CRAN Package Check Results for Package strataG

Last updated on 2016-03-07 23:47:40.

Check Details

Version: 0.9.4
Check: S3 generic/method consistency
Result: NOTE
    Found the following apparent S3 methods exported but not registered:
     as.data.frame.gtypes as.matrix.gtypes gtypes.character gtypes.default
     gtypes.list label.haplotypes.default label.haplotypes.gtypes
     merge.gtypes na.omit.gtypes plot.jack.influential print.gtypeSummary
     subset.gtypes summary.gtypes
    See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
    manual.
Flavors: 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-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-x86_64

Version: 0.9.4
Check: R code for possible problems
Result: NOTE
    allele.freqs : <anonymous>: no visible global function definition for
     ‘na.omit’
    allelic.richness : <anonymous>: no visible global function definition
     for ‘na.omit’
    check.genotypes: no visible global function definition for ‘write.csv’
    check.genotypes: no visible global function definition for ‘pdf’
    check.genotypes: no visible global function definition for ‘plot’
    check.genotypes: no visible global function definition for ‘dev.off’
    check.seqs: no visible global function definition for ‘write.csv’
    clumpp.run: no visible global function definition for ‘file_test’
    clumpp.run: no visible global function definition for ‘write.table’
    diversity: no visible global function definition for ‘na.omit’
    dup.genotypes: no visible global function definition for ‘write.csv’
    fisher.method.p: no visible global function definition for ‘pchisq’
    fixed.differences: no visible global function definition for ‘combn’
    gelato.plot: no visible global function definition for ‘par’
    gelato.plot: no visible global function definition for ‘hist’
    gelato.plot: no visible global function definition for ‘dnorm’
    gelato.plot: no visible global function definition for ‘curve’
    gelato.plot: no visible global function definition for ‘axis’
    gelato.plot: no visible global function definition for ‘mtext’
    gelato.run : <anonymous> : <anonymous>: no visible global function
     definition for ‘dnorm’
    gelato.run : <anonymous> : <anonymous>: no visible global function
     definition for ‘median’
    gen.data.from.freq : <anonymous>: no visible global function definition
     for ‘complete.cases’
    gtypes.default: no visible global function definition for ‘na.omit’
    haplotype.likelihoods : <anonymous>: no visible global function
     definition for ‘dgamma’
    haplotype.likelihoods: no visible global function definition for
     ‘dotchart’
    is.gtypes: no visible global function definition for ‘na.omit’
    jack.hwe: no visible global function definition for ‘combn’
    label.haplotypes.default: no visible global function definition for
     ‘combn’
    most.distant.sequences: no visible global function definition for
     ‘cmdscale’
    most.distant.sequences : <anonymous>: no visible global function
     definition for ‘var’
    nei.Da: no visible global function definition for ‘combn’
    nucleotide.divergence : pair.dist.summary: no visible global function
     definition for ‘quantile’
    nucleotide.divergence : <anonymous>: no visible global function
     definition for ‘combn’
    nucleotide.divergence: no visible global function definition for
     ‘combn’
    num.alleles : <anonymous>: no visible global function definition for
     ‘na.omit’
    obsvd.het : <anonymous>: no visible global function definition for
     ‘na.omit’
    overall.test: no visible global function definition for ‘write.csv’
    pairwise.shared.loci: no visible global function definition for ‘combn’
    pairwise.shared.loci : <anonymous>: no visible global function
     definition for ‘na.omit’
    pairwise.test: no visible global function definition for ‘combn’
    pairwise.test: no visible global function definition for ‘write.csv’
    plot.jack.influential: no visible global function definition for ‘plot’
    plot.jack.influential: no visible global function definition for
     ‘abline’
    plot.jack.influential: no visible global function definition for ‘text’
    read.gen.data: no visible global function definition for ‘read.csv’
    shared.haps: no visible global function definition for ‘combn’
    sim.gamma.haps: no visible global function definition for ‘dgamma’
    sim.gamma.haps : gamma.func: no visible global function definition for
     ‘dgamma’
    sim.gamma.haps: no visible global function definition for ‘layout’
    sim.gamma.haps: no visible global function definition for ‘par’
    sim.gamma.haps: no visible global function definition for ‘curve’
    sim.gamma.haps: no visible global function definition for ‘hist’
    sim.gamma.haps: no visible global function definition for ‘box’
    smry.by.locus : by.locus.smry: no visible global function definition
     for ‘write.csv’
    smry.by.sample : <anonymous> : <anonymous>: no visible global function
     definition for ‘na.omit’
    smry.by.sample: no visible global function definition for ‘write.csv’
    stat.d.jost : <anonymous>: no visible global function definition for
     ‘na.omit’
    strata.pairs: no visible global function definition for ‘combn’
    strata.split: no visible global function definition for ‘na.omit’
    structure.evanno: no visible binding for global variable ‘sd’
    structure.evanno: no visible global function definition for ‘par’
    structure.evanno: no visible global function definition for ‘layout’
    structure.evanno : plot.func: no visible global function definition for
     ‘segments’
    structure.evanno : plot.func: no visible global function definition for
     ‘axis’
    structure.evanno : plot.func: no visible global function definition for
     ‘box’
    structure.plot : <anonymous> : <anonymous>: no visible global function
     definition for ‘median’
    structure.plot: no visible global function definition for ‘rainbow’
    structure.plot: no visible global function definition for ‘barplot’
    structure.plot: no visible global function definition for ‘axis’
    structure.plot: no visible global function definition for ‘mtext’
    structure.run: no visible global function definition for ‘file_test’
    summarize.sequences : summary.stats: no visible global function
     definition for ‘median’
    tajimas.d: no visible global function definition for ‘qbeta’
    tajimas.d: no visible global function definition for ‘integrate’
    theta: no visible global function definition for ‘na.omit’
    theta : <anonymous>: no visible global function definition for
     ‘na.omit’
    ti.tv.ratio : <anonymous>: no visible global function definition for
     ‘combn’
    write.gtypes: no visible global function definition for ‘write.csv’
    Undefined global functions or variables:
     abline axis barplot box cmdscale combn complete.cases curve dev.off
     dgamma dnorm dotchart file_test hist integrate layout median mtext
     na.omit par pchisq pdf plot qbeta quantile rainbow read.csv sd
     segments text var write.csv write.table
    Consider adding
     importFrom("grDevices", "dev.off", "pdf", "rainbow")
     importFrom("graphics", "abline", "axis", "barplot", "box", "curve",
     "dotchart", "hist", "layout", "mtext", "par", "plot",
     "segments", "text")
     importFrom("stats", "cmdscale", "complete.cases", "dgamma", "dnorm",
     "integrate", "median", "na.omit", "pchisq", "qbeta",
     "quantile", "sd", "var")
     importFrom("utils", "combn", "file_test", "read.csv", "write.csv",
     "write.table")
    to your NAMESPACE file.
Flavors: 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