93 NOTE
r-devel-linux-x86_64-fedora-gcc 3.3 163.50 NOTE
r-devel-osx-x86_64-clang 3.3 141.71 OK
r-devel-windows-ix86+x86_64 3.3 83.00 148.00 231.00 NOTE
r-patched-linux-x86_64 3.3 9.56 79.18 88.74 OK
r-patched-solaris-sparc 3.3 1039.30 OK
r-patched-solaris-x86 3.3 194.00 OK
r-release-linux-x86_64 3.3 9.74 79.81 89.55 OK
r-release-osx-x86_64-mavericks 3.3 OK
r-release-windows-ix86+x86_64 3.3 65.00 152.00 217.00 OK
r-oldrel-windows-ix86+x86_64 3.3 49.00 231.00 280.00 OK

Check Details

Version: 3.3
Check: R code for possible problems
Result: NOTE
    .CDF.birth.death2: no visible global function definition for
     ‘integrate’
    .DNAAlignment2DNAbinMatrix: no visible global function definition for
     ‘as’
    .getRHOetINT : RHO: no visible global function definition for
     ‘integrate’
    .getRHOetINT : INT: no visible global function definition for
     ‘integrate’
    BOTHlabels: no visible global function definition for ‘par’
    BOTHlabels: no visible global function definition for ‘strwidth’
    BOTHlabels: no visible global function definition for ‘strheight’
    BOTHlabels: no visible global function definition for ‘xinch’
    BOTHlabels: no visible global function definition for ‘yinch’
    BOTHlabels: no visible global function definition for ‘rect’
    BOTHlabels: no visible global function definition for ‘symbols’
    BOTHlabels: no visible global function definition for ‘rainbow’
    BOTHlabels: no visible global function definition for ‘points’
    CADM.global: no visible global function definition for ‘as.dist’
    CADM.global: no visible global function definition for ‘var’
    CADM.post: no visible global function definition for ‘as.dist’
    CADM.post: no visible global function definition for ‘var’
    CADM.post: no visible global function definition for ‘cor’
    CADM.post: no visible global function definition for ‘p.adjust’
    Initialize.corPhyl: no visible global function definition for ‘formula’
    LTT: no visible global function definition for ‘qbinom’
    Moran.I: no visible global function definition for ‘sd’
    Moran.I: no visible global function definition for ‘pnorm’
    ace: no visible global function definition for ‘nlm’
    ace: no visible global function definition for ‘qt’
    ace: no visible global function definition for ‘qnorm’
    ace: no visible global function definition for ‘nlminb’
    add.scale.bar: no visible global function definition for ‘locator’
    add.scale.bar: no visible global function definition for ‘text’
    additive: no visible global function definition for ‘as.dist’
    alex: no visible global function definition for ‘dev.cur’
    alex: no visible global function definition for ‘dev.set’
    alex: no visible global function definition for ‘locator’
    alex: no visible global function definition for ‘dev.new’
    alex: no visible global function definition for ‘image’
    alex: no visible global function definition for ‘axTicks’
    alex: no visible global function definition for ‘axis’
    alex: no visible global function definition for ‘title’
    anova.ace: no visible global function definition for ‘pchisq’
    axisPhylo: no visible global function definition for ‘axis’
    axisPhylo: no visible global function definition for ‘text’
    bd.ext: no visible global function definition for ‘nlm’
    bd.time: no visible global function definition for ‘nlminb’
    binaryPGLMM: no visible global function definition for ‘model.frame’
    binaryPGLMM: no visible global function definition for ‘model.matrix’
    binaryPGLMM: no visible global function definition for ‘model.response’
    binaryPGLMM: no visible global function definition for ‘var’
    binaryPGLMM: no visible global function definition for ‘glm’
    binaryPGLMM: no visible global function definition for ‘optim’
    binaryPGLMM: no visible global function definition for ‘pnorm’
    binaryPGLMM: no visible global function definition for ‘pchisq’
    binaryPGLMM.sim: no visible global function definition for
     ‘model.frame’
    binaryPGLMM.sim: no visible global function definition for
     ‘model.matrix’
    binaryPGLMM.sim: no visible global function definition for ‘rnorm’
    binaryPGLMM.sim: no visible global function definition for ‘runif’
    bind.tree: no visible global function definition for ‘locator’
    bionj: no visible global function definition for ‘as.dist’
    bionjs: no visible global function definition for ‘as.dist’
    biplot.pcoa: no visible global function definition for ‘par’
    biplot.pcoa: no visible global function definition for ‘text’
    biplot.pcoa: no visible global function definition for ‘title’
    biplot.pcoa: no visible global function definition for ‘cov’
    birth.step: no visible global function definition for ‘runif’
    birthdeath: no visible global function definition for ‘nlm’
    cherry: no visible global function definition for ‘pnorm’
    chronoMPL: no visible global function definition for ‘pnorm’
    chronopl : minusploglik: no visible global function definition for
     ‘var’
    chronopl: no visible global function definition for ‘nlminb’
    chronos: no visible global function definition for ‘runif’
    chronos : <anonymous>: no visible global function definition for
     ‘dgamma’
    chronos : <anonymous>: no visible global function definition for
     ‘pgamma’
    chronos : <anonymous>: no visible global function definition for ‘var’
    chronos: no visible global function definition for ‘nlminb’
    chronos: no visible global function definition for ‘var’
    chronos: no visible global function definition for ‘pgamma’
    compar.gee: no visible binding for global variable ‘gaussian’
    compar.gee: no visible global function definition for ‘model.matrix’
    compar.gee: no visible global function definition for ‘glm’
    compar.gee: no visible binding for global variable ‘quasibinomial’
    compar.lynch: no visible global function definition for ‘runif’
    compar.lynch: no visible global function definition for ‘var’
    compar.ou: no visible global function definition for ‘nlm’
    compute.brtime: no visible global function definition for ‘rexp’
    cophyloplot: no visible global function definition for ‘par’
    corMatrix.corMartins: no visible global function definition for
     ‘cov2cor’
    corphylo : corphylo.LL: no visible global function definition for
     ‘show’
    corphylo: no visible global function definition for ‘sd’
    corphylo: no visible global function definition for ‘lm’
    corphylo: no visible global function definition for ‘resid’
    corphylo: no visible global function definition for ‘cov’
    corphylo: no visible global function definition for ‘optim’
    corphylo: no visible global function definition for ‘pnorm’
    correlogram.formula: no visible global function definition for
     ‘na.fail’
    correlogram.formula: no visible global function definition for
     ‘complete.cases’
    death.step: no visible global function definition for ‘runif’
    delta.plot: no visible global function definition for ‘as.dist’
    delta.plot: no visible global function definition for ‘layout’
    delta.plot: no visible global function definition for ‘barplot’
    delta.plot: no visible global function definition for ‘axTicks’
    delta.plot: no visible global function definition for ‘axis’
    diversi.time: no visible global function definition for ‘uniroot’
    diversi.time: no visible global function definition for ‘median’
    diversi.time: no visible global function definition for ‘pchisq’
    diversity.contrast.test: no visible global function definition for
     ‘wilcox.test’
    drop.tip: no visible global function definition for ‘locator’
    drop1.compar.gee: no visible global function definition for ‘formula’
    drop1.compar.gee: no visible global function definition for ‘terms’
    drop1.compar.gee: no visible global function definition for ‘pf’
    ewLasso: no visible global function definition for ‘as.dist’
    extract.popsize: no visible global function definition for ‘median’
    extract.popsize: no visible global function definition for ‘quantile’
    fancyarrows: no visible global function definition for ‘par’
    fancyarrows : foo: no visible global function definition for ‘par’
    fancyarrows : arrow.triangle: no visible global function definition for
     ‘xinch’
    fancyarrows : arrow.triangle: no visible global function definition for
     ‘yinch’
    fancyarrows : arrow.triangle: no visible global function definition for
     ‘polygon’
    fancyarrows : arrow.harpoon: no visible global function definition for
     ‘xinch’
    fancyarrows : arrow.harpoon: no visible global function definition for
     ‘yinch’
    fancyarrows : arrow.harpoon: no visible global function definition for
     ‘polygon’
    fastme.bal: no visible global function definition for ‘as.dist’
    fastme.ols: no visible global function definition for ‘as.dist’
    floating.pie.asp: no visible global function definition for ‘par’
    floating.pie.asp: no visible global function definition for ‘rainbow’
    floating.pie.asp: no visible global function definition for ‘symbols’
    floating.pie.asp: no visible global function definition for ‘polygon’
    ht.move: no visible global function definition for ‘runif’
    identify.phylo: no visible global function definition for ‘locator’
    identify.phylo: no visible global function definition for ‘par’
    image.DNAbin: no visible global function definition for ‘mtext’
    image.DNAbin: no visible global function definition for ‘par’
    is.monophyletic: no visible global function definition for ‘mtext’
    is.ultrametric: no visible global function definition for ‘var’
    kronoviz: no visible global function definition for ‘par’
    kronoviz: no visible global function definition for ‘devAskNewPage’
    lmorigin: no visible global function definition for ‘lm’
    lmorigin: no visible global function definition for ‘rbinom’
    ltt.coplot: no visible global function definition for ‘layout’
    ltt.coplot: no visible global function definition for ‘par’
    ltt.coplot: no visible global function definition for ‘axis’
    mantel.test: no visible global function definition for ‘density’
    mantel.test: no visible global function definition for ‘abline’
    mcconwaysims.test: no visible global function definition for ‘pchisq’
    mcmc.popsize: no visible global function definition for ‘dpois’
    mcmc.popsize: no visible global function definition for ‘ppois’
    mcmc.popsize: no visible global function definition for ‘dev.new’
    mcmc.popsize: no visible global function definition for ‘par’
    mcmc.popsize: no visible global function definition for ‘polygon’
    mcmc.popsize: no visible global function definition for ‘rgamma’
    mcmc.popsize: no visible global function definition for ‘dev.off’
    mltt.plot: no visible global function definition for ‘topo.colors’
    mvr: no visible global function definition for ‘as.dist’
    mvrs: no visible global function definition for ‘as.dist’
    nj: no visible global function definition for ‘as.dist’
    njs: no visible global function definition for ‘as.dist’
    parafit: no visible global function definition for ‘runif’
    phydataplot: no visible global function definition for ‘barplot’
    phydataplot: no visible global function definition for ‘axis’
    phydataplot: no visible global function definition for ‘image’
    phydataplot: no visible global function definition for ‘mtext’
    plot.correlogram: no visible global function definition for ‘axis’
    plot.correlogramList: no visible global function definition for ‘axis’
    plot.evonet: no visible global function definition for ‘rgb’
    plot.evonet: no visible global function definition for ‘col2rgb’
    plot.mst: no visible global function definition for ‘points’
    plot.mst: no visible global function definition for ‘text’
    plot.multiPhylo: no visible global function definition for
     ‘devAskNewPage’
    plot.multiPhylo: no visible global function definition for ‘dev.cur’
    plot.phylo: no visible global function definition for ‘par’
    plot.phylo: no visible global function definition for ‘strwidth’
    plot.phylo: no visible global function definition for ‘uniroot’
    plot.phylo: no visible global function definition for ‘text’
    plot.phylo: no visible global function definition for ‘strheight’
    plot.phymltest: no visible global function definition for ‘axis’
    plot.phymltest: no visible global function definition for ‘abline’
    plot.phymltest: no visible global function definition for ‘text’
    plot.prop.part: no visible global function definition for ‘layout’
    plot.prop.part: no visible global function definition for ‘par’
    plot.prop.part: no visible global function definition for ‘mtext’
    plotCophylo2: no visible global function definition for ‘text’
    plotCophylo2: no visible global function definition for ‘strwidth’
    pos.move: no visible global function definition for ‘runif’
    predict.compar.gee: no visible global function definition for ‘formula’
    predict.compar.gee: no visible global function definition for
     ‘model.matrix’
    print.binaryPGLMM: no visible global function definition for
     ‘printCoefmat’
    print.compar.gee: no visible global function definition for ‘pt’
    print.compar.gee: no visible global function definition for ‘quantile’
    print.corphylo: no visible global function definition for
     ‘printCoefmat’
    print.lmorigin: no visible global function definition for
     ‘printCoefmat’
    print.lmorigin: no visible global function definition for ‘pf’
    rbdtree : rtimetospe : <anonymous>: no visible global function
     definition for ‘integrate’
    rbdtree : rtimetospe: no visible global function definition for ‘runif’
    rbdtree : foo: no visible global function definition for ‘rbinom’
    rcoal: no visible global function definition for ‘rexp’
    read.FASTA: no visible global function definition for ‘download.file’
    read.caic: no visible global function definition for ‘read.table’
    reconstruct: no visible global function definition for ‘qt’
    reconstruct: no visible global function definition for ‘nlm’
    reconstruct: no visible global function definition for ‘qnorm’
    richness.yule.test: no visible global function definition for ‘nlminb’
    richness.yule.test: no visible global function definition for ‘pchisq’
    ring: no visible global function definition for ‘polygon’
    rlineage : rTimeToEvent : Foo: no visible global function definition
     for ‘integrate’
    rlineage : rTimeToEvent: no visible global function definition for
     ‘runif’
    rlineage : foo: no visible global function definition for ‘rbinom’
    rmtree: no visible binding for global variable ‘runif’
    rphylo : rTimeToEvent: no visible global function definition for ‘rexp’
    rphylo : Foo: no visible global function definition for ‘integrate’
    rphylo : rTimeToEvent: no visible global function definition for
     ‘runif’
    rphylo: no visible global function definition for ‘rbinom’
    rtree: no visible binding for global variable ‘runif’
    rtt : objective: no visible global function definition for ‘cor.test’
    rtt : objective: no visible global function definition for ‘lm’
    rtt: no visible global function definition for ‘optimize’
    skylineplot.deluxe: no visible global function definition for ‘grey’
    slowinskiguyer.test: no visible global function definition for ‘pchisq’
    speciesTree: no visible global function definition for ‘as.dist’
    str.multiPhylo: no visible global function definition for ‘str’
    subtreeplot: no visible global function definition for ‘split.screen’
    subtreeplot: no visible global function definition for ‘screen’
    subtreeplot: no visible global function definition for ‘close.screen’
    summary.phylo: no visible global function definition for ‘var’
    summary.phymltest: no visible global function definition for ‘pchisq’
    trex: no visible global function definition for ‘dev.cur’
    trex : restore: no visible global function definition for ‘dev.set’
    trex: no visible global function definition for ‘dev.new’
    trex: no visible global function definition for ‘par’
    trex: no visible global function definition for ‘dev.set’
    triangMtd: no visible global function definition for ‘as.dist’
    triangMtds: no visible global function definition for ‘as.dist’
    ultrametric: no visible global function definition for ‘as.dist’
    yule.cov: no visible global function definition for ‘model.matrix’
    yule.cov: no visible global function definition for ‘nlm’
    yule.cov: no visible global function definition for ‘pchisq’
    yule.time : Foo: no visible global function definition for ‘integrate’
    yule.time : half.dev: no visible global function definition for
     ‘integrate’
    yule.time: no visible global function definition for ‘nlm’
    yule.time: no visible global function definition for ‘nlminb’
    yule.time: no visible global function definition for ‘optim’
    zoom: no visible binding for global variable ‘rainbow’
    zoom: no visible global function definition for ‘grey’
    zoom: no visible global function definition for ‘layout’
    Undefined global functions or variables:
     abline as as.dist axTicks axis barplot close.screen col2rgb
     complete.cases cor cor.test cov cov2cor density dev.cur dev.new
     dev.off dev.set devAskNewPage dgamma download.file dpois formula
     gaussian glm grey image integrate layout lm locator median
     model.frame model.matrix model.response mtext na.fail nlm nlminb
     optim optimize p.adjust par pchisq pf pgamma pnorm points polygon
     ppois printCoefmat pt qbinom qnorm qt quantile quasibinomial rainbow
     rbinom read.table rect resid rexp rgamma rgb rnorm runif screen sd
     show split.screen str strheight strwidth symbols terms text title
     topo.colors uniroot var wilcox.test xinch yinch
    Consider adding
     importFrom("grDevices", "col2rgb", "dev.cur", "dev.new", "dev.off",
     "dev.set", "devAskNewPage", "grey", "rainbow", "rgb",
     "topo.colors")
     importFrom("graphics", "abline", "axTicks", "axis", "barplot",
     "close.screen", "image", "layout", "locator", "mtext",
     "par", "points", "polygon", "rect", "screen",
     "split.screen", "strheight", "strwidth", "symbols", "text",
     "title", "xinch", "yinch")
     importFrom("methods", "as", "show")
     importFrom("stats", "as.dist", "complete.cases", "cor", "cor.test",
     "cov", "cov2cor", "density", "dgamma", "dpois", "formula",
     "gaussian", "glm", "integrate", "lm", "median",
     "model.frame", "model.matrix", "model.response", "na.fail",
     "nlm", "nlminb", "optim", "optimize", "p.adjust", "pchisq",
     "pf", "pgamma", "pnorm", "ppois", "printCoefmat", "pt",
     "qbinom", "qnorm", "qt", "quantile", "quasibinomial",
     "rbinom", "resid", "rexp", "rgamma", "rnorm", "runif", "sd",
     "terms", "uniroot", "var", "wilcox.test")
     importFrom("utils", "download.file", "read.table", "str")
    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

Version: 3.3
Check: R code for possible problems
Result: NOTE
    .CDF.birth.death2: no visible global function definition for
     'integrate'
    .DNAAlignment2DNAbinMatrix: no visible global function definition for
     'as'
    .getRHOetINT : RHO: no visible global function definition for
     'integrate'
    .getRHOetINT : INT: no visible global function definition for
     'integrate'
    BOTHlabels: no visible global function definition for 'par'
    BOTHlabels: no visible global function definition for 'strwidth'
    BOTHlabels: no visible global function definition for 'strheight'
    BOTHlabels: no visible global function definition for 'xinch'
    BOTHlabels: no visible global function definition for 'yinch'
    BOTHlabels: no visible global function definition for 'rect'
    BOTHlabels: no visible global function definition for 'symbols'
    BOTHlabels: no visible global function definition for 'rainbow'
    BOTHlabels: no visible global function definition for 'points'
    CADM.global: no visible global function definition for 'as.dist'
    CADM.global: no visible global function definition for 'var'
    CADM.post: no visible global function definition for 'as.dist'
    CADM.post: no visible global function definition for 'var'
    CADM.post: no visible global function definition for 'cor'
    CADM.post: no visible global function definition for 'p.adjust'
    Initialize.corPhyl: no visible global function definition for 'formula'
    LTT: no visible global function definition for 'qbinom'
    Moran.I: no visible global function definition for 'sd'
    Moran.I: no visible global function definition for 'pnorm'
    ace: no visible global function definition for 'nlm'
    ace: no visible global function definition for 'qt'
    ace: no visible global function definition for 'qnorm'
    ace: no visible global function definition for 'nlminb'
    add.scale.bar: no visible global function definition for 'locator'
    add.scale.bar: no visible global function definition for 'text'
    additive: no visible global function definition for 'as.dist'
    alex: no visible global function definition for 'dev.cur'
    alex: no visible global function definition for 'dev.set'
    alex: no visible global function definition for 'locator'
    alex: no visible global function definition for 'dev.new'
    alex: no visible global function definition for 'image'
    alex: no visible global function definition for 'axTicks'
    alex: no visible global function definition for 'axis'
    alex: no visible global function definition for 'title'
    anova.ace: no visible global function definition for 'pchisq'
    axisPhylo: no visible global function definition for 'axis'
    axisPhylo: no visible global function definition for 'text'
    bd.ext: no visible global function definition for 'nlm'
    bd.time: no visible global function definition for 'nlminb'
    binaryPGLMM: no visible global function definition for 'model.frame'
    binaryPGLMM: no visible global function definition for 'model.matrix'
    binaryPGLMM: no visible global function definition for 'model.response'
    binaryPGLMM: no visible global function definition for 'var'
    binaryPGLMM: no visible global function definition for 'glm'
    binaryPGLMM: no visible global function definition for 'optim'
    binaryPGLMM: no visible global function definition for 'pnorm'
    binaryPGLMM: no visible global function definition for 'pchisq'
    binaryPGLMM.sim: no visible global function definition for
     'model.frame'
    binaryPGLMM.sim: no visible global function definition for
     'model.matrix'
    binaryPGLMM.sim: no visible global function definition for 'rnorm'
    binaryPGLMM.sim: no visible global function definition for 'runif'
    bind.tree: no visible global function definition for 'locator'
    bionj: no visible global function definition for 'as.dist'
    bionjs: no visible global function definition for 'as.dist'
    biplot.pcoa: no visible global function definition for 'par'
    biplot.pcoa: no visible global function definition for 'text'
    biplot.pcoa: no visible global function definition for 'title'
    biplot.pcoa: no visible global function definition for 'cov'
    birth.step: no visible global function definition for 'runif'
    birthdeath: no visible global function definition for 'nlm'
    cherry: no visible global function definition for 'pnorm'
    chronoMPL: no visible global function definition for 'pnorm'
    chronopl : minusploglik: no visible global function definition for
     'var'
    chronopl: no visible global function definition for 'nlminb'
    chronos: no visible global function definition for 'runif'
    chronos : <anonymous>: no visible global function definition for
     'dgamma'
    chronos : <anonymous>: no visible global function definition for
     'pgamma'
    chronos : <anonymous>: no visible global function definition for 'var'
    chronos: no visible global function definition for 'nlminb'
    chronos: no visible global function definition for 'var'
    chronos: no visible global function definition for 'pgamma'
    clustal: no visible global function definition for 'shortPathName'
    compar.gee: no visible binding for global variable 'gaussian'
    compar.gee: no visible global function definition for 'model.matrix'
    compar.gee: no visible global function definition for 'glm'
    compar.gee: no visible binding for global variable 'quasibinomial'
    compar.lynch: no visible global function definition for 'runif'
    compar.lynch: no visible global function definition for 'var'
    compar.ou: no visible global function definition for 'nlm'
    compute.brtime: no visible global function definition for 'rexp'
    cophyloplot: no visible global function definition for 'par'
    corMatrix.corMartins: no visible global function definition for
     'cov2cor'
    corphylo : corphylo.LL: no visible global function definition for
     'show'
    corphylo: no visible global function definition for 'sd'
    corphylo: no visible global function definition for 'lm'
    corphylo: no visible global function definition for 'resid'
    corphylo: no visible global function definition for 'cov'
    corphylo: no visible global function definition for 'optim'
    corphylo: no visible global function definition for 'pnorm'
    correlogram.formula: no visible global function definition for
     'na.fail'
    correlogram.formula: no visible global function definition for
     'complete.cases'
    death.step: no visible global function definition for 'runif'
    delta.plot: no visible global function definition for 'as.dist'
    delta.plot: no visible global function definition for 'layout'
    delta.plot: no visible global function definition for 'barplot'
    delta.plot: no visible global function definition for 'axTicks'
    delta.plot: no visible global function definition for 'axis'
    diversi.time: no visible global function definition for 'uniroot'
    diversi.time: no visible global function definition for 'median'
    diversi.time: no visible global function definition for 'pchisq'
    diversity.contrast.test: no visible global function definition for
     'wilcox.test'
    drop.tip: no visible global function definition for 'locator'
    drop1.compar.gee: no visible global function definition for 'formula'
    drop1.compar.gee: no visible global function definition for 'terms'
    drop1.compar.gee: no visible global function definition for 'pf'
    ewLasso: no visible global function definition for 'as.dist'
    extract.popsize: no visible global function definition for 'median'
    extract.popsize: no visible global function definition for 'quantile'
    fancyarrows: no visible global function definition for 'par'
    fancyarrows : foo: no visible global function definition for 'par'
    fancyarrows : arrow.triangle: no visible global function definition for
     'xinch'
    fancyarrows : arrow.triangle: no visible global function definition for
     'yinch'
    fancyarrows : arrow.triangle: no visible global function definition for
     'polygon'
    fancyarrows : arrow.harpoon: no visible global function definition for
     'xinch'
    fancyarrows : arrow.harpoon: no visible global function definition for
     'yinch'
    fancyarrows : arrow.harpoon: no visible global function definition for
     'polygon'
    fastme.bal: no visible global function definition for 'as.dist'
    fastme.ols: no visible global function definition for 'as.dist'
    floating.pie.asp: no visible global function definition for 'par'
    floating.pie.asp: no visible global function definition for 'rainbow'
    floating.pie.asp: no visible global function definition for 'symbols'
    floating.pie.asp: no visible global function definition for 'polygon'
    ht.move: no visible global function definition for 'runif'
    identify.phylo: no visible global function definition for 'locator'
    identify.phylo: no visible global function definition for 'par'
    image.DNAbin: no visible global function definition for 'mtext'
    image.DNAbin: no visible global function definition for 'par'
    is.monophyletic: no visible global function definition for 'mtext'
    is.ultrametric: no visible global function definition for 'var'
    kronoviz: no visible global function definition for 'par'
    kronoviz: no visible global function definition for 'devAskNewPage'
    lmorigin: no visible global function definition for 'lm'
    lmorigin: no visible global function definition for 'rbinom'
    ltt.coplot: no visible global function definition for 'layout'
    ltt.coplot: no visible global function definition for 'par'
    ltt.coplot: no visible global function definition for 'axis'
    mantel.test: no visible global function definition for 'density'
    mantel.test: no visible global function definition for 'abline'
    mcconwaysims.test: no visible global function definition for 'pchisq'
    mcmc.popsize: no visible global function definition for 'dpois'
    mcmc.popsize: no visible global function definition for 'ppois'
    mcmc.popsize: no visible global function definition for 'dev.new'
    mcmc.popsize: no visible global function definition for 'par'
    mcmc.popsize: no visible global function definition for 'polygon'
    mcmc.popsize: no visible global function definition for 'rgamma'
    mcmc.popsize: no visible global function definition for 'dev.off'
    mltt.plot: no visible global function definition for 'topo.colors'
    mvr: no visible global function definition for 'as.dist'
    mvrs: no visible global function definition for 'as.dist'
    nj: no visible global function definition for 'as.dist'
    njs: no visible global function definition for 'as.dist'
    parafit: no visible global function definition for 'runif'
    phydataplot: no visible global function definition for 'barplot'
    phydataplot: no visible global function definition for 'axis'
    phydataplot: no visible global function definition for 'image'
    phydataplot: no visible global function definition for 'mtext'
    plot.correlogram: no visible global function definition for 'axis'
    plot.correlogramList: no visible global function definition for 'axis'
    plot.evonet: no visible global function definition for 'rgb'
    plot.evonet: no visible global function definition for 'col2rgb'
    plot.mst: no visible global function definition for 'points'
    plot.mst: no visible global function definition for 'text'
    plot.multiPhylo: no visible global function definition for
     'devAskNewPage'
    plot.multiPhylo: no visible global function definition for 'dev.cur'
    plot.phylo: no visible global function definition for 'par'
    plot.phylo: no visible global function definition for 'strwidth'
    plot.phylo: no visible global function definition for 'uniroot'
    plot.phylo: no visible global function definition for 'text'
    plot.phylo: no visible global function definition for 'strheight'
    plot.phymltest: no visible global function definition for 'axis'
    plot.phymltest: no visible global function definition for 'abline'
    plot.phymltest: no visible global function definition for 'text'
    plot.prop.part: no visible global function definition for 'layout'
    plot.prop.part: no visible global function definition for 'par'
    plot.prop.part: no visible global function definition for 'mtext'
    plotCophylo2: no visible global function definition for 'text'
    plotCophylo2: no visible global function definition for 'strwidth'
    pos.move: no visible global function definition for 'runif'
    predict.compar.gee: no visible global function definition for 'formula'
    predict.compar.gee: no visible global function definition for
     'model.matrix'
    print.binaryPGLMM: no visible global function definition for
     'printCoefmat'
    print.compar.gee: no visible global function definition for 'pt'
    print.compar.gee: no visible global function definition for 'quantile'
    print.corphylo: no visible global function definition for
     'printCoefmat'
    print.lmorigin: no visible global function definition for
     'printCoefmat'
    print.lmorigin: no visible global function definition for 'pf'
    rbdtree : rtimetospe : <anonymous>: no visible global function
     definition for 'integrate'
    rbdtree : rtimetospe: no visible global function definition for 'runif'
    rbdtree : foo: no visible global function definition for 'rbinom'
    rcoal: no visible global function definition for 'rexp'
    read.FASTA: no visible global function definition for 'download.file'
    read.caic: no visible global function definition for 'read.table'
    reconstruct: no visible global function definition for 'qt'
    reconstruct: no visible global function definition for 'nlm'
    reconstruct: no visible global function definition for 'qnorm'
    richness.yule.test: no visible global function definition for 'nlminb'
    richness.yule.test: no visible global function definition for 'pchisq'
    ring: no visible global function definition for 'polygon'
    rlineage : rTimeToEvent : Foo: no visible global function definition
     for 'integrate'
    rlineage : rTimeToEvent: no visible global function definition for
     'runif'
    rlineage : foo: no visible global function definition for 'rbinom'
    rmtree: no visible binding for global variable 'runif'
    rphylo : rTimeToEvent: no visible global function definition for 'rexp'
    rphylo : Foo: no visible global function definition for 'integrate'
    rphylo : rTimeToEvent: no visible global function definition for
     'runif'
    rphylo: no visible global function definition for 'rbinom'
    rtree: no visible binding for global variable 'runif'
    rtt : objective: no visible global function definition for 'cor.test'
    rtt : objective: no visible global function definition for 'lm'
    rtt: no visible global function definition for 'optimize'
    skylineplot.deluxe: no visible global function definition for 'grey'
    slowinskiguyer.test: no visible global function definition for 'pchisq'
    speciesTree: no visible global function definition for 'as.dist'
    str.multiPhylo: no visible global function definition for 'str'
    subtreeplot: no visible global function definition for 'split.screen'
    subtreeplot: no visible global function definition for 'screen'
    subtreeplot: no visible global function definition for 'close.screen'
    summary.phylo: no visible global function definition for 'var'
    summary.phymltest: no visible global function definition for 'pchisq'
    trex: no visible global function definition for 'dev.cur'
    trex : restore: no visible global function definition for 'dev.set'
    trex: no visible global function definition for 'dev.new'
    trex: no visible global function definition for 'par'
    trex: no visible global function definition for 'dev.set'
    triangMtd: no visible global function definition for 'as.dist'
    triangMtds: no visible global function definition for 'as.dist'
    ultrametric: no visible global function definition for 'as.dist'
    yule.cov: no visible global function definition for 'model.matrix'
    yule.cov: no visible global function definition for 'nlm'
    yule.cov: no visible global function definition for 'pchisq'
    yule.time : Foo: no visible global function definition for 'integrate'
    yule.time : half.dev: no visible global function definition for
     'integrate'
    yule.time: no visible global function definition for 'nlm'
    yule.time: no visible global function definition for 'nlminb'
    yule.time: no visible global function definition for 'optim'
    zoom: no visible binding for global variable 'rainbow'
    zoom: no visible global function definition for 'grey'
    zoom: no visible global function definition for 'layout'
    Undefined global functions or variables:
     abline as as.dist axTicks axis barplot close.screen col2rgb
     complete.cases cor cor.test cov cov2cor density dev.cur dev.new
     dev.off dev.set devAskNewPage dgamma download.file dpois formula
     gaussian glm grey image integrate layout lm locator median
     model.frame model.matrix model.response mtext na.fail nlm nlminb
     optim optimize p.adjust par pchisq pf pgamma pnorm points polygon
     ppois printCoefmat pt qbinom qnorm qt quantile quasibinomial rainbow
     rbinom read.table rect resid rexp rgamma rgb rnorm runif screen sd
     shortPathName show split.screen str strheight strwidth symbols terms
     text title topo.colors uniroot var wilcox.test xinch yinch
    Consider adding
     importFrom("grDevices", "col2rgb", "dev.cur", "dev.new", "dev.off",
     "dev.set", "devAskNewPage", "grey", "rainbow", "rgb",
     "topo.colors")
     importFrom("graphics", "abline", "axTicks", "axis", "barplot",
     "close.screen", "image", "layout", "locator", "mtext",
     "par", "points", "polygon", "rect", "screen",
     "split.screen", "strheight", "strwidth", "symbols", "text",
     "title", "xinch", "yinch")
     importFrom("methods", "as", "show")
     importFrom("stats", "as.dist", "complete.cases", "cor", "cor.test",
     "cov", "cov2cor", "density", "dgamma", "dpois", "formula",
     "gaussian", "glm", "integrate", "lm", "median",
     "model.frame", "model.matrix", "model.response", "na.fail",
     "nlm", "nlminb", "optim", "optimize", "p.adjust", "pchisq",
     "pf", "pgamma", "pnorm", "ppois", "printCoefmat", "pt",
     "qbinom", "qnorm", "qt", "quantile", "quasibinomial",
     "rbinom", "resid", "rexp", "rgamma", "rnorm", "runif", "sd",
     "terms", "uniroot", "var", "wilcox.test")
     importFrom("utils", "download.file", "read.table", "shortPathName",
     "str")
    to your NAMESPACE.
Flavor: r-devel-windows-ix86+x86_64