CRAN Package Check Results for Package diversitree

Last updated on 2015-07-02 23:47:05.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.9-7 27.65 65.34 92.99 NOTE
r-devel-linux-x86_64-debian-gcc 0.9-7 31.02 61.05 92.07 NOTE
r-devel-linux-x86_64-fedora-clang 0.9-7 175.65 NOTE
r-devel-linux-x86_64-fedora-gcc 0.9-7 167.40 NOTE
r-devel-osx-x86_64-clang 0.9-7 142.99 NOTE
r-devel-windows-ix86+x86_64 0.9-7 115.00 122.00 237.00 NOTE
r-patched-linux-x86_64 0.9-7 30.80 59.88 90.68 NOTE
r-patched-solaris-sparc 0.9-7 1110.60 NOTE
r-patched-solaris-x86 0.9-7 202.70 NOTE
r-release-linux-x86_64 0.9-7 32.02 59.81 91.82 NOTE
r-release-osx-x86_64-mavericks 0.9-7 NOTE
r-release-windows-ix86+x86_64 0.9-7 113.00 133.00 246.00 NOTE
r-oldrel-windows-ix86+x86_64 0.9-7 123.00 141.00 264.00 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 ‘matplot’
    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 matplot 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
Flavors: r-devel-linux-x86_64-debian-clang, 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 5.1Mb
     sub-directories of 1Mb or more:
     libs 4.3Mb
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-patched-solaris-sparc, r-release-linux-x86_64, r-release-osx-x86_64-mavericks

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 ‘matplot’
    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’
Flavor: r-devel-linux-x86_64-debian-gcc

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