CRAN Package Check Results for Package geomorph

Last updated on 2015-09-02 13:46:57.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 2.1.6 5.64 64.07 69.70 NOTE
r-devel-linux-x86_64-debian-gcc 2.1.6 5.75 62.88 68.63 NOTE
r-devel-linux-x86_64-fedora-clang 2.1.6 136.06 NOTE
r-devel-linux-x86_64-fedora-gcc 2.1.6 130.28 NOTE
r-devel-osx-x86_64-clang 2.1.6 112.35 OK
r-devel-windows-ix86+x86_64 2.1.6 30.00 188.00 218.00 NOTE
r-patched-linux-x86_64 2.1.6 5.88 66.70 72.58 OK
r-patched-solaris-sparc 2.1.6 846.60 OK
r-patched-solaris-x86 2.1.6 196.10 OK
r-release-linux-x86_64 2.1.6 6.03 64.54 70.57 OK
r-release-osx-x86_64-mavericks 2.1.6 ERROR
r-release-windows-ix86+x86_64 2.1.6 26.00 206.00 232.00 OK
r-oldrel-windows-ix86+x86_64 2.1.6 41.00 229.00 270.00 OK

Check Details

Version: 2.1.6
Check: R code for possible problems
Result: NOTE
    Gower.center: no visible global function definition for ‘dist’
    Hat.anova.tab: no visible global function definition for ‘formula’
    Hat.anova.tab: no visible global function definition for ‘terms’
    Hat.anova.tab: no visible global function definition for ‘model.matrix’
    RRP.submodels: no visible global function definition for ‘lm’
    SS.pgls.random: no visible global function definition for ‘lm’
    SS.random: no visible global function definition for ‘lm’
    SSE: no visible global function definition for ‘resid’
    advanced.procD.lm: no visible global function definition for
     ‘as.formula’
    advanced.procD.lm: no visible global function definition for ‘terms’
    advanced.procD.lm: no visible global function definition for
     ‘model.matrix’
    advanced.procD.lm: no visible global function definition for ‘lm’
    advanced.procD.lm: no visible global function definition for ‘resid’
    advanced.procD.lm: no visible global function definition for ‘predict’
    advanced.procD.lm: no visible global function definition for ‘dist’
    advanced.procD.lm: no visible global function definition for
     ‘model.frame’
    anova.parts: no visible global function definition for ‘formula’
    anova.parts: no visible global function definition for ‘terms’
    anova.parts: no visible global function definition for ‘model.frame’
    anova.parts: no visible global function definition for ‘lm’
    anova.parts: no visible global function definition for ‘coef’
    anova.pgls.parts: no visible global function definition for ‘formula’
    anova.pgls.parts: no visible global function definition for ‘terms’
    anova.pgls.parts: no visible global function definition for
     ‘model.frame’
    anova.pgls.parts: no visible global function definition for ‘lm’
    anova.pgls.parts: no visible global function definition for ‘coef’
    bilat.symmetry: no visible global function definition for ‘as.formula’
    bilat.symmetry: no visible global function definition for ‘pf’
    bilat.symmetry: no visible global function definition for ‘aov’
    bilat.symmetry: no visible global function definition for ‘predict’
    bilat.symmetry: no visible global function definition for ‘lm’
    bilat.symmetry: no visible global function definition for ‘manova’
    bilat.symmetry: no visible global function definition for ‘par’
    bilat.symmetry: no visible global function definition for ‘mtext’
    bilat.symmetry: no visible global function definition for ‘layout’
    buildtemplate: no visible global function definition for ‘kmeans’
    buildtemplate: no visible global function definition for ‘write.table’
    buildtemplate: no visible global function definition for ‘write.csv’
    compare.evol.rates : sigma.d: no visible global function definition for
     ‘prcomp’
    compare.evol.rates : sigma.d: no visible global function definition for
     ‘dist’
    compare.evol.rates: no visible global function definition for ‘hist’
    compare.evol.rates: no visible global function definition for ‘arrows’
    compare.modular.partitions: no visible global function definition for
     ‘cov’
    compare.modular.partitions: no visible global function definition for
     ‘hist’
    compare.modular.partitions: no visible global function definition for
     ‘arrows’
    csize: no visible binding for global variable ‘var’
    define.links: no visible global function definition for ‘plot’
    define.links: no visible global function definition for ‘text’
    define.links: no visible global function definition for ‘identify’
    define.links: no visible global function definition for ‘segments’
    define.modules: no visible global function definition for ‘rainbow’
    define.modules: no visible global function definition for ‘plot’
    define.modules: no visible global function definition for ‘text’
    define.sliders: no visible global function definition for ‘write.table’
    define.sliders: no visible global function definition for ‘plot’
    define.sliders: no visible global function definition for ‘text’
    define.sliders: no visible global function definition for ‘identify’
    define.sliders: no visible global function definition for ‘points’
    define.sliders: no visible global function definition for ‘arrows’
    define.sliders: no visible global function definition for ‘read.csv’
    digitize2d: no visible global function definition for ‘na.omit’
    digitize2d: no visible global function definition for ‘plot’
    digitize2d: no visible global function definition for ‘rasterImage’
    digitize2d: no visible global function definition for ‘locator’
    digitize2d: no visible global function definition for ‘points’
    digitsurface: no visible global function definition for ‘read.table’
    editTemplate: no visible global function definition for ‘write.table’
    estimate.missing: no visible global function definition for ‘cov’
    estimate.missing: no visible global function definition for ‘coef’
    estimate.missing: no visible global function definition for ‘lm’
    findMeanSpec: no visible global function definition for ‘dist’
    globalIntegration: no visible global function definition for ‘dist’
    globalIntegration: no visible global function definition for ‘var’
    globalIntegration: no visible global function definition for ‘coef’
    globalIntegration: no visible global function definition for ‘lm’
    globalIntegration: no visible global function definition for ‘plot’
    globalIntegration: no visible global function definition for ‘abline’
    globalIntegration: no visible global function definition for ‘lines’
    gpagen: no visible global function definition for ‘prcomp’
    identifyPch: no visible global function definition for ‘xy.coords’
    identifyPch: no visible global function definition for ‘identify’
    identifyPch: no visible global function definition for ‘points’
    ls.means: no visible global function definition for ‘model.matrix’
    ls.means: no visible global function definition for ‘predict’
    ls.means: no visible global function definition for ‘lm’
    ls.means: no visible global function definition for ‘terms’
    ls.means: no visible global function definition for ‘coef’
    ls.means: no visible global function definition for ‘aggregate’
    mod.mats: no visible global function definition for ‘terms’
    mod.mats: no visible global function definition for ‘model.matrix’
    mod.mats.w.cov: no visible global function definition for ‘terms’
    mod.mats.w.cov: no visible global function definition for ‘as.formula’
    mod.mats.w.cov: no visible global function definition for
     ‘model.matrix’
    morphol.disparity: no visible global function definition for ‘resid’
    morphol.disparity: no visible global function definition for ‘lm’
    morphol.disparity : procvar: no visible global function definition for
     ‘dist’
    morphol.disparity: no visible global function definition for ‘dist’
    morphol.integr: no visible global function definition for ‘cov’
    morphol.integr: no visible global function definition for ‘cor’
    morphol.integr: no visible global function definition for ‘plot’
    morphol.integr: no visible global function definition for ‘text’
    morphol.integr: no visible global function definition for ‘layout’
    morphol.integr: no visible global function definition for ‘hist’
    morphol.integr: no visible global function definition for ‘arrows’
    pathdist: no visible global function definition for ‘dist’
    pgpa: no visible global function definition for ‘dist’
    phylo.pls: no visible global function definition for ‘cor’
    phylo.pls: no visible global function definition for ‘plot’
    phylo.pls: no visible global function definition for ‘text’
    phylo.pls: no visible global function definition for ‘par’
    phylo.pls: no visible global function definition for ‘split.screen’
    phylo.pls: no visible global function definition for ‘screen’
    phylo.pls: no visible global function definition for ‘close.screen’
    physignal : Kmult: no visible global function definition for ‘dist’
    physignal: no visible global function definition for ‘dist’
    picscale: no visible global function definition for ‘locator’
    plotAllSpecimens: no visible global function definition for ‘plot’
    plotAllSpecimens: no visible global function definition for ‘points’
    plotAllSpecimens: no visible global function definition for ‘segments’
    plotAllometry: no visible global function definition for ‘model.frame’
    plotAllometry: no visible global function definition for ‘as.formula’
    plotAllometry: no visible global function definition for ‘terms’
    plotAllometry: no visible global function definition for ‘predict’
    plotAllometry: no visible global function definition for ‘lm’
    plotAllometry: no visible global function definition for ‘coef’
    plotAllometry: no visible global function definition for ‘prcomp’
    plotAllometry: no visible global function definition for ‘layout’
    plotAllometry: no visible global function definition for ‘plot’
    plotAllometry: no visible global function definition for ‘points’
    plotAllometry: no visible global function definition for ‘text’
    plotAllometry: no visible global function definition for ‘arrows’
    plotGMPhyloMorphoSpace: no visible global function definition for
     ‘prcomp’
    plotGMPhyloMorphoSpace: no visible global function definition for
     ‘plot’
    plotGMPhyloMorphoSpace: no visible global function definition for
     ‘lines’
    plotGMPhyloMorphoSpace: no visible global function definition for
     ‘points’
    plotGMPhyloMorphoSpace: no visible global function definition for
     ‘text’
    plotOutliers : <anonymous>: no visible global function definition for
     ‘dist’
    plotOutliers : <anonymous>: no visible global function definition for
     ‘plot’
    plotOutliers : <anonymous>: no visible global function definition for
     ‘abline’
    plotOutliers : <anonymous>: no visible global function definition for
     ‘text’
    plotOutliers : <anonymous>: no visible global function definition for
     ‘points’
    plotRefToTarget: no visible global function definition for ‘segments’
    plotRefToTarget: no visible global function definition for ‘text’
    plotRefToTarget: no visible global function definition for ‘points’
    plotRefToTarget: no visible global function definition for ‘plot’
    plotRefToTarget: no visible global function definition for ‘arrows’
    plotRefToTarget: no visible global function definition for ‘par’
    plotRefToTarget: no visible global function definition for ‘layout’
    plotRefToTarget: no visible global function definition for ‘title’
    plotTangentSpace: no visible global function definition for ‘prcomp’
    plotTangentSpace: no visible global function definition for ‘plot’
    plotTangentSpace: no visible global function definition for ‘points’
    plotTangentSpace: no visible global function definition for ‘segments’
    plotTangentSpace: no visible global function definition for ‘text’
    plotTangentSpace: no visible global function definition for ‘layout’
    plotTangentSpace: no visible global function definition for ‘arrows’
    pls: no visible global function definition for ‘var’
    pls: no visible global function definition for ‘cor’
    procD.lm: no visible global function definition for ‘formula’
    procD.lm: no visible global function definition for ‘model.frame’
    procD.lm: no visible global function definition for ‘as.formula’
    procD.lm: no visible global function definition for ‘terms’
    procD.pgls: no visible global function definition for ‘formula’
    procD.pgls: no visible global function definition for ‘as.formula’
    procD.pgls: no visible global function definition for ‘terms’
    procD.pgls: no visible global function definition for ‘model.frame’
    read.ply: no visible global function definition for ‘rgb’
    single.factor: no visible global function definition for ‘formula’
    single.factor: no visible global function definition for ‘terms’
    single.factor: no visible global function definition for ‘model.frame’
    slopes: no visible global function definition for ‘lm’
    slopes: no visible global function definition for ‘coef’
    tps: no visible global function definition for ‘plot’
    tps: no visible global function definition for ‘lines’
    tps: no visible global function definition for ‘points’
    tps2d3d: no visible global function definition for ‘dist’
    trajectory.analysis: no visible global function definition for
     ‘formula’
    trajectory.analysis: no visible global function definition for
     ‘as.formula’
    trajectory.analysis: no visible global function definition for ‘terms’
    trajectory.analysis: no visible global function definition for
     ‘model.frame’
    trajectory.analysis: no visible global function definition for ‘prcomp’
    trajectory.analysis: no visible global function definition for
     ‘model.matrix’
    trajectory.analysis: no visible global function definition for ‘lm’
    trajectory.analysis: no visible global function definition for ‘dist’
    trajorient: no visible global function definition for ‘var’
    trajplot: no visible global function definition for ‘plot’
    trajplot: no visible global function definition for ‘points’
    trajsize: no visible global function definition for ‘dist’
    two.b.pls: no visible global function definition for ‘plot’
    two.b.pls: no visible global function definition for ‘text’
    two.b.pls: no visible global function definition for ‘par’
    two.b.pls: no visible global function definition for ‘split.screen’
    two.b.pls: no visible global function definition for ‘screen’
    two.b.pls: no visible global function definition for ‘close.screen’
    warpRefOutline: no visible global function definition for ‘read.table’
    warpRefOutline: no visible global function definition for ‘read.csv’
    warpRefOutline: no visible global function definition for ‘plot’
    warpRefOutline: no visible global function definition for ‘points’
    writeland.nts: no visible global function definition for ‘write.table’
    writeland.tps: no visible global function definition for ‘write.table’
    Undefined global functions or variables:
     abline aggregate aov arrows as.formula close.screen coef cor cov dist
     formula hist identify kmeans layout lines lm locator manova
     model.frame model.matrix mtext na.omit par pf plot points prcomp
     predict rainbow rasterImage read.csv read.table resid rgb screen
     segments split.screen terms text title var write.csv write.table
     xy.coords
    Consider adding
     importFrom("grDevices", "rainbow", "rgb", "xy.coords")
     importFrom("graphics", "abline", "arrows", "close.screen", "hist",
     "identify", "layout", "lines", "locator", "mtext", "par",
     "plot", "points", "rasterImage", "screen", "segments",
     "split.screen", "text", "title")
     importFrom("stats", "aggregate", "aov", "as.formula", "coef", "cor",
     "cov", "dist", "formula", "kmeans", "lm", "manova",
     "model.frame", "model.matrix", "na.omit", "pf", "prcomp",
     "predict", "resid", "terms", "var")
     importFrom("utils", "read.csv", "read.table", "write.csv",
     "write.table")
    to your NAMESPACE.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64

Version: 2.1.6
Check: examples
Result: ERROR
    Running examples in ‘geomorph-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: bilat.symmetry
    > ### Title: Analysis of bilateral symmetry
    > ### Aliases: bilat.symmetry
    > ### Keywords: analysis
    >
    > ### ** Examples
    >
    > #Example of matching symmetry
    >
    > data(mosquito)
    > bilat.symmetry(mosquito$wingshape,ind=mosquito$ind,side=mosquito$side,
    + replicate=mosquito$replicate,object.sym=FALSE)
    $ANOVA.size
     df SS MS F P
    ind 9 4.1497e-09 4.6107e-10 0.5965 0.77333
    side 1 3.4740e-10 3.4738e-10 0.4494 0.51945
    ind:side 9 6.9569e-09 7.7299e-10 1.4170 0.24590
    replicate 20 1.0910e-08 5.4549e-10
    
    $ANOVA.Shape
     df SS MS Goodall.F P.param
    ind 288 0.104888 0.00036419 2.69010 0.00001
    side 32 0.003221 0.00010065 0.74346 0.84331
    ind:side 288 0.038990 0.00013538 1.04068 0.34061
    ind:side:replicate 640 0.083259 0.00013009
    
    >
    > #Example of object symmetry
    >
    > data(scallops)
    > bilat.symmetry(scallops$coorddata,ind=scallops$ind,object.sym=TRUE,land.pairs=scallops$land.pairs)
    Error in rgl.open(useNULL) : rgl.open failed
    Calls: bilat.symmetry -> open3d -> rgl.open
    Execution halted
Flavor: r-release-osx-x86_64-mavericks