CRAN Package Check Results for Package caper

Last updated on 2016-10-25 23:47:30.

Check Details

Version: 0.5.2
Check: S3 generic/method consistency
Result: NOTE
    Found the following apparent S3 methods exported but not registered:
     anova.caic anova.caiclist anova.pgls anova.pglslist
     as.comparative.data.growTree coef.caic coef.pgls fitted.pgls
     logLik.caic logLik.pgls na.omit.comparative.data nobs.pgls plot.caic
     plot.fusco plot.pgls plot.pgls.profile plot.phylo.d predict.caic
     predict.pgls print.caic print.caic.diagnostics print.comparative.data
     print.fusco print.pgls print.phylo.d print.phylo.d.subset
     print.summary.pgls reorder.comparative.data residuals.caic
     residuals.pgls subset.comparative.data summary.caic summary.fusco
     summary.pgls summary.phylo.d summary.phylo.d.subset
    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-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-macos-x86_64-clang, r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-x86_64

Version: 0.5.2
Check: R code for possible problems
Result: NOTE
    [.comparative.data: no visible global function definition for ‘na.omit’
    anova.caic: no visible global function definition for ‘anova’
    anova.pgls: no visible global function definition for ‘terms’
    anova.pgls: no visible global function definition for ‘as.formula’
    anova.pgls: no visible global function definition for ‘pf’
    anova.pgls: no visible global function definition for ‘formula’
    anova.pglslist : <anonymous>: no visible global function definition for
     ‘terms’
    anova.pglslist: no visible global function definition for ‘anova’
    anova.pglslist : <anonymous>: no visible global function definition for
     ‘formula’
    anova.pglslist: no visible global function definition for ‘stat.anova’
    brunch: no visible global function definition for ‘update’
    brunch: no visible global function definition for ‘model.frame’
    brunch: no visible binding for global variable ‘na.pass’
    brunch: no visible global function definition for ‘complete.cases’
    brunch: no visible global function definition for ‘model.matrix’
    brunch: no visible global function definition for ‘model.response’
    brunch: no visible global function definition for ‘is.empty.model’
    brunch: no visible global function definition for ‘rstudent’
    caic.diagnostics: no visible global function definition for ‘terms’
    caic.diagnostics: no visible global function definition for ‘formula’
    caic.diagnostics : text.id: no visible global function definition for
     ‘text’
    caic.diagnostics: no visible global function definition for ‘lm’
    caic.diagnostics: no visible global function definition for
     ‘summary.lm’
    caic.diagnostics: no visible global function definition for ‘abline’
    caic.robust: no visible global function definition for ‘lm.fit’
    caic.robust: no visible binding for global variable ‘formula’
    coef.caic: no visible global function definition for ‘coef’
    contrCalc: no visible global function definition for ‘reorder’
    contrCalc: no visible global function definition for ‘complete.cases’
    contrCalc: no visible global function definition for ‘var’
    crunch: no visible global function definition for ‘update’
    crunch: no visible global function definition for ‘model.frame’
    crunch: no visible binding for global variable ‘na.pass’
    crunch: no visible global function definition for ‘complete.cases’
    crunch: no visible global function definition for ‘model.matrix’
    crunch: no visible global function definition for ‘model.response’
    crunch: no visible global function definition for ‘is.empty.model’
    crunch: no visible global function definition for ‘lm.fit’
    crunch: no visible global function definition for ‘rstudent’
    fusco.test: no visible global function definition for ‘reorder’
    fusco.test: no visible global function definition for ‘median’
    fusco.test: no visible global function definition for ‘IQR’
    fusco.test : expFun: no visible global function definition for ‘runif’
    fusco.test: no visible global function definition for ‘quantile’
    growTree : waitTime: no visible global function definition for ‘rexp’
    logLik.caic: no visible global function definition for ‘logLik’
    macrocaic: no visible global function definition for ‘update’
    macrocaic: no visible global function definition for ‘is.empty.model’
    macrocaic: no visible global function definition for ‘model.frame’
    macrocaic: no visible global function definition for ‘complete.cases’
    macrocaic: no visible global function definition for ‘model.response’
    macrocaic: no visible binding for global variable ‘na.pass’
    macrocaic: no visible global function definition for ‘model.matrix’
    macrocaic: no visible global function definition for ‘rstudent’
    na.omit.comparative.data: no visible global function definition for
     ‘complete.cases’
    nobs.pgls: no visible global function definition for ‘resid’
    pgls: no visible global function definition for ‘model.frame’
    pgls: no visible binding for global variable ‘na.pass’
    pgls: no visible global function definition for ‘model.matrix’
    pgls: no visible binding for global variable ‘var’
    pgls: no visible global function definition for ‘optim’
    pgls.confint: no visible global function definition for ‘qchisq’
    pgls.confint: no visible global function definition for ‘pchisq’
    pgls.confint: no visible global function definition for ‘uniroot’
    phylo.d: no visible binding for global variable ‘quantile’
    phylo.d: no visible global function definition for ‘reorder’
    plot.caic: no visible global function definition for ‘plot’
    plot.fusco: no visible global function definition for ‘hist’
    plot.fusco : <anonymous>: no visible global function definition for
     ‘hist’
    plot.fusco: no visible global function definition for ‘abline’
    plot.fusco: no visible global function definition for ‘median’
    plot.pgls: no visible global function definition for ‘residuals’
    plot.pgls: no visible global function definition for ‘var’
    plot.pgls: no visible global function definition for ‘plot’
    plot.pgls: no visible global function definition for ‘density’
    plot.pgls: no visible global function definition for ‘qqnorm’
    plot.pgls: no visible global function definition for ‘qqline’
    plot.pgls: no visible global function definition for ‘fitted’
    plot.pgls.profile: no visible global function definition for ‘title’
    plot.pgls.profile: no visible global function definition for ‘par’
    plot.pgls.profile: no visible global function definition for ‘abline’
    plot.phylo.d: no visible global function definition for ‘density’
    plot.phylo.d: no visible global function definition for ‘plot’
    plot.phylo.d: no visible global function definition for ‘lines’
    plot.phylo.d: no visible global function definition for ‘abline’
    predict.caic: no visible global function definition for ‘predict’
    predict.pgls: no visible global function definition for ‘model.matrix’
    predict.pgls: no visible global function definition for
     ‘delete.response’
    predict.pgls: no visible global function definition for ‘terms’
    predict.pgls: no visible global function definition for ‘formula’
    predict.pgls: no visible global function definition for ‘coef’
    print.caic: no visible global function definition for ‘na.omit’
    print.caic.diagnostics: no visible global function definition for
     ‘printCoefmat’
    print.comparative.data: no visible global function definition for ‘str’
    print.pgls: no visible global function definition for ‘coef’
    print.summary.pgls: no visible global function definition for
     ‘quantile’
    print.summary.pgls: no visible global function definition for
     ‘printCoefmat’
    print.summary.pgls: no visible global function definition for ‘naprint’
    print.summary.pgls: no visible global function definition for ‘pf’
    reorder.comparative.data: no visible global function definition for
     ‘packageVersion’
    reorder.comparative.data: no visible global function definition for
     ‘reorder’
    residuals.caic: no visible global function definition for ‘residuals’
    summary.fusco: no visible global function definition for ‘wilcox.test’
    summary.pgls: no visible global function definition for ‘pt’
    Undefined global functions or variables:
     IQR abline anova as.formula coef complete.cases delete.response
     density fitted formula hist is.empty.model lines lm lm.fit logLik
     median model.frame model.matrix model.response na.omit na.pass
     naprint optim packageVersion par pchisq pf plot predict printCoefmat
     pt qchisq qqline qqnorm quantile reorder resid residuals rexp
     rstudent runif stat.anova str summary.lm terms text title uniroot
     update var wilcox.test
    Consider adding
     importFrom("graphics", "abline", "hist", "lines", "par", "plot",
     "text", "title")
     importFrom("stats", "IQR", "anova", "as.formula", "coef",
     "complete.cases", "delete.response", "density", "fitted",
     "formula", "is.empty.model", "lm", "lm.fit", "logLik",
     "median", "model.frame", "model.matrix", "model.response",
     "na.omit", "na.pass", "naprint", "optim", "pchisq", "pf",
     "predict", "printCoefmat", "pt", "qchisq", "qqline",
     "qqnorm", "quantile", "reorder", "resid", "residuals",
     "rexp", "rstudent", "runif", "stat.anova", "summary.lm",
     "terms", "uniroot", "update", "var", "wilcox.test")
     importFrom("utils", "packageVersion", "str")
    to your NAMESPACE file.
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-macos-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