CRAN Package Check Results for Package BiodiversityR

Last updated on 2014-11-24 09:48:08.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 2.5-1 6.79 103.26 110.05 OK
r-devel-linux-x86_64-debian-gcc 2.5-1 6.08 97.15 103.23 OK
r-devel-linux-x86_64-fedora-clang 2.5-1 128.32 OK
r-devel-linux-x86_64-fedora-gcc 2.5-1 121.37 OK
r-devel-osx-x86_64-clang 2.5-1 117.64 OK
r-devel-windows-ix86+x86_64 2.5-1 31.00 148.00 179.00 OK
r-patched-linux-x86_64 2.4-4 3.13 68.20 71.33 ERROR
r-patched-solaris-sparc 2.5-1 1182.50 OK
r-patched-solaris-x86 2.5-1 232.40 OK
r-release-linux-ix86 2.4-4 4.62 85.39 90.00 ERROR
r-release-linux-x86_64 2.4-4 3.16 68.59 71.76 ERROR
r-release-osx-x86_64-mavericks 2.5-1 NOTE
r-release-osx-x86_64-snowleopard 2.4-4 OK
r-release-windows-ix86+x86_64 2.5-1 25.00 136.00 161.00 OK
r-oldrel-windows-ix86+x86_64 2.5-1 27.00 150.00 177.00 OK

Check Details

Version: 2.4-4
Check: R code for possible problems
Result: NOTE
    CAPdiscrim : CAPresult: no visible global function definition for ‘lda’
    CAPdiscrim: no visible global function definition for ‘vegdist’
    NMSrandom: no visible global function definition for ‘isoMDS’
    NMSrandom: no visible global function definition for ‘initMDS’
    NMSrandom: no visible global function definition for ‘sammon’
    accumresult: no visible global function definition for ‘specaccum’
    add.spec.scores: no visible global function definition for ‘scores’
    add.spec.scores: no visible global function definition for ‘wascores’
    caprescale: no visible global function definition for ‘scores’
    caprescale: no visible global function definition for ‘vegdist’
    check.ordiscores: no visible global function definition for ‘scores’
    dist.eval: no visible global function definition for ‘vegdist’
    dist.eval: no visible global function definition for ‘no.shared’
    dist.eval: no visible global function definition for ‘distconnected’
    distdisplayed: no visible global function definition for ‘vegdist’
    distdisplayed: no visible global function definition for ‘scores’
    distdisplayed: no visible global function definition for ‘mantel’
    disttransform: no visible global function definition for ‘decostand’
    diversityresult : diversityresult0: no visible global function
     definition for ‘diversity’
    diversityresult : diversityresult0: no visible global function
     definition for ‘fisher.alpha’
    diversityresult : diversityresult0: no visible global function
     definition for ‘specpool’
    ensemble.accepted.categories: no visible global function definition for
     ‘file_ext’
    ensemble.accepted.categories: no visible global function definition for
     ‘freq’
    ensemble.accepted.categories: no visible global function definition for
     ‘subs’
    ensemble.batch: no visible global function definition for ‘nlayers’
    ensemble.batch: no visible global function definition for
     ‘randomPoints’
    ensemble.category.simplify: no visible global function definition for
     ‘randomPoints’
    ensemble.category.simplify: no visible global function definition for
     ‘prepareData’
    ensemble.category.simplify: no visible global function definition for
     ‘freq’
    ensemble.category.simplify: no visible global function definition for
     ‘subs’
    ensemble.drop1: no visible global function definition for ‘dropLayer’
    ensemble.drop1 : loglik.calculation: no visible global function
     definition for ‘calc.deviance’
    ensemble.dummy.variables: no visible global function definition for
     ‘freq’
    ensemble.dummy.variables: no visible global function definition for
     ‘filename’
    ensemble.dummy.variables: no visible global function definition for
     ‘file_ext’
    ensemble.dummy.variables: no visible global function definition for
     ‘writeRaster’
    ensemble.habitat.change: no visible global function definition for
     ‘raster’
    ensemble.habitat.change: no visible global function definition for
     ‘setMinMax’
    ensemble.habitat.change: no visible global function definition for
     ‘maxValue’
    ensemble.habitat.change: no visible global function definition for
     ‘freq’
    ensemble.habitat.change: no visible global function definition for
     ‘overlay’
    ensemble.habitat.change: no visible global function definition for
     ‘writeRaster’
    ensemble.habitat.change: no visible global function definition for
     ‘KML’
    ensemble.mean: no visible global function definition for ‘setMinMax’
    ensemble.mean: no visible global function definition for ‘writeRaster’
    ensemble.mean: no visible global function definition for ‘raster’
    ensemble.mean: no visible global function definition for ‘extract’
    ensemble.mean: no visible global function definition for ‘evaluate’
    ensemble.mean: no visible global function definition for ‘KML’
    ensemble.raster: no visible global function definition for ‘crop’
    ensemble.raster: no visible global function definition for ‘dropLayer’
    ensemble.raster: no visible global function definition for ‘nlayers’
    ensemble.raster: no visible global function definition for ‘setMinMax’
    ensemble.raster: no visible global function definition for ‘projection’
    ensemble.raster: no visible global function definition for
     ‘projection<-’
    ensemble.raster: no visible global function definition for
     ‘writeRaster’
    ensemble.raster: no visible global function definition for ‘extract’
    ensemble.raster: no visible global function definition for ‘NAvalue’
    ensemble.raster: no visible global function definition for ‘minValue’
    ensemble.raster: no visible global function definition for ‘maxValue’
    ensemble.raster: no visible global function definition for ‘KML’
    ensemble.raster: no visible global function definition for ‘raster’
    ensemble.simplified.categories: no visible global function definition
     for ‘file_ext’
    ensemble.simplified.categories: no visible global function definition
     for ‘randomPoints’
    ensemble.simplified.categories: no visible global function definition
     for ‘prepareData’
    ensemble.simplified.categories: no visible global function definition
     for ‘freq’
    ensemble.simplified.categories: no visible global function definition
     for ‘subs’
    ensemble.strategy: no visible global function definition for ‘evaluate’
    ensemble.test: no visible global function definition for ‘projection’
    ensemble.test: no visible global function definition for ‘projection<-’
    ensemble.test: no visible global function definition for ‘nlayers’
    ensemble.test: no visible global function definition for ‘crop’
    ensemble.test: no visible global function definition for ‘dropLayer’
    ensemble.test: no visible global function definition for ‘setMinMax’
    ensemble.test: no visible global function definition for ‘kfold’
    ensemble.test: no visible global function definition for ‘randomPoints’
    ensemble.test: no visible global function definition for ‘prepareData’
    ensemble.test: no visible global function definition for ‘freq’
    ensemble.test: no visible global function definition for
     ‘sampleStratified’
    ensemble.test: no visible global function definition for ‘xyFromCell’
    ensemble.test: no visible global function definition for ‘extract’
    ensemble.test: no visible global function definition for ‘vif’
    ensemble.test: no visible global function definition for ‘maxent’
    ensemble.test: no visible global function definition for
     ‘calc.deviance’
    ensemble.test: no visible global function definition for ‘evaluate’
    ensemble.test: no visible global function definition for ‘threshold’
    ensemble.test: no visible global function definition for ‘gbm’
    ensemble.test: no visible global function definition for ‘gbm.step’
    ensemble.test: no visible global function definition for ‘randomForest’
    ensemble.test: no visible global function definition for ‘stepAIC’
    ensemble.test: no visible global function definition for ‘gam’
    ensemble.test: no visible global function definition for ‘gam.control’
    ensemble.test: no visible global function definition for ‘step.gam’
    ensemble.test: no visible global function definition for ‘earth’
    ensemble.test: no visible global function definition for ‘rpart’
    ensemble.test: no visible global function definition for
     ‘rpart.control’
    ensemble.test: no visible global function definition for ‘nnet’
    ensemble.test: no visible global function definition for ‘fda’
    ensemble.test: no visible binding for global variable ‘mars’
    ensemble.test: no visible global function definition for ‘ksvm’
    ensemble.test: no visible global function definition for ‘svm’
    ensemble.test: no visible global function definition for ‘bioclim’
    ensemble.test: no visible global function definition for ‘domain’
    ensemble.test: no visible global function definition for ‘mahal’
    ensemble.test: no visible global function definition for ‘geoDist’
    ensemble.test.gbm: no visible global function definition for
     ‘projection’
    ensemble.test.gbm: no visible global function definition for
     ‘projection<-’
    ensemble.test.gbm: no visible global function definition for ‘nlayers’
    ensemble.test.gbm: no visible global function definition for ‘crop’
    ensemble.test.gbm: no visible global function definition for
     ‘dropLayer’
    ensemble.test.gbm: no visible global function definition for
     ‘setMinMax’
    ensemble.test.gbm: no visible global function definition for
     ‘randomPoints’
    ensemble.test.gbm: no visible global function definition for
     ‘prepareData’
    ensemble.test.gbm: no visible global function definition for ‘kfold’
    ensemble.test.nnet: no visible global function definition for
     ‘projection’
    ensemble.test.nnet: no visible global function definition for
     ‘projection<-’
    ensemble.test.nnet: no visible global function definition for ‘nlayers’
    ensemble.test.nnet: no visible global function definition for ‘crop’
    ensemble.test.nnet: no visible global function definition for
     ‘dropLayer’
    ensemble.test.nnet: no visible global function definition for
     ‘setMinMax’
    ensemble.test.nnet: no visible global function definition for
     ‘randomPoints’
    ensemble.test.nnet: no visible global function definition for
     ‘prepareData’
    ensemble.test.nnet: no visible global function definition for ‘kfold’
    ensemble.test.splits: no visible global function definition for
     ‘dropLayer’
    ensemble.test.splits: no visible global function definition for ‘kfold’
    ensemble.test.splits: no visible global function definition for
     ‘evaluate’
    evaluation.strip.data: no visible global function definition for ‘crop’
    evaluation.strip.data: no visible global function definition for
     ‘dropLayer’
    evaluation.strip.data: no visible global function definition for
     ‘nlayers’
    evaluation.strip.data: no visible global function definition for
     ‘setMinMax’
    evaluation.strip.data: no visible global function definition for
     ‘projection’
    evaluation.strip.data: no visible global function definition for
     ‘projection<-’
    evaluation.strip.data: no visible global function definition for ‘freq’
    evaluation.strip.data: no visible global function definition for
     ‘cellStats’
    evaluation.strip.data: no visible global function definition for
     ‘minValue’
    evaluation.strip.data: no visible global function definition for
     ‘maxValue’
    multiconstrained: no visible global function definition for ‘rda’
    multiconstrained: no visible global function definition for ‘cca’
    multiconstrained: no visible global function definition for ‘capscale’
    multiconstrained: no visible global function definition for ‘anova.cca’
    nested.anova.dbrda: no visible global function definition for ‘vegdist’
    nested.anova.dbrda: no visible global function definition for
     ‘capscale’
    nested.npmanova: no visible global function definition for ‘vegdist’
    nested.npmanova: no visible global function definition for ‘adonis’
    nnetrandom : nnet.1: no visible global function definition for ‘nnet’
    ordibubble: no visible global function definition for ‘scores’
    ordicluster2: no visible global function definition for ‘ordihull’
    ordicoeno: no visible global function definition for ‘scores’
    ordicoeno: no visible global function definition for ‘gam’
    ordiequilibriumcircle: no visible global function definition for
     ‘scores’
    ordihull.centroids: no visible global function definition for ‘scores’
    ordihull.centroids: no visible global function definition for ‘vegdist’
    ordinearest: no visible global function definition for ‘scores’
    ordispider.centroids: no visible global function definition for
     ‘scores’
    ordispider.centroids : ordispidercentres: no visible global function
     definition for ‘scores’
    ordispider.centroids: no visible global function definition for
     ‘vegdist’
    ordivector: no visible global function definition for ‘scores’
    radfitresult: no visible global function definition for ‘radfit’
    radfitresult: no visible global function definition for ‘fisherfit’
    radfitresult: no visible global function definition for ‘prestonfit’
    renyiaccumresult: no visible global function definition for
     ‘renyiaccum’
    renyiresult: no visible global function definition for ‘renyi’
    residualssurface: no visible global function definition for ‘surf.ls’
    residualssurface: no visible global function definition for ‘interp’
    spatialsample: no visible global function definition for ‘inout’
Flavors: r-patched-linux-x86_64, r-release-linux-ix86, r-release-linux-x86_64

Version: 2.4-4
Check: examples
Result: ERROR
    Running examples in ‘BiodiversityR-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: deviancepercentage
    > ### Title: Calculate Percentage and Significance of Deviance Explained by a
    > ### GLM
    > ### Aliases: deviancepercentage
    > ### Keywords: multivariate
    >
    > ### ** Examples
    >
    > library(vegan)
    Loading required package: permute
    Loading required package: lattice
    This is vegan 2.2-0
    > data(dune)
    > data(dune.env)
    > dune.env$Agrsto<- dune$Agrsto
    > Count.model1 <- glm(Agrsto ~ Management + A1, family=quasipoisson(link=log),
    + data=dune.env, na.action=na.omit)
    Error in eval(expr, envir, enclos) : object 'Agrsto' not found
    Calls: glm ... eval -> <Anonymous> -> model.frame.default -> eval -> eval
    Execution halted
Flavors: r-patched-linux-x86_64, r-release-linux-ix86, r-release-linux-x86_64

Version: 2.5-1
Check: package dependencies
Result: NOTE
    Packages suggested but not available for checking: ‘RODBC’ ‘rgdal’
Flavor: r-release-osx-x86_64-mavericks