CRAN Package Check Results for Package geiger

Last updated on 2015-09-01 23:48:24.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 2.0.3 17.87 54.42 72.29 NOTE --no-vignettes
r-devel-linux-x86_64-debian-gcc 2.0.3 21.31 52.22 73.53 NOTE --no-vignettes
r-devel-linux-x86_64-fedora-clang 2.0.3 141.36 NOTE
r-devel-linux-x86_64-fedora-gcc 2.0.3 137.49 NOTE
r-devel-osx-x86_64-clang 2.0.3 119.53 NOTE --no-build-vignettes
r-devel-windows-ix86+x86_64 2.0.3 76.00 141.00 217.00 NOTE
r-patched-linux-x86_64 2.0.3 22.65 56.08 78.73 NOTE --no-vignettes
r-patched-solaris-sparc 2.0.3 867.70 NOTE --no-vignettes
r-patched-solaris-x86 2.0.3 166.30 NOTE
r-release-linux-x86_64 2.0.3 21.82 53.84 75.66 NOTE --no-vignettes
r-release-osx-x86_64-mavericks 2.0.3 NOTE
r-release-windows-ix86+x86_64 2.0.3 77.00 150.00 227.00 NOTE
r-oldrel-windows-ix86+x86_64 2.0.3 85.00 177.00 262.00 NOTE

Check Details

Version: 2.0.3
Flags: --no-vignettes
Check: DESCRIPTION meta-information
Result: NOTE
    Malformed Description field: should contain one or more complete sentences.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-patched-solaris-sparc, r-release-linux-x86_64

Version: 2.0.3
Flags: --no-vignettes
Check: dependencies in R code
Result: NOTE
    'library' or 'require' calls in package code:
     ‘colorspace’ ‘msm’ ‘ncbit’ ‘parallel’ ‘pls’
     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-patched-linux-x86_64, r-patched-solaris-sparc, r-release-linux-x86_64

Version: 2.0.3
Flags: --no-vignettes
Check: S3 generic/method consistency
Result: NOTE
    Found the following apparent S3 methods exported but not registered:
     as.phylo.hphylo
    See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
    manual.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-patched-solaris-sparc, r-release-linux-x86_64

Version: 2.0.3
Flags: --no-vignettes
Check: foreign function calls
Result: NOTE
    Call with DUP:
     .C("r_mkn_core", k = as.integer(k), n = length(order.C) - 1L,
     order = order.C, children = children.C, pij = pij, init = branch.init,
     base = branch.base, lq = lq, NAOK = TRUE, DUP = FALSE, PACKAGE = "geiger")
    DUP is no longer supported and will be ignored.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-patched-solaris-sparc, r-release-linux-x86_64

Version: 2.0.3
Flags: --no-vignettes
Check: R code for possible problems
Result: NOTE
    .TESTING.ultrametricize.phylo: no visible global function definition
     for ‘reorder’
    .acegram: no visible global function definition for ‘plot’
    .acegram: no visible global function definition for ‘lines’
    .acegram: no visible global function definition for ‘text’
    .acegram: no visible global function definition for ‘points’
    .adjustrate: no visible global function definition for ‘runif’
    .adjustvalue: no visible global function definition for ‘runif’
    .back.step.medusa: no visible global function definition for
     ‘weighted.mean’
    .bm.lik.fn.reml: no visible global function definition for ‘dnorm’
    .bm.rate.mle: no visible global function definition for ‘var’
    .bnd.hessian: no visible global function definition for ‘qnorm’
    .branchcol.plot : <anonymous>: no visible global function definition
     for ‘median’
    .branchcol.plot: no visible global function definition for ‘median’
    .branchcol.plot: no visible global function definition for
     ‘diverge_hcl’
    .cache.descendants: no visible global function definition for ‘reorder’
    .check.control.mkn: no visible global function definition for
     ‘modifyList’
    .check.control.ode: no visible global function definition for
     ‘modifyList’
    .check.parallel: no visible global function definition for
     ‘installed.packages’
    .check.states: no visible global function definition for ‘na.omit’
    .constrain.parse: no visible global function definition for
     ‘as.formula’
    .disparity: no visible global function definition for ‘dist’
    .drop.tip: no visible global function definition for ‘reorder’
    .dtt.polygon : <anonymous>: no visible global function definition for
     ‘quantile’
    .fit.partition.medusa: no visible global function definition for
     ‘optim’
    .fit.partition.medusa: no visible global function definition for
     ‘optimize’
    .get.parallel: no visible global function definition for ‘detectCores’
    .get.parallel : fx: no visible global function definition for
     ‘mclapply’
    .get.profile.likelihoods: no visible global function definition for
     ‘uniroot’
    .jumps.plot: no visible global function definition for ‘reorder’
    .jumps.plot: no visible global function definition for ‘diverge_hcl’
    .jumps.plot: no visible global function definition for ‘par’
    .jumps.plot: no visible global function definition for ‘layout’
    .jumps.plot: no visible global function definition for ‘plot’
    .jumps.plot: no visible global function definition for ‘mtext’
    .jumps.plot: no visible global function definition for ‘text’
    .laser.getlambda: no visible global function definition for ‘optimize’
    .make.ode.deSolve: no visible global function definition for
     ‘packageVersion’
    .make.ode.deSolve: no visible global function definition for
     ‘packageDescription’
    .mcmc : unipr : <anonymous>: no visible global function definition for
     ‘dunif’
    .mcmc : tnormpr: no visible global function definition for ‘pnorm’
    .mcmc : tnormpr : <anonymous>: no visible global function definition
     for ‘dnorm’
    .mcmc : getstart : fx: no visible global function definition for
     ‘runif’
    .mcmc: no visible global function definition for ‘runif’
    .mecca.acceptance: no visible global function definition for ‘dnorm’
    .mecca.acceptance: no visible global function definition for ‘runif’
    .mecca.calproposal: no visible global function definition for ‘runif’
    .mecca.fastbm: no visible global function definition for ‘rnorm’
    .mecca.fasttreesim: no visible global function definition for ‘runif’
    .mecca.generatetipsummaries: no visible global function definition for
     ‘var’
    .mecca.getproposal: no visible global function definition for ‘runif’
    .mecca.nodestatestworate: no visible global function definition for
     ‘rnorm’
    .mecca.normalpriorratio: no visible global function definition for
     ‘dnorm’
    .mecca.normalpriorratio: no visible global function definition for
     ‘runif’
    .mecca.priordrawbirth: no visible global function definition for
     ‘runif’
    .mecca.priordrawdeath: no visible global function definition for
     ‘runif’
    .mecca.priordrawmean: no visible global function definition for ‘runif’
    .mecca.priordrawmean: no visible global function definition for ‘rnorm’
    .mecca.priordrawsig: no visible global function definition for ‘runif’
    .mecca.priordrawsig: no visible global function definition for ‘rnorm’
    .mecca.singletiptrait: no visible global function definition for
     ‘rnorm’
    .nodeheights: no visible global function definition for ‘reorder’
    .oldestyle.gfit.continuous: no visible global function definition for
     ‘logLik’
    .oldestyle.gfit.discrete: no visible global function definition for
     ‘logLik’
    .ou.smartstart: no visible global function definition for ‘var’
    .parlog.rjmcmc: no visible global function definition for ‘write.table’
    .parlog.rjmcmc: no visible global function definition for ‘median’
    .paths.phylo: no visible global function definition for ‘reorder’
    .pic_variance.phylo: no visible global function definition for
     ‘reorder’
    .pp.getproposal: no visible global function definition for ‘runif’
    .prepare.bm.univariate: no visible global function definition for
     ‘reorder’
    .prepare.gbm.univariate : <anonymous>: no visible global function
     definition for ‘dexp’
    .prepare.gbm.univariate : <anonymous>: no visible global function
     definition for ‘dunif’
    .proposal.multiplier: no visible global function definition for ‘runif’
    .proposal.slidingwindow: no visible global function definition for
     ‘runif’
    .rcount: no visible global function definition for ‘runif’
    .replace.tip.with.subtree: no visible global function definition for
     ‘reorder’
    .root.bm.direct: no visible global function definition for ‘dnorm’
    .set.seed.clock: no visible global function definition for ‘runif’
    .shifts.plot: no visible global function definition for ‘reorder’
    .shifts.plot: no visible binding for global variable ‘median’
    .shifts.plot: no visible global function definition for ‘diverge_hcl’
    .shifts.plot: no visible global function definition for ‘par’
    .shifts.plot: no visible global function definition for ‘layout’
    .shifts.plot: no visible global function definition for ‘plot’
    .shifts.plot: no visible global function definition for ‘mtext’
    .shifts.plot: no visible global function definition for ‘text’
    .slater.dnodeprior: no visible global function definition for ‘dnorm’
    .slater.dnodeprior: no visible global function definition for ‘dunif’
    .slater.dnodeprior: no visible global function definition for ‘dexp’
    .slater.generatestartingvalues: no visible global function definition
     for ‘rnorm’
    .slater.generatestartingvalues: no visible global function definition
     for ‘runif’
    .slater.generatestartingvalues: no visible global function definition
     for ‘rexp’
    .slater.getproposal: no visible global function definition for ‘runif’
    .slater.initiate: no visible global function definition for ‘na.omit’
    .splitormerge : .splitrate: no visible global function definition for
     ‘runif’
    .startingpt.bm: no visible global function definition for ‘runif’
    .subset.auteurRAW : trim: no visible global function definition for
     ‘as’
    .subset.auteurRAW: no visible global function definition for
     ‘read.table’
    .traceplot : .infer.y: no visible global function definition for ‘lm’
    .traceplot : .infer.y: no visible global function definition for ‘coef’
    .traceplot: no visible global function definition for ‘gray.colors’
    .traceplot : <anonymous>: no visible global function definition for
     ‘density’
    .traceplot: no visible global function definition for ‘plot’
    .traceplot: no visible global function definition for ‘polygon’
    .traceplot: no visible global function definition for ‘lines’
    .traceplot: no visible global function definition for ‘arrows’
    .traceplot: no visible global function definition for ‘points’
    .traceplot: no visible global function definition for ‘legend’
    .transparency: no visible global function definition for ‘col2rgb’
    .transparency: no visible global function definition for ‘rgb’
    .treeslide: no visible global function definition for ‘runif’
    .tune.SE: no visible global function definition for ‘runif’
    .tune.rate: no visible global function definition for ‘runif’
    .tune.value: no visible global function definition for ‘runif’
    aicm: no visible global function definition for ‘var’
    aov.phylo: no visible global function definition for ‘summary.manova’
    aov.phylo: no visible global function definition for ‘manova’
    aov.phylo : FUN: no visible global function definition for
     ‘summary.manova’
    aov.phylo : FUN: no visible global function definition for ‘manova’
    aov.phylo: no visible global function definition for ‘anova’
    aov.phylo: no visible global function definition for ‘lm’
    aov.phylo : FUN: no visible global function definition for ‘anova’
    aov.phylo : FUN: no visible global function definition for ‘lm’
    calibrate.mecca: no visible global function definition for
     ‘txtProgressBar’
    calibrate.mecca: no visible global function definition for ‘runif’
    calibrate.mecca: no visible global function definition for
     ‘setTxtProgressBar’
    calibrate.mecca : lmreturn: no visible global function definition for
     ‘as.formula’
    calibrate.mecca : lmreturn: no visible global function definition for
     ‘optimize’
    calibrate.mecca: no visible global function definition for ‘sd’
    calibrate.rjmcmc: no visible global function definition for ‘spline’
    coef.gfits: no visible binding for global variable ‘coef’
    crown.limits: no visible global function definition for ‘optim’
    dtpois: no visible global function definition for ‘dpois’
    dtt: no visible binding for global variable ‘median’
    dtt: no visible global function definition for ‘polygon’
    dtt: no visible global function definition for ‘lines’
    ex.jumpsimulator : .jumpsim: no visible global function definition for
     ‘reorder’
    ex.jumpsimulator : .jumpsim: no visible global function definition for
     ‘rexp’
    ex.jumpsimulator : .jumpsim: no visible global function definition for
     ‘rnorm’
    ex.ratesimulator: no visible global function definition for ‘dev.new’
    ex.ratesimulator: no visible global function definition for ‘plot’
    ex.ratesimulator: no visible global function definition for ‘mtext’
    ex.traitgram: no visible global function definition for ‘plot’
    ex.traitgram: no visible global function definition for ‘lines’
    ex.traitgram: no visible global function definition for ‘points’
    fitContinuous : <anonymous> : <anonymous>: no visible global function
     definition for ‘runif’
    fitContinuous : <anonymous>: no visible global function definition for
     ‘runif’
    fitContinuous : <anonymous>: no visible global function definition for
     ‘var’
    fitContinuous : <anonymous>: no visible global function definition for
     ‘optim’
    fitContinuousMCMC: no visible global function definition for ‘runif’
    fitContinuousMCMC: no visible global function definition for ‘na.omit’
    fitDiscrete : <anonymous> : <anonymous>: no visible global function
     definition for ‘runif’
    fitDiscrete : <anonymous>: no visible global function definition for
     ‘runif’
    fitDiscrete : <anonymous>: no visible global function definition for
     ‘optim’
    gbcontain: no visible global function definition for ‘ncbit’
    gbresolve.default: no visible global function definition for ‘ncbit’
    hdr : hdr.uniroot: no visible global function definition for ‘ecdf’
    hdr : hdr.uniroot: no visible global function definition for
     ‘approxfun’
    hdr : hdr.uniroot: no visible global function definition for ‘optimize’
    hdr: no visible global function definition for ‘quantile’
    heights.phylo: no visible global function definition for ‘reorder’
    mecca: no visible global function definition for ‘write.table’
    mecca: no visible global function definition for ‘runif’
    mecca: no visible global function definition for ‘dist’
    medusa : medusa_runner : runStepwiseAIC: no visible global function
     definition for ‘tail’
    mkn.lik: no visible global function definition for ‘reorder’
    nh.test: no visible global function definition for ‘plot’
    nh.test: no visible global function definition for ‘lm’
    plot.medusa: no visible global function definition for ‘plot’
    plot.rjmcmc: no visible global function definition for
     ‘dev.interactive’
    plot.rjmcmc: no visible global function definition for ‘par’
    plot.rjmcmc: no visible global function definition for ‘start’
    plot.rjmcmc: no visible global function definition for ‘end’
    plot.rjmcmc.list: no visible global function definition for
     ‘dev.interactive’
    plot.rjmcmc.list: no visible global function definition for ‘par’
    pp.mcmc: no visible global function definition for ‘runif’
    pp.mcmc: no visible global function definition for ‘lm’
    print.gfit : solnfreq: no visible global function definition for
     ‘logLik’
    print.mcmc.list: no visible global function definition for ‘start’
    print.mcmc.list: no visible global function definition for ‘end’
    print.rjmcmc: no visible global function definition for ‘start’
    print.rjmcmc: no visible global function definition for ‘end’
    print.rjmcmcmc: no visible global function definition for ‘start’
    print.rjmcmcmc: no visible global function definition for ‘end’
    rjmcmc.bm: no visible global function definition for ‘runif’
    sem: no visible global function definition for ‘sd’
    sim.bd: no visible global function definition for ‘rexp’
    sim.bd: no visible global function definition for ‘runif’
    sim.bdtree: no visible global function definition for ‘rexp’
    sim.bdtree: no visible global function definition for ‘runif’
    sim.char : .get.state: no visible global function definition for
     ‘runif’
    sim.mecca: no visible global function definition for ‘var’
    startingpt.mecca: no visible global function definition for ‘dist’
    startingpt.mecca: no visible global function definition for ‘sd’
    Undefined global functions or variables:
     anova approxfun arrows as as.formula coef col2rgb density detectCores
     dev.interactive dev.new dexp dist diverge_hcl dnorm dpois dunif ecdf
     end gray.colors installed.packages layout legend lines lm logLik
     manova mclapply median modifyList mtext na.omit ncbit optim optimize
     packageDescription packageVersion par plot pnorm points polygon qnorm
     quantile read.table reorder rexp rgb rnorm runif sd setTxtProgressBar
     spline start summary.manova tail text txtProgressBar uniroot var
     weighted.mean write.table
    Consider adding
     importFrom("grDevices", "col2rgb", "dev.interactive", "dev.new",
     "gray.colors", "rgb")
     importFrom("graphics", "arrows", "layout", "legend", "lines", "mtext",
     "par", "plot", "points", "polygon", "text")
     importFrom("methods", "as")
     importFrom("stats", "anova", "approxfun", "as.formula", "coef",
     "density", "dexp", "dist", "dnorm", "dpois", "dunif",
     "ecdf", "end", "lm", "logLik", "manova", "median",
     "na.omit", "optim", "optimize", "pnorm", "qnorm",
     "quantile", "reorder", "rexp", "rnorm", "runif", "sd",
     "spline", "start", "summary.manova", "uniroot", "var",
     "weighted.mean")
     importFrom("utils", "installed.packages", "modifyList",
     "packageDescription", "packageVersion", "read.table",
     "setTxtProgressBar", "tail", "txtProgressBar",
     "write.table")
    to your NAMESPACE (and ensure that your DESCRIPTION Imports field
    contains 'methods').
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Version: 2.0.3
Check: DESCRIPTION meta-information
Result: NOTE
    Malformed Description field: should contain one or more complete sentences.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64, r-patched-solaris-x86, r-release-osx-x86_64-mavericks, r-release-windows-ix86+x86_64

Version: 2.0.3
Check: dependencies in R code
Result: NOTE
    'library' or 'require' calls in package code:
     ‘colorspace’ ‘msm’ ‘ncbit’ ‘parallel’ ‘pls’
     Please use :: or requireNamespace() instead.
     See section 'Suggested packages' in the 'Writing R Extensions' manual.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64, r-patched-solaris-x86, r-release-osx-x86_64-mavericks, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 2.0.3
Check: S3 generic/method consistency
Result: NOTE
    Found the following apparent S3 methods exported but not registered:
     as.phylo.hphylo
    See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
    manual.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-solaris-x86

Version: 2.0.3
Check: foreign function calls
Result: NOTE
    Call with DUP:
     .C("r_mkn_core", k = as.integer(k), n = length(order.C) - 1L,
     order = order.C, children = children.C, pij = pij, init = branch.init,
     base = branch.base, lq = lq, NAOK = TRUE, DUP = FALSE, PACKAGE = "geiger")
    DUP is no longer supported and will be ignored.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64, r-patched-solaris-x86, r-release-osx-x86_64-mavericks, r-release-windows-ix86+x86_64

Version: 2.0.3
Check: R code for possible problems
Result: NOTE
    .TESTING.ultrametricize.phylo: no visible global function definition
     for ‘reorder’
    .acegram: no visible global function definition for ‘plot’
    .acegram: no visible global function definition for ‘lines’
    .acegram: no visible global function definition for ‘text’
    .acegram: no visible global function definition for ‘points’
    .adjustrate: no visible global function definition for ‘runif’
    .adjustvalue: no visible global function definition for ‘runif’
    .back.step.medusa: no visible global function definition for
     ‘weighted.mean’
    .bm.lik.fn.reml: no visible global function definition for ‘dnorm’
    .bm.rate.mle: no visible global function definition for ‘var’
    .bnd.hessian: no visible global function definition for ‘qnorm’
    .branchcol.plot : <anonymous>: no visible global function definition
     for ‘median’
    .branchcol.plot: no visible global function definition for ‘median’
    .branchcol.plot: no visible global function definition for
     ‘diverge_hcl’
    .cache.descendants: no visible global function definition for ‘reorder’
    .check.control.mkn: no visible global function definition for
     ‘modifyList’
    .check.control.ode: no visible global function definition for
     ‘modifyList’
    .check.parallel: no visible global function definition for
     ‘installed.packages’
    .check.states: no visible global function definition for ‘na.omit’
    .constrain.parse: no visible global function definition for
     ‘as.formula’
    .disparity: no visible global function definition for ‘dist’
    .drop.tip: no visible global function definition for ‘reorder’
    .dtt.polygon : <anonymous>: no visible global function definition for
     ‘quantile’
    .fit.partition.medusa: no visible global function definition for
     ‘optim’
    .fit.partition.medusa: no visible global function definition for
     ‘optimize’
    .get.parallel: no visible global function definition for ‘detectCores’
    .get.parallel : fx: no visible global function definition for
     ‘mclapply’
    .get.profile.likelihoods: no visible global function definition for
     ‘uniroot’
    .jumps.plot: no visible global function definition for ‘reorder’
    .jumps.plot: no visible global function definition for ‘diverge_hcl’
    .jumps.plot: no visible global function definition for ‘par’
    .jumps.plot: no visible global function definition for ‘layout’
    .jumps.plot: no visible global function definition for ‘plot’
    .jumps.plot: no visible global function definition for ‘mtext’
    .jumps.plot: no visible global function definition for ‘text’
    .laser.getlambda: no visible global function definition for ‘optimize’
    .make.ode.deSolve: no visible global function definition for
     ‘packageVersion’
    .make.ode.deSolve: no visible global function definition for
     ‘packageDescription’
    .mcmc : unipr : <anonymous>: no visible global function definition for
     ‘dunif’
    .mcmc : tnormpr: no visible global function definition for ‘pnorm’
    .mcmc : tnormpr : <anonymous>: no visible global function definition
     for ‘dnorm’
    .mcmc : getstart : fx: no visible global function definition for
     ‘runif’
    .mcmc: no visible global function definition for ‘runif’
    .mecca.acceptance: no visible global function definition for ‘dnorm’
    .mecca.acceptance: no visible global function definition for ‘runif’
    .mecca.calproposal: no visible global function definition for ‘runif’
    .mecca.fastbm: no visible global function definition for ‘rnorm’
    .mecca.fasttreesim: no visible global function definition for ‘runif’
    .mecca.generatetipsummaries: no visible global function definition for
     ‘var’
    .mecca.getproposal: no visible global function definition for ‘runif’
    .mecca.nodestatestworate: no visible global function definition for
     ‘rnorm’
    .mecca.normalpriorratio: no visible global function definition for
     ‘dnorm’
    .mecca.normalpriorratio: no visible global function definition for
     ‘runif’
    .mecca.priordrawbirth: no visible global function definition for
     ‘runif’
    .mecca.priordrawdeath: no visible global function definition for
     ‘runif’
    .mecca.priordrawmean: no visible global function definition for ‘runif’
    .mecca.priordrawmean: no visible global function definition for ‘rnorm’
    .mecca.priordrawsig: no visible global function definition for ‘runif’
    .mecca.priordrawsig: no visible global function definition for ‘rnorm’
    .mecca.singletiptrait: no visible global function definition for
     ‘rnorm’
    .nodeheights: no visible global function definition for ‘reorder’
    .oldestyle.gfit.continuous: no visible global function definition for
     ‘logLik’
    .oldestyle.gfit.discrete: no visible global function definition for
     ‘logLik’
    .ou.smartstart: no visible global function definition for ‘var’
    .parlog.rjmcmc: no visible global function definition for ‘write.table’
    .parlog.rjmcmc: no visible global function definition for ‘median’
    .paths.phylo: no visible global function definition for ‘reorder’
    .pic_variance.phylo: no visible global function definition for
     ‘reorder’
    .pp.getproposal: no visible global function definition for ‘runif’
    .prepare.bm.univariate: no visible global function definition for
     ‘reorder’
    .prepare.gbm.univariate : <anonymous>: no visible global function
     definition for ‘dexp’
    .prepare.gbm.univariate : <anonymous>: no visible global function
     definition for ‘dunif’
    .proposal.multiplier: no visible global function definition for ‘runif’
    .proposal.slidingwindow: no visible global function definition for
     ‘runif’
    .rcount: no visible global function definition for ‘runif’
    .replace.tip.with.subtree: no visible global function definition for
     ‘reorder’
    .root.bm.direct: no visible global function definition for ‘dnorm’
    .set.seed.clock: no visible global function definition for ‘runif’
    .shifts.plot: no visible global function definition for ‘reorder’
    .shifts.plot: no visible binding for global variable ‘median’
    .shifts.plot: no visible global function definition for ‘diverge_hcl’
    .shifts.plot: no visible global function definition for ‘par’
    .shifts.plot: no visible global function definition for ‘layout’
    .shifts.plot: no visible global function definition for ‘plot’
    .shifts.plot: no visible global function definition for ‘mtext’
    .shifts.plot: no visible global function definition for ‘text’
    .slater.dnodeprior: no visible global function definition for ‘dnorm’
    .slater.dnodeprior: no visible global function definition for ‘dunif’
    .slater.dnodeprior: no visible global function definition for ‘dexp’
    .slater.generatestartingvalues: no visible global function definition
     for ‘rnorm’
    .slater.generatestartingvalues: no visible global function definition
     for ‘runif’
    .slater.generatestartingvalues: no visible global function definition
     for ‘rexp’
    .slater.getproposal: no visible global function definition for ‘runif’
    .slater.initiate: no visible global function definition for ‘na.omit’
    .splitormerge : .splitrate: no visible global function definition for
     ‘runif’
    .startingpt.bm: no visible global function definition for ‘runif’
    .subset.auteurRAW : trim: no visible global function definition for
     ‘as’
    .subset.auteurRAW: no visible global function definition for
     ‘read.table’
    .traceplot : .infer.y: no visible global function definition for ‘lm’
    .traceplot : .infer.y: no visible global function definition for ‘coef’
    .traceplot: no visible global function definition for ‘gray.colors’
    .traceplot : <anonymous>: no visible global function definition for
     ‘density’
    .traceplot: no visible global function definition for ‘plot’
    .traceplot: no visible global function definition for ‘polygon’
    .traceplot: no visible global function definition for ‘lines’
    .traceplot: no visible global function definition for ‘arrows’
    .traceplot: no visible global function definition for ‘points’
    .traceplot: no visible global function definition for ‘legend’
    .transparency: no visible global function definition for ‘col2rgb’
    .transparency: no visible global function definition for ‘rgb’
    .treeslide: no visible global function definition for ‘runif’
    .tune.SE: no visible global function definition for ‘runif’
    .tune.rate: no visible global function definition for ‘runif’
    .tune.value: no visible global function definition for ‘runif’
    aicm: no visible global function definition for ‘var’
    aov.phylo: no visible global function definition for ‘summary.manova’
    aov.phylo: no visible global function definition for ‘manova’
    aov.phylo : FUN: no visible global function definition for
     ‘summary.manova’
    aov.phylo : FUN: no visible global function definition for ‘manova’
    aov.phylo: no visible global function definition for ‘anova’
    aov.phylo: no visible global function definition for ‘lm’
    aov.phylo : FUN: no visible global function definition for ‘anova’
    aov.phylo : FUN: no visible global function definition for ‘lm’
    calibrate.mecca: no visible global function definition for
     ‘txtProgressBar’
    calibrate.mecca: no visible global function definition for ‘runif’
    calibrate.mecca: no visible global function definition for
     ‘setTxtProgressBar’
    calibrate.mecca : lmreturn: no visible global function definition for
     ‘as.formula’
    calibrate.mecca : lmreturn: no visible global function definition for
     ‘optimize’
    calibrate.mecca: no visible global function definition for ‘sd’
    calibrate.rjmcmc: no visible global function definition for ‘spline’
    coef.gfits: no visible binding for global variable ‘coef’
    crown.limits: no visible global function definition for ‘optim’
    dtpois: no visible global function definition for ‘dpois’
    dtt: no visible binding for global variable ‘median’
    dtt: no visible global function definition for ‘polygon’
    dtt: no visible global function definition for ‘lines’
    ex.jumpsimulator : .jumpsim: no visible global function definition for
     ‘reorder’
    ex.jumpsimulator : .jumpsim: no visible global function definition for
     ‘rexp’
    ex.jumpsimulator : .jumpsim: no visible global function definition for
     ‘rnorm’
    ex.ratesimulator: no visible global function definition for ‘dev.new’
    ex.ratesimulator: no visible global function definition for ‘plot’
    ex.ratesimulator: no visible global function definition for ‘mtext’
    ex.traitgram: no visible global function definition for ‘plot’
    ex.traitgram: no visible global function definition for ‘lines’
    ex.traitgram: no visible global function definition for ‘points’
    fitContinuous : <anonymous> : <anonymous>: no visible global function
     definition for ‘runif’
    fitContinuous : <anonymous>: no visible global function definition for
     ‘runif’
    fitContinuous : <anonymous>: no visible global function definition for
     ‘var’
    fitContinuous : <anonymous>: no visible global function definition for
     ‘optim’
    fitContinuousMCMC: no visible global function definition for ‘runif’
    fitContinuousMCMC: no visible global function definition for ‘na.omit’
    fitDiscrete : <anonymous> : <anonymous>: no visible global function
     definition for ‘runif’
    fitDiscrete : <anonymous>: no visible global function definition for
     ‘runif’
    fitDiscrete : <anonymous>: no visible global function definition for
     ‘optim’
    gbcontain: no visible global function definition for ‘ncbit’
    gbresolve.default: no visible global function definition for ‘ncbit’
    hdr : hdr.uniroot: no visible global function definition for ‘ecdf’
    hdr : hdr.uniroot: no visible global function definition for
     ‘approxfun’
    hdr : hdr.uniroot: no visible global function definition for ‘optimize’
    hdr: no visible global function definition for ‘quantile’
    heights.phylo: no visible global function definition for ‘reorder’
    mecca: no visible global function definition for ‘write.table’
    mecca: no visible global function definition for ‘runif’
    mecca: no visible global function definition for ‘dist’
    medusa : medusa_runner : runStepwiseAIC: no visible global function
     definition for ‘tail’
    mkn.lik: no visible global function definition for ‘reorder’
    nh.test: no visible global function definition for ‘plot’
    nh.test: no visible global function definition for ‘lm’
    plot.medusa: no visible global function definition for ‘plot’
    plot.rjmcmc: no visible global function definition for
     ‘dev.interactive’
    plot.rjmcmc: no visible global function definition for ‘par’
    plot.rjmcmc: no visible global function definition for ‘start’
    plot.rjmcmc: no visible global function definition for ‘end’
    plot.rjmcmc.list: no visible global function definition for
     ‘dev.interactive’
    plot.rjmcmc.list: no visible global function definition for ‘par’
    pp.mcmc: no visible global function definition for ‘runif’
    pp.mcmc: no visible global function definition for ‘lm’
    print.gfit : solnfreq: no visible global function definition for
     ‘logLik’
    print.mcmc.list: no visible global function definition for ‘start’
    print.mcmc.list: no visible global function definition for ‘end’
    print.rjmcmc: no visible global function definition for ‘start’
    print.rjmcmc: no visible global function definition for ‘end’
    print.rjmcmcmc: no visible global function definition for ‘start’
    print.rjmcmcmc: no visible global function definition for ‘end’
    rjmcmc.bm: no visible global function definition for ‘runif’
    sem: no visible global function definition for ‘sd’
    sim.bd: no visible global function definition for ‘rexp’
    sim.bd: no visible global function definition for ‘runif’
    sim.bdtree: no visible global function definition for ‘rexp’
    sim.bdtree: no visible global function definition for ‘runif’
    sim.char : .get.state: no visible global function definition for
     ‘runif’
    sim.mecca: no visible global function definition for ‘var’
    startingpt.mecca: no visible global function definition for ‘dist’
    startingpt.mecca: no visible global function definition for ‘sd’
    Undefined global functions or variables:
     anova approxfun arrows as as.formula coef col2rgb density detectCores
     dev.interactive dev.new dexp dist diverge_hcl dnorm dpois dunif ecdf
     end gray.colors installed.packages layout legend lines lm logLik
     manova mclapply median modifyList mtext na.omit ncbit optim optimize
     packageDescription packageVersion par plot pnorm points polygon qnorm
     quantile read.table reorder rexp rgb rnorm runif sd setTxtProgressBar
     spline start summary.manova tail text txtProgressBar uniroot var
     weighted.mean write.table
    Consider adding
     importFrom("grDevices", "col2rgb", "dev.interactive", "dev.new",
     "gray.colors", "rgb")
     importFrom("graphics", "arrows", "layout", "legend", "lines", "mtext",
     "par", "plot", "points", "polygon", "text")
     importFrom("methods", "as")
     importFrom("stats", "anova", "approxfun", "as.formula", "coef",
     "density", "dexp", "dist", "dnorm", "dpois", "dunif",
     "ecdf", "end", "lm", "logLik", "manova", "median",
     "na.omit", "optim", "optimize", "pnorm", "qnorm",
     "quantile", "reorder", "rexp", "rnorm", "runif", "sd",
     "spline", "start", "summary.manova", "uniroot", "var",
     "weighted.mean")
     importFrom("utils", "installed.packages", "modifyList",
     "packageDescription", "packageVersion", "read.table",
     "setTxtProgressBar", "tail", "txtProgressBar",
     "write.table")
    to your NAMESPACE (and ensure that your DESCRIPTION Imports field
    contains 'methods').
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64

Version: 2.0.3
Flags: --no-build-vignettes
Check: DESCRIPTION meta-information
Result: NOTE
    Malformed Description field: should contain one or more complete sentences.
Flavor: r-devel-osx-x86_64-clang

Version: 2.0.3
Flags: --no-build-vignettes
Check: dependencies in R code
Result: NOTE
    'library' or 'require' calls in package code:
     ‘colorspace’ ‘msm’ ‘ncbit’ ‘parallel’ ‘pls’
     Please use :: or requireNamespace() instead.
     See section 'Suggested packages' in the 'Writing R Extensions' manual.
Flavor: r-devel-osx-x86_64-clang

Version: 2.0.3
Flags: --no-build-vignettes
Check: S3 generic/method consistency
Result: NOTE
    Found the following apparent S3 methods exported but not registered:
     as.phylo.hphylo
    See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
    manual.
Flavor: r-devel-osx-x86_64-clang

Version: 2.0.3
Flags: --no-build-vignettes
Check: foreign function calls
Result: NOTE
    Call with DUP:
     .C("r_mkn_core", k = as.integer(k), n = length(order.C) - 1L,
     order = order.C, children = children.C, pij = pij, init = branch.init,
     base = branch.base, lq = lq, NAOK = TRUE, DUP = FALSE, PACKAGE = "geiger")
    DUP is no longer supported and will be ignored.
Flavor: r-devel-osx-x86_64-clang

Version: 2.0.3
Flags: --no-build-vignettes
Check: R code for possible problems
Result: NOTE
    .branchcol.plot: no visible global function definition for
     ‘diverge_hcl’
    .get.parallel: no visible global function definition for ‘detectCores’
    .get.parallel : fx: no visible global function definition for
     ‘mclapply’
    .jumps.plot: no visible global function definition for ‘diverge_hcl’
    .shifts.plot: no visible global function definition for ‘diverge_hcl’
    gbcontain: no visible global function definition for ‘ncbit’
    gbresolve.default: no visible global function definition for ‘ncbit’
    Undefined global functions or variables:
     detectCores diverge_hcl mclapply ncbit
Flavor: r-devel-osx-x86_64-clang

Version: 2.0.3
Flags: --no-vignettes
Check: R code for possible problems
Result: NOTE
    .branchcol.plot: no visible global function definition for
     ‘diverge_hcl’
    .get.parallel: no visible global function definition for ‘detectCores’
    .get.parallel : fx: no visible global function definition for
     ‘mclapply’
    .jumps.plot: no visible global function definition for ‘diverge_hcl’
    .shifts.plot: no visible global function definition for ‘diverge_hcl’
    gbcontain: no visible global function definition for ‘ncbit’
    gbresolve.default: no visible global function definition for ‘ncbit’
Flavors: r-patched-linux-x86_64, r-patched-solaris-sparc, r-release-linux-x86_64

Version: 2.0.3
Check: R code for possible problems
Result: NOTE
    .branchcol.plot: no visible global function definition for
     ‘diverge_hcl’
    .get.parallel: no visible global function definition for ‘detectCores’
    .get.parallel : fx: no visible global function definition for
     ‘mclapply’
    .jumps.plot: no visible global function definition for ‘diverge_hcl’
    .shifts.plot: no visible global function definition for ‘diverge_hcl’
    gbcontain: no visible global function definition for ‘ncbit’
    gbresolve.default: no visible global function definition for ‘ncbit’
Flavors: r-patched-solaris-x86, r-release-osx-x86_64-mavericks, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 2.0.3
Check: foreign function calls
Result: NOTE
    Call with DUP != TRUE:
     .C("r_mkn_core", k = as.integer(k), n = length(order.C) - 1L,
     order = order.C, children = children.C, pij = pij, init = branch.init,
     base = branch.base, lq = lq, NAOK = TRUE, DUP = FALSE, PACKAGE = "geiger")
    DUP = FALSE is deprecated and will be disabled in future versions of R.
Flavor: r-oldrel-windows-ix86+x86_64