CRAN Package Check Results for Package diversitree

Last updated on 2015-09-04 11:47:32.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.9-7 27.37 63.48 90.84 NOTE
r-devel-linux-x86_64-debian-gcc 0.9-7 30.89 64.27 95.16 NOTE
r-devel-linux-x86_64-fedora-clang 0.9-7 175.86 NOTE
r-devel-linux-x86_64-fedora-gcc 0.9-7 170.52 NOTE
r-devel-osx-x86_64-clang 0.9-7 139.58 NOTE
r-devel-windows-ix86+x86_64 0.9-7 114.00 108.00 222.00 WARN
r-patched-linux-x86_64 0.9-7 30.57 62.27 92.84 NOTE
r-patched-solaris-sparc 0.9-7 1029.10 NOTE
r-patched-solaris-x86 0.9-7 192.00 NOTE
r-release-linux-x86_64 0.9-7 30.80 61.16 91.96 NOTE
r-release-osx-x86_64-mavericks 0.9-7 NOTE
r-release-windows-ix86+x86_64 0.9-7 146.00 178.00 324.00 NOTE
r-oldrel-windows-ix86+x86_64 0.9-7 105.00 141.00 246.00 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.ode.gslode: no visible binding for global variable ‘GslOdeTime’
    make.ode.gslode: no visible binding for global variable
     ‘GslOdeCompiled’
    make.ode.gslode: no visible binding for global variable ‘GslOdeR’
    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.time.machine: no visible binding for global variable ‘TimeMachine’
    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 GslOdeCompiled GslOdeR GslOdeTime TimeMachine 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

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: whether the namespace can be loaded with stated dependencies
Result: WARN
    
    This application has requested the Runtime to terminate it in an unusual way.
    Please contact the application's support team for more information.
    terminate called after throwing an instance of 'Rcpp::eval_error'
     what(): could not find function "new"
    
    A namespace must be able to be loaded with just the base namespace
    loaded: otherwise if the namespace gets loaded by a saved object, the
    session will be unable to start.
    
    Probably some imports need to be declared in the NAMESPACE file.
Flavors: r-devel-windows-ix86+x86_64, r-devel-windows-ix86+x86_64

Version: 0.9-7
Check: R code for possible problems
Result: NOTE
    
    This application has requested the Runtime to terminate it in an unusual way.
    Please contact the application's support team for more information.
    terminate called after throwing an instance of 'Rcpp::eval_error'
     what(): could not find function "new"
Flavor: r-devel-windows-ix86+x86_64

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