CRAN Package Check Results for Package diversitree

Last updated on 2015-08-02 23:47:59.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.9-7 27.54 60.64 88.19 NOTE
r-devel-linux-x86_64-debian-gcc 0.9-7 31.26 62.92 94.18 NOTE
r-devel-linux-x86_64-fedora-clang 0.9-7 178.67 NOTE
r-devel-linux-x86_64-fedora-gcc 0.9-7 168.61 NOTE
r-devel-osx-x86_64-clang 0.9-7 135.79 NOTE
r-devel-windows-ix86+x86_64 0.9-7 124.00 149.00 273.00 NOTE
r-patched-linux-x86_64 0.9-7 30.95 60.17 91.12 NOTE
r-patched-solaris-sparc 0.9-7 1029.10 NOTE
r-patched-solaris-x86 0.9-7 192.40 NOTE
r-release-linux-x86_64 0.9-7 30.68 62.88 93.56 NOTE
r-release-osx-x86_64-mavericks 0.9-7 NOTE
r-release-windows-ix86+x86_64 0.9-7 157.00 150.00 307.00 NOTE
r-oldrel-windows-ix86+x86_64 0.9-7 154.00 154.00 308.00 NOTE

Check Details

Version: 0.9-7
Check: dependencies in R code
Result: NOTE
    'library' or 'require' calls in package code:
     ‘lubridate’ ‘minqa’ ‘numDeriv’
     Please use :: or requireNamespace() instead.
     See section 'Suggested packages' in 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-x86_64, r-release-osx-x86_64-mavericks, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 0.9-7
Check: R code for possible problems
Result: NOTE
    add.alpha: no visible global function definition for ‘col2rgb’
    add.alpha: no visible global function definition for ‘rgb’
    add.profile.outline: no visible global function definition for ‘lines’
    add.profile.shading: no visible global function definition for
     ‘polygon’
    anova.fit.mle: no visible binding for global variable ‘logLik’
    anova.fit.mle : check: no visible global function definition for ‘coef’
    anova.fit.mle: no visible binding for global variable ‘AIC’
    anova.fit.mle: no visible global function definition for ‘pchisq’
    arcs: no visible global function definition for ‘par’
    arcs: no visible global function definition for ‘segments’
    branching.heights: no visible global function definition for ‘reorder’
    check.control.bd: no visible global function definition for
     ‘modifyList’
    check.control.continuous: no visible global function definition for
     ‘modifyList’
    check.control.expokit: no visible global function definition for
     ‘modifyList’
    check.control.mk2: no visible global function definition for
     ‘modifyList’
    check.control.mkn: no visible global function definition for
     ‘modifyList’
    check.control.ode: no visible global function definition for
     ‘modifyList’
    check.control.pgls: no visible global function definition for
     ‘modifyList’
    check.control.quasse: no visible global function definition for
     ‘modifyList’
    check.data.pgls: no visible global function definition for
     ‘model.frame’
    check.data.pgls: no visible binding for global variable ‘na.fail’
    check.data.pgls: no visible global function definition for
     ‘model.matrix’
    check.spline.data: no visible global function definition for ‘spline’
    check.states: no visible global function definition for ‘na.omit’
    check.states.musse.multitrait : f: no visible global function
     definition for ‘na.omit’
    clades.from.sample : f: no visible global function definition for
     ‘na.omit’
    clades.from.sample: no visible global function definition for ‘runif’
    constrain.parse: no visible global function definition for ‘as.formula’
    dmvnorm2: no visible global function definition for ‘mahalanobis’
    dmvnorm3: no visible global function definition for ‘mahalanobis’
    do.mle.search.int1d: no visible global function definition for
     ‘modifyList’
    do.mle.search.minqa: no visible global function definition for
     ‘modifyList’
    do.mle.search.mixed: no visible global function definition for
     ‘modifyList’
    do.mle.search.nlm: no visible global function definition for
     ‘modifyList’
    do.mle.search.nlm: no visible global function definition for ‘nlm’
    do.mle.search.nlminb: no visible global function definition for
     ‘nlminb’
    do.mle.search.optim: no visible global function definition for
     ‘modifyList’
    do.mle.search.optim: no visible global function definition for ‘optim’
    do.mle.search.optimize: no visible global function definition for
     ‘modifyList’
    do.mle.search.optimize: no visible global function definition for
     ‘optimize’
    do.mle.search.subplex: no visible global function definition for
     ‘modifyList’
    do.mle.search.subplexR: no visible global function definition for
     ‘modifyList’
    drop.tip.fixed: no visible global function definition for ‘reorder’
    extractAIC.fit.mle: no visible global function definition for ‘coef’
    extractAIC.fit.mle: no visible global function definition for ‘AIC’
    fftR.make.kern: no visible global function definition for ‘dnorm’
    fftR.propagate.x : ifft: no visible global function definition for
     ‘fft’
    fftR.propagate.x : f: no visible global function definition for ‘fft’
    fftR.propagate.x: no visible binding for global variable ‘fft’
    filled.arcs: no visible global function definition for ‘par’
    filled.arcs: no visible global function definition for ‘polygon’
    fitted.fit.mle.pgls: no visible global function definition for ‘fitted’
    fitted.fit.mle.pgls: no visible global function definition for ‘coef’
    fitted.mcmcsamples.pgls: no visible global function definition for
     ‘coef’
    fitted.mcmcsamples.pgls : <anonymous>: no visible global function
     definition for ‘fitted’
    group.label.tip: no visible global function definition for ‘par’
    group.label.tip: no visible global function definition for ‘segments’
    group.label.tip: no visible global function definition for ‘text’
    hdr: no visible global function definition for ‘quantile’
    hdr.new: no visible global function definition for ‘ecdf’
    hdr.uniroot: no visible global function definition for ‘ecdf’
    hdr.uniroot: no visible global function definition for ‘approxfun’
    hdr.uniroot: no visible global function definition for ‘optimize’
    hyperg: no visible global function definition for ‘dhyper’
    initial.tip.quasse : <anonymous>: no visible global function definition
     for ‘dnorm’
    initial.tip.quasse.split : <anonymous>: no visible global function
     definition for ‘dnorm’
    make.all.branches.rescale.contrasts: no visible global function
     definition for ‘reorder’
    make.br.bbm : <anonymous>: no visible global function definition for
     ‘rnorm’
    make.br.bm : <anonymous>: no visible global function definition for
     ‘rnorm’
    make.br.mk2 : <anonymous>: no visible global function definition for
     ‘rexp’
    make.br.mkn : <anonymous>: no visible global function definition for
     ‘rexp’
    make.br.ou : <anonymous>: no visible global function definition for
     ‘rnorm’
    make.brownian.with.drift : <anonymous>: no visible global function
     definition for ‘rnorm’
    make.cache.bisse: no visible global function definition for ‘na.omit’
    make.every.so.often: no visible global function definition for ‘now’
    make.every.so.often : check: no visible global function definition for
     ‘now’
    make.prior.ExpBeta : <anonymous>: no visible global function definition
     for ‘dexp’
    make.prior.ExpBeta : <anonymous>: no visible global function definition
     for ‘dbeta’
    make.prior.exponential : <anonymous>: no visible global function
     definition for ‘dexp’
    make.tree.bd: no visible global function definition for ‘rexp’
    make.tree.bd: no visible global function definition for ‘runif’
    make.tree.bisse: no visible global function definition for ‘rexp’
    make.tree.bisse: no visible global function definition for ‘runif’
    make.tree.bisse.R.core: no visible global function definition for
     ‘rexp’
    make.tree.bisse.R.core: no visible global function definition for
     ‘runif’
    make.tree.bisseness: no visible global function definition for ‘rexp’
    make.tree.bisseness: no visible global function definition for ‘runif’
    make.tree.classe: no visible global function definition for ‘rexp’
    make.tree.musse: no visible global function definition for ‘rexp’
    mcmc.default : <anonymous>: no visible global function definition for
     ‘write.csv’
    mcmc.default: no visible global function definition for ‘coef’
    mcmc.norm.1d: no visible global function definition for ‘rnorm’
    mcmc.norm.1d: no visible global function definition for ‘runif’
    me.to.ape.bd: no visible global function definition for ‘reorder’
    me.to.ape.bisse: no visible global function definition for ‘reorder’
    me.to.ape.quasse: no visible global function definition for ‘reorder’
    minimise.int1d: no visible global function definition for ‘modifyList’
    node.depth: no visible global function definition for ‘reorder’
    node.depth.edgelength: no visible global function definition for
     ‘reorder’
    node.height: no visible global function definition for ‘reorder’
    plot.dtlik.t: no visible global function definition for ‘predict’
    plot.dtlik.t: no visible global function definition for ‘plot’
    plot.dtlik.t: no visible global function definition for ‘polygon’
    plot.dtlik.t: no visible global function definition for ‘lines’
    plot.dtlik.t: no visible global function definition for ‘legend’
    plot.history: no visible global function definition for ‘par’
    plot.history: no visible global function definition for ‘plot’
    plot.history: no visible global function definition for ‘heat.colors’
    plot2.phylo: no visible global function definition for ‘par’
    plot2.phylo: no visible global function definition for ‘plot’
    pp.clades.phylogram: no visible global function definition for
     ‘polygon’
    pp.coords.phylogram: no visible global function definition for
     ‘reorder’
    pp.lim.fan: no visible global function definition for ‘par’
    pp.lim.fan: no visible global function definition for ‘strwidth’
    pp.node.coords: no visible global function definition for ‘reorder’
    pp.nodelabel.phylogram: no visible global function definition for
     ‘text’
    pp.nodepoints.phylogram: no visible global function definition for
     ‘points’
    pp.segments.phylogram: no visible global function definition for
     ‘segments’
    pp.tiplabel.phylogram: no visible global function definition for
     ‘strwidth’
    pp.tiplabel.phylogram: no visible global function definition for ‘text’
    predict.dtlik.t: no visible global function definition for ‘coef’
    profiles.plot : f: no visible global function definition for ‘hist’
    profiles.plot: no visible global function definition for ‘plot’
    profiles.plot: no visible global function definition for ‘par’
    profiles.plot: no visible global function definition for ‘arrows’
    profiles.plot: no visible global function definition for ‘legend’
    quasse.integrate.fftR: no visible global function definition for ‘fft’
    radial.text: no visible global function definition for ‘text’
    reparam.1: no visible binding for global variable ‘combn’
    residuals.fit.mle.pgls: no visible global function definition for
     ‘fitted’
    residuals.mcmcsamples.pgls: no visible global function definition for
     ‘fitted’
    residuals.pgls.dt: no visible global function definition for ‘fitted’
    rootfunc.bm.contrasts: no visible global function definition for
     ‘dnorm’
    rootfunc.bm.pruning: no visible global function definition for ‘dnorm’
    run.until.change: no visible global function definition for ‘runif’
    sampler.hmc.bounded: no visible global function definition for ‘rnorm’
    sampler.hmc.bounded: no visible global function definition for ‘runif’
    sectors: no visible global function definition for ‘polygon’
    slice.1d: no visible global function definition for ‘rexp’
    slice.isolate: no visible global function definition for ‘runif’
    slice.sample: no visible global function definition for ‘runif’
    starting.point.bd: no visible global function definition for ‘coef’
    starting.point.quasse: no visible global function definition for ‘coef’
    subplexR: no visible global function definition for ‘modifyList’
    trait.plot: no visible global function definition for ‘par’
    trait.plot: no visible global function definition for ‘rect’
    tree.bisse: no visible global function definition for ‘runif’
    tree.bisseness: no visible global function definition for ‘runif’
    Undefined global functions or variables:
     AIC approxfun arrows as.formula coef col2rgb combn dbeta dexp dhyper
     dnorm ecdf fft fitted heat.colors hist legend lines logLik
     mahalanobis model.frame model.matrix modifyList na.fail na.omit nlm
     nlminb now optim optimize par pchisq plot points polygon predict
     quantile rect reorder rexp rgb rnorm runif segments spline strwidth
     text write.csv
    Consider adding
     importFrom("grDevices", "col2rgb", "heat.colors", "rgb")
     importFrom("graphics", "arrows", "hist", "legend", "lines", "par",
     "plot", "points", "polygon", "rect", "segments", "strwidth",
     "text")
     importFrom("stats", "AIC", "approxfun", "as.formula", "coef", "dbeta",
     "dexp", "dhyper", "dnorm", "ecdf", "fft", "fitted",
     "logLik", "mahalanobis", "model.frame", "model.matrix",
     "na.fail", "na.omit", "nlm", "nlminb", "optim", "optimize",
     "pchisq", "predict", "quantile", "reorder", "rexp", "rnorm",
     "runif", "spline")
     importFrom("utils", "combn", "modifyList", "write.csv")
    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: 0.9-7
Check: installed package size
Result: NOTE
     installed size is 5.2Mb
     sub-directories of 1Mb or more:
     libs 4.4Mb
Flavors: r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-osx-x86_64-mavericks

Version: 0.9-7
Check: R code for possible problems
Result: NOTE
    make.every.so.often: no visible global function definition for ‘now’
    make.every.so.often : check: no visible global function definition for
     ‘now’
    Undefined global functions or variables:
     now
Flavor: r-devel-osx-x86_64-clang

Version: 0.9-7
Check: R code for possible problems
Result: NOTE
    make.every.so.often: no visible global function definition for ‘now’
    make.every.so.often : check: no visible global function definition for
     ‘now’
Flavors: r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-x86_64, r-release-osx-x86_64-mavericks, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64