CRAN Package Check Results for Package GenABEL

Last updated on 2017-02-24 23:52:28.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.8-0 28.94 105.55 134.50 NOTE
r-devel-linux-x86_64-debian-gcc 1.8-0 32.88 109.35 142.22 NOTE
r-devel-linux-x86_64-fedora-clang 1.8-0 275.73 NOTE --no-stop-on-test-error
r-devel-linux-x86_64-fedora-gcc 1.8-0 257.24 NOTE --no-stop-on-test-error
r-devel-macos-x86_64-clang 1.8-0 186.10 NOTE --no-stop-on-test-error
r-devel-windows-ix86+x86_64 1.8-0 220.00 291.00 511.00 NOTE
r-patched-linux-x86_64 1.8-0 29.59 103.01 132.61 NOTE
r-patched-solaris-sparc 1.8-0 781.70 NOTE --no-examples
r-patched-solaris-x86 1.8-0 280.40 NOTE
r-release-linux-x86_64 1.8-0 29.61 97.72 127.33 NOTE
r-release-osx-x86_64-mavericks 1.8-0 NOTE
r-release-windows-ix86+x86_64 1.8-0 153.00 279.00 432.00 NOTE
r-oldrel-windows-ix86+x86_64 1.8-0 207.00 283.00 490.00 NOTE

Check Details

Version: 1.8-0
Check: whether the namespace can be loaded with stated dependencies
Result: NOTE
    Warning: no function found corresponding to methods exports from ‘GenABEL’ for: ‘show’
    
    A namespace must be able to be loaded with just the base namespace
    loaded: otherwise if the namespace gets loaded by a saved object, the
    session will be unable to start.
    
    Probably some imports need to be declared in the NAMESPACE file.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-windows-ix86+x86_64, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-osx-x86_64-mavericks, r-release-windows-ix86+x86_64, r-release-windows-ix86+x86_64

Version: 1.8-0
Check: dependencies in R code
Result: NOTE
    'library' or 'require' calls in package code:
     ‘DatABEL’ ‘genetics’ ‘haplo.stats’ ‘hglm’ ‘qvalue’
     Please use :: or requireNamespace() instead.
     See section 'Suggested packages' in the 'Writing R Extensions' manual.
    Packages in Depends field not imported from:
     ‘GenABEL.data’ ‘MASS’ ‘methods’
     These packages need to be imported from (in the NAMESPACE file)
     for when this namespace is loaded but not attached.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-osx-x86_64-mavericks, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 1.8-0
Check: S3 generic/method consistency
Result: NOTE
    Found the following apparent S3 methods exported but not registered:
     as.character.snp.coding as.character.snp.strand merge.gwaa.data
     merge.snp.data summary.snp.data_old
    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-x86, r-release-linux-x86_64

Version: 1.8-0
Check: R code for possible problems
Result: NOTE
    GASurv: no visible global function definition for ‘is’
    HWE.show: no visible global function definition for ‘is’
    HWE.show: no visible global function definition for ‘pchisq’
    LiLog: no visible global function definition for ‘binomial’
    PGC: no visible global function definition for ‘median’
    PGC: no visible global function definition for ‘qchisq’
    PGC: no visible global function definition for ‘ppoints’
    PGC: no visible global function definition for ‘quantile’
    PGC : f2: no visible global function definition for ‘ks.test’
    PGC : f2: no visible global function definition for ‘median’
    PGC : f2: no visible global function definition for ‘qchisq’
    PGC: no visible global function definition for ‘abline’
    PGC: no visible global function definition for ‘lines’
    VIFGC : Clust: no visible global function definition for ‘as.dist’
    VIFGC : Clust: no visible global function definition for ‘cmdscale’
    VIFGC : ClustN: no visible global function definition for ‘kmeans’
    VIFGC : GC_VIF_nlm: no visible global function definition for ‘ks.test’
    VIFGC : GC_VIF_nlm: no visible global function definition for ‘qchisq’
    VIFGC : GC_VIF_nlm: no visible global function definition for ‘median’
    VIFGC : GC_VIF: no visible global function definition for ‘ks.test’
    VIFGC : GC_VIF: no visible global function definition for ‘qchisq’
    VIFGC : GC_VIF: no visible global function definition for ‘median’
    VIFGC: no visible global function definition for ‘qchisq’
    VIFGC: no visible global function definition for ‘median’
    VIFGC: no visible global function definition for ‘ppoints’
    VIFGC: no visible global function definition for ‘optimize’
    VIFGC: no visible global function definition for ‘nlm’
    VIFGC: no visible global function definition for ‘abline’
    VIFGC: no visible global function definition for ‘lines’
    VIFGC_ovdom : Clust: no visible global function definition for
     ‘as.dist’
    VIFGC_ovdom : Clust: no visible global function definition for
     ‘cmdscale’
    VIFGC_ovdom : ClustN: no visible global function definition for
     ‘kmeans’
    VIFGC_ovdom : GC_VIF_nlm: no visible global function definition for
     ‘ks.test’
    VIFGC_ovdom : GC_VIF_nlm: no visible global function definition for
     ‘qchisq’
    VIFGC_ovdom : GC_VIF_nlm: no visible global function definition for
     ‘median’
    VIFGC_ovdom : GC_VIF: no visible global function definition for
     ‘ks.test’
    VIFGC_ovdom : GC_VIF: no visible global function definition for
     ‘qchisq’
    VIFGC_ovdom : GC_VIF: no visible global function definition for
     ‘median’
    VIFGC_ovdom: no visible global function definition for ‘qchisq’
    VIFGC_ovdom: no visible global function definition for ‘ppoints’
    VIFGC_ovdom: no visible global function definition for ‘optimize’
    VIFGC_ovdom: no visible global function definition for ‘median’
    VIFGC_ovdom: no visible global function definition for ‘nlm’
    VIFGC_ovdom: no visible global function definition for ‘abline’
    Xcheck: no visible global function definition for ‘is’
    Xfix: no visible global function definition for ‘is’
    Xfix.internal: no visible global function definition for ‘is’
    add.phdata: no visible global function definition for ‘is’
    add.plot: no visible global function definition for ‘is’
    add.plot: no visible global function definition for ‘points’
    add.plot: no visible global function definition for ‘image’
    arrange_probabel_phe: no visible global function definition for
     ‘read.table’
    arrange_probabel_phe: no visible global function definition for
     ‘databel’
    arrange_probabel_phe: no visible global function definition for
     ‘write.table’
    as.character.gwaa.data: no visible global function definition for ‘is’
    as.character.snp.data: no visible global function definition for ‘is’
    as.double.gwaa.data: no visible global function definition for ‘is’
    as.double.snp.data: no visible global function definition for ‘is’
    as.genotype.gwaa.data: no visible global function definition for ‘is’
    as.genotype.snp.data: no visible global function definition for ‘is’
    as.genotype.snp.data: no visible global function definition for
     ‘genotype’
    as.hsgeno.gwaa.data: no visible global function definition for ‘is’
    as.hsgeno.snp.data: no visible global function definition for ‘is’
    as.raw.snp.data: no visible global function definition for ‘is’
    as.raw.snp.mx: no visible global function definition for ‘is’
    autosomal: no visible global function definition for ‘is’
    blurGenotype: no visible global function definition for ‘is’
    catable: no visible global function definition for ‘quantile’
    catable: no visible global function definition for ‘is’
    ccfast: no visible global function definition for ‘is’
    ccfast: no visible global function definition for ‘flush.console’
    ccfast: no visible global function definition for ‘pchisq’
    ccfast: no visible global function definition for ‘new’
    ccfast.new: no visible global function definition for ‘is’
    check.marker: no visible global function definition for ‘is’
    check.marker.internal: no visible global function definition for ‘is’
    check.marker.internal: no visible global function definition for
     ‘flush.console’
    check.marker.internal: no visible global function definition for
     ‘qvalue’
    check.marker.internal: no visible global function definition for ‘sd’
    check.marker.internal: no visible global function definition for
     ‘pchisq’
    check.trait: no visible global function definition for ‘is’
    checkphengen: no visible global function definition for ‘is’
    cocohet: no visible global function definition for ‘is’
    cocohet: no visible global function definition for ‘pchisq’
    convert.snp.affymetrix: no visible global function definition for ‘is’
    convert.snp.mach: no visible global function definition for
     ‘read.table’
    convert.snp.mach: no visible global function definition for ‘new’
    descriptives.marker: no visible global function definition for ‘is’
    descriptives.marker: no visible global function definition for ‘sd’
    descriptives.marker: no visible global function definition for
     ‘write.table’
    descriptives.scan: no visible global function definition for ‘is’
    descriptives.scan: no visible global function definition for
     ‘write.table’
    descriptives.trait: no visible global function definition for ‘is’
    descriptives.trait: no visible global function definition for ‘sd’
    descriptives.trait: no visible global function definition for ‘t.test’
    descriptives.trait: no visible global function definition for
     ‘kruskal.test’
    descriptives.trait: no visible global function definition for
     ‘fisher.test’
    descriptives.trait: no visible global function definition for
     ‘write.table’
    dprfast: no visible global function definition for ‘is’
    drop.out.points: no visible global function definition for ‘var’
    dump.piece: no visible global function definition for ‘write.table’
    egscore: no visible global function definition for ‘is’
    egscore: no visible global function definition for ‘as’
    egscore: no visible global function definition for ‘model.frame’
    egscore: no visible binding for global variable ‘na.omit’
    egscore: no visible global function definition for ‘model.response’
    egscore: no visible global function definition for ‘model.matrix’
    egscore: no visible global function definition for ‘glm.fit’
    egscore: no visible global function definition for ‘lm’
    egscore: no visible global function definition for ‘flush.console’
    egscore: no visible global function definition for ‘pchisq’
    egscore: no visible global function definition for ‘new’
    egscore.old: no visible global function definition for ‘is’
    egscore.old: no visible global function definition for ‘as’
    egscore.old: no visible global function definition for ‘model.frame’
    egscore.old: no visible binding for global variable ‘na.omit’
    egscore.old: no visible global function definition for ‘model.response’
    egscore.old: no visible global function definition for ‘model.matrix’
    egscore.old: no visible global function definition for ‘glm.fit’
    egscore.old: no visible global function definition for ‘lm’
    egscore.old: no visible global function definition for ‘flush.console’
    egscore.old: no visible global function definition for ‘pchisq’
    estLambdaKS: no visible global function definition for ‘optimize’
    estlambda: no visible global function definition for ‘qchisq’
    estlambda: no visible global function definition for ‘ppoints’
    estlambda: no visible global function definition for ‘lm’
    estlambda: no visible global function definition for ‘median’
    estlambda: no visible global function definition for ‘par’
    estlambda: no visible global function definition for ‘abline’
    export.impute: no visible global function definition for ‘is’
    export.impute: no visible global function definition for ‘write.table’
    export.merlin: no visible global function definition for ‘is’
    export.merlin: no visible global function definition for ‘new’
    export.merlin: no visible global function definition for ‘write.table’
    export.plink: no visible global function definition for ‘write.table’
    extract.annotation.impute: no visible global function definition for
     ‘extract_text_file_columns’
    extract.annotation.mach: no visible global function definition for
     ‘extract_text_file_columns’
    fcc: no visible global function definition for ‘is’
    fcc.new: no visible global function definition for ‘is’
    findRelatives: no visible global function definition for ‘is’
    findRelatives: no visible global function definition for
     ‘txtProgressBar’
    findRelatives: no visible global function definition for
     ‘setTxtProgressBar’
    formetascore: no visible global function definition for ‘is’
    formetascore: no visible global function definition for ‘as’
    formetascore: no visible global function definition for ‘model.frame’
    formetascore: no visible binding for global variable ‘na.omit’
    generateOffspring : genSOG: no visible global function definition for
     ‘runif’
    generateOffspring : infer: no visible global function definition for
     ‘rbinom’
    generateOffspring: no visible global function definition for ‘rbinom’
    get.snp.distr.plot: no visible global function definition for ‘na.omit’
    get.snp.distr.plot: no visible global function definition for ‘bitmap’
    get.snp.distr.plot: no visible global function definition for ‘par’
    get.snp.distr.plot: no visible global function definition for
     ‘bartlett.test’
    get.snp.distr.plot: no visible global function definition for ‘boxplot’
    get.snp.distr.plot: no visible global function definition for ‘plot’
    get.snp.distr.plot: no visible global function definition for ‘density’
    get.snp.distr.plot: no visible global function definition for ‘dev.off’
    grammar: no visible global function definition for ‘pchisq’
    grammar.old: no visible global function definition for ‘is’
    grammar.old: no visible global function definition for ‘flush.console’
    grammar.old: no visible global function definition for ‘pchisq’
    hom: no visible global function definition for ‘is’
    hom.old: no visible global function definition for ‘is’
    ibs: no visible global function definition for ‘is’
    ibs.old: no visible global function definition for ‘is’
    imphetcheck: no visible global function definition for ‘is’
    impute2databel: no visible global function definition for
     ‘get_temporary_file_name’
    impute2databel: no visible global function definition for
     ‘text2databel’
    impute2databel: no visible global function definition for
     ‘get_dimnames’
    impute2databel: no visible global function definition for ‘apply2dfo’
    impute2databel: no visible global function definition for ‘databel’
    impute2databel: no visible global function definition for
     ‘set_dimnames<-’
    impute2databel: no visible global function definition for ‘disconnect’
    impute2mach: no visible global function definition for ‘write.table’
    impute2mach: no visible global function definition for ‘get_dimnames’
    impute2mach: no visible global function definition for ‘as’
    impute2mach: no visible global function definition for ‘disconnect’
    load.gwaa.data: no visible global function definition for ‘read.table’
    load.gwaa.data: no visible global function definition for ‘new’
    lossFunctionLambdaKS: no visible global function definition for
     ‘ks.test’
    mach2databel: no visible global function definition for
     ‘get_temporary_file_name’
    mach2databel: no visible global function definition for ‘text2databel’
    mach2databel: no visible global function definition for ‘get_dimnames’
    makeTransitionMatrix: no visible global function definition for ‘is’
    merge.gwaa.data: no visible global function definition for ‘is’
    merge.gwaa.data: no visible global function definition for ‘new’
    merge.snp.data: no visible global function definition for ‘is’
    merge.snp.data: no visible global function definition for ‘write.table’
    merge.snp.data: no visible global function definition for ‘new’
    minimac2databel: no visible global function definition for
     ‘get_temporary_file_name’
    minimac2databel: no visible global function definition for
     ‘text2databel’
    minimac2databel: no visible global function definition for
     ‘get_dimnames’
    mlreg: no visible global function definition for ‘is’
    mlreg: no visible global function definition for ‘model.matrix’
    mlreg: no visible global function definition for ‘model.extract’
    mlreg: no visible global function definition for ‘pchisq’
    mlreg: no visible global function definition for ‘new’
    mlreg.p: no visible global function definition for ‘is’
    mlreg.p: no visible global function definition for ‘model.matrix’
    mlreg.p: no visible global function definition for ‘model.extract’
    mlreg.p: no visible global function definition for ‘pchisq’
    mmscore: no visible global function definition for ‘is’
    mmscore: no visible global function definition for ‘flush.console’
    mmscore: no visible global function definition for ‘pchisq’
    mmscore: no visible global function definition for ‘new’
    palinear2LiLog: no visible global function definition for ‘read.table’
    palinear2LiLog: no visible global function definition for ‘write.table’
    patch_strand: no visible global function definition for ‘new’
    perid.summary: no visible global function definition for ‘is’
    plot.check.marker: no visible global function definition for ‘is’
    plot.check.marker: no visible global function definition for ‘plot’
    plot.check.marker: no visible global function definition for ‘text’
    plot.check.marker: no visible global function definition for ‘lines’
    plot.check.marker: no visible global function definition for ‘points’
    plot.check.marker: no visible global function definition for ‘abline’
    plot.check.marker: no visible global function definition for ‘rug’
    plot.scan.gwaa: no visible global function definition for ‘is’
    plot.scan.gwaa: no visible global function definition for ‘plot’
    plot.scan.gwaa: no visible global function definition for ‘points’
    plot.scan.gwaa: no visible global function definition for ‘axis’
    plot.scan.gwaa.2D: no visible global function definition for ‘image’
    polygenic: no visible global function definition for ‘is’
    polygenic: no visible global function definition for ‘gaussian’
    polygenic: no visible global function definition for ‘binomial’
    polygenic: no visible global function definition for ‘as’
    polygenic: no visible global function definition for ‘model.frame’
    polygenic: no visible binding for global variable ‘na.omit’
    polygenic: no visible global function definition for ‘as.formula’
    polygenic: no visible global function definition for ‘model.response’
    polygenic: no visible global function definition for ‘sd’
    polygenic: no visible global function definition for ‘model.matrix’
    polygenic: no visible global function definition for ‘glm’
    polygenic: no visible global function definition for ‘var’
    polygenic: no visible global function definition for ‘ginv’
    polygenic: no visible global function definition for ‘flush.console’
    polygenic: no visible global function definition for ‘nlm’
    polygenic: no visible global function definition for ‘optim’
    polygenic: no visible global function definition for ‘runif’
    polygenic_hglm: no visible global function definition for ‘gaussian’
    polygenic_hglm: no visible global function definition for ‘is’
    polygenic_hglm: no visible global function definition for ‘as.formula’
    polygenic_hglm: no visible global function definition for ‘model.frame’
    polygenic_hglm: no visible binding for global variable ‘na.omit’
    polygenic_hglm: no visible global function definition for
     ‘model.response’
    polygenic_hglm: no visible global function definition for
     ‘model.matrix’
    polygenic_hglm: no visible global function definition for ‘hglm’
    polygenic_hglm: no visible global function definition for ‘ginv’
    qqplot.plot: no visible global function definition for ‘na.omit’
    qqplot.plot: no visible global function definition for ‘rchisq’
    qqplot.plot: no visible global function definition for ‘bitmap’
    qqplot.plot: no visible global function definition for ‘qqplot’
    qqplot.plot: no visible global function definition for ‘abline’
    qqplot.plot: no visible global function definition for ‘dev.off’
    qqplot.plot: no visible global function definition for ‘pchisq’
    qtscore: no visible global function definition for ‘is’
    qtscore: no visible global function definition for ‘as’
    qtscore: no visible global function definition for ‘model.frame’
    qtscore: no visible binding for global variable ‘na.omit’
    qtscore: no visible global function definition for ‘model.response’
    qtscore: no visible global function definition for ‘gaussian’
    qtscore: no visible global function definition for ‘binomial’
    qtscore: no visible global function definition for ‘model.matrix’
    qtscore: no visible global function definition for ‘glm.fit’
    qtscore: no visible global function definition for ‘residuals’
    qtscore: no visible global function definition for ‘txtProgressBar’
    qtscore: no visible global function definition for ‘setTxtProgressBar’
    qtscore: no visible global function definition for ‘pchisq’
    qtscore: no visible global function definition for ‘new’
    r2fast: no visible global function definition for ‘is’
    r2fast.old: no visible global function definition for ‘is’
    reconstructNPs: no visible global function definition for ‘is’
    redundant: no visible global function definition for ‘is’
    refresh.gwaa.data: no visible global function definition for ‘is’
    refresh.gwaa.data: no visible global function definition for ‘new’
    rhofast: no visible global function definition for ‘is’
    rntransform: no visible binding for global variable ‘gaussian’
    rntransform: no visible global function definition for ‘is’
    rntransform: no visible global function definition for ‘as’
    rntransform: no visible global function definition for ‘qnorm’
    save.gwaa.data: no visible global function definition for ‘write.table’
    save.snp.data: no visible global function definition for ‘is’
    scan.glm: no visible global function definition for ‘gaussian’
    scan.glm: no visible global function definition for ‘is’
    scan.glm: no visible global function definition for ‘as.formula’
    scan.glm: no visible global function definition for ‘glm’
    scan.glm: no visible global function definition for ‘anova’
    scan.glm: no visible global function definition for ‘lm’
    scan.glm: no visible global function definition for ‘flush.console’
    scan.glm: no visible global function definition for ‘median’
    scan.glm: no visible global function definition for ‘qchisq’
    scan.glm.2D: no visible global function definition for ‘gaussian’
    scan.glm.2D: no visible global function definition for ‘is’
    scan.glm.2D: no visible global function definition for ‘as.formula’
    scan.glm.2D: no visible global function definition for ‘glm’
    scan.glm.2D: no visible global function definition for ‘anova’
    scan.glm.2D: no visible global function definition for ‘lm’
    scan.glm.2D: no visible global function definition for ‘flush.console’
    scan.glm.2D: no visible global function definition for ‘median’
    scan.glm.2D: no visible global function definition for ‘qchisq’
    scan.haplo: no visible global function definition for ‘is’
    scan.haplo: no visible global function definition for ‘as.formula’
    scan.haplo: no visible global function definition for
     ‘haplo.score.slide’
    scan.haplo: no visible global function definition for ‘flush.console’
    scan.haplo: no visible global function definition for ‘new’
    scan.haplo.2D: no visible global function definition for ‘is’
    scan.haplo.2D: no visible global function definition for ‘as.formula’
    scan.haplo.2D: no visible global function definition for
     ‘haplo.score.slide’
    scan.haplo.2D: no visible global function definition for
     ‘score.sim.control’
    scan.haplo.2D: no visible global function definition for
     ‘flush.console’
    show.ncbi: no visible global function definition for ‘browseURL’
    show.ncbi: no visible global function definition for ‘is’
    snp.data: no visible global function definition for ‘new’
    snp.names: no visible global function definition for ‘is’
    snp.names.gwaa.data: no visible global function definition for ‘is’
    snp.subset: no visible global function definition for ‘is’
    snp.subset.scan.gwaa: no visible global function definition for ‘new’
    summary.snp.data: no visible global function definition for ‘is’
    summary.snp.data: no visible global function definition for ‘pchisq’
    summary.snp.data_old: no visible global function definition for ‘is’
    summary.snp.data_old: no visible global function definition for
     ‘pchisq’
    ztransform: no visible binding for global variable ‘gaussian’
    ztransform: no visible global function definition for ‘is’
    ztransform: no visible global function definition for ‘as’
    ztransform: no visible global function definition for ‘model.frame’
    ztransform: no visible binding for global variable ‘na.pass’
    ztransform: no visible global function definition for ‘complete.cases’
    ztransform: no visible global function definition for ‘model.response’
    ztransform: no visible global function definition for ‘model.matrix’
    ztransform: no visible global function definition for ‘glm.fit’
    ztransform: no visible global function definition for ‘sd’
    [,gwaa.data-ANY-ANY-ANY: no visible global function definition for
     ‘new’
    [,snp.coding-ANY-missing-missing: no visible global function definition
     for ‘new’
    [,snp.data-ANY-ANY-ANY: no visible global function definition for ‘new’
    [,snp.mx-ANY-ANY-ANY: no visible global function definition for ‘new’
    [,snp.strand-ANY-missing-missing: no visible global function definition
     for ‘new’
    coding<-,snp.data: no visible global function definition for ‘new’
    results,scan.gwaa: no visible global function definition for ‘pchisq’
    show,gwaa.data: no visible global function definition for ‘show’
    show,snp.data: no visible global function definition for ‘show’
    Undefined global functions or variables:
     abline anova apply2dfo as as.dist as.formula axis bartlett.test
     binomial bitmap boxplot browseURL cmdscale complete.cases databel
     density dev.off disconnect extract_text_file_columns fisher.test
     flush.console gaussian genotype get_dimnames get_temporary_file_name
     ginv glm glm.fit haplo.score.slide hglm image is kmeans kruskal.test
     ks.test lines lm median model.extract model.frame model.matrix
     model.response na.omit na.pass new nlm optim optimize par pchisq plot
     points ppoints qchisq qnorm qqplot quantile qvalue rbinom rchisq
     read.table residuals rug runif score.sim.control sd setTxtProgressBar
     set_dimnames<- show t.test text text2databel txtProgressBar var
     write.table
    Consider adding
     importFrom("grDevices", "bitmap", "dev.off")
     importFrom("graphics", "abline", "axis", "boxplot", "image", "lines",
     "par", "plot", "points", "rug", "text")
     importFrom("methods", "as", "is", "new", "show")
     importFrom("stats", "anova", "as.dist", "as.formula", "bartlett.test",
     "binomial", "cmdscale", "complete.cases", "density",
     "fisher.test", "gaussian", "glm", "glm.fit", "kmeans",
     "kruskal.test", "ks.test", "lm", "median", "model.extract",
     "model.frame", "model.matrix", "model.response", "na.omit",
     "na.pass", "nlm", "optim", "optimize", "pchisq", "ppoints",
     "qchisq", "qnorm", "qqplot", "quantile", "rbinom", "rchisq",
     "residuals", "runif", "sd", "t.test", "var")
     importFrom("utils", "browseURL", "flush.console", "read.table",
     "setTxtProgressBar", "txtProgressBar", "write.table")
    to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
    contains 'methods').
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-osx-x86_64-mavericks, r-release-windows-ix86+x86_64

Version: 1.8-0
Check: line endings in Makefiles
Result: NOTE
    Found the following Makefile(s) without a final LF:
     inst/unitTests/Makefile
    Some ‘make’ programs ignore lines not ending in LF.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-osx-x86_64-mavericks, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 1.8-0
Check: compiled code
Result: NOTE
    File ‘GenABEL/libs/GenABEL.so’:
     Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’
    
    It is good practice to register native routines and to disable symbol
    search.
    
    See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Version: 1.8-0
Flags: --no-stop-on-test-error
Check: installed package size
Result: NOTE
     installed size is 7.5Mb
     sub-directories of 1Mb or more:
     doc 2.3Mb
     libs 4.3Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 1.8-0
Flags: --no-stop-on-test-error
Check: whether the namespace can be loaded with stated dependencies
Result: NOTE
    Warning: no function found corresponding to methods exports from ‘GenABEL’ for: ‘show’
    
    A namespace must be able to be loaded with just the base namespace
    loaded: otherwise if the namespace gets loaded by a saved object, the
    session will be unable to start.
    
    Probably some imports need to be declared in the NAMESPACE file.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-macos-x86_64-clang

Version: 1.8-0
Flags: --no-stop-on-test-error
Check: dependencies in R code
Result: NOTE
    'library' or 'require' calls in package code:
     ‘DatABEL’ ‘genetics’ ‘haplo.stats’ ‘hglm’ ‘qvalue’
     Please use :: or requireNamespace() instead.
     See section 'Suggested packages' in the 'Writing R Extensions' manual.
    Packages in Depends field not imported from:
     ‘GenABEL.data’ ‘MASS’ ‘methods’
     These packages need to be imported from (in the NAMESPACE file)
     for when this namespace is loaded but not attached.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-macos-x86_64-clang

Version: 1.8-0
Flags: --no-stop-on-test-error
Check: S3 generic/method consistency
Result: NOTE
    Found the following apparent S3 methods exported but not registered:
     as.character.snp.coding as.character.snp.strand merge.gwaa.data
     merge.snp.data summary.snp.data_old
    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-devel-macos-x86_64-clang

Version: 1.8-0
Flags: --no-stop-on-test-error
Check: R code for possible problems
Result: NOTE
    GASurv: no visible global function definition for ‘is’
    HWE.show: no visible global function definition for ‘is’
    HWE.show: no visible global function definition for ‘pchisq’
    LiLog: no visible global function definition for ‘binomial’
    PGC: no visible global function definition for ‘median’
    PGC: no visible global function definition for ‘qchisq’
    PGC: no visible global function definition for ‘ppoints’
    PGC: no visible global function definition for ‘quantile’
    PGC : f2: no visible global function definition for ‘ks.test’
    PGC : f2: no visible global function definition for ‘median’
    PGC : f2: no visible global function definition for ‘qchisq’
    PGC: no visible global function definition for ‘abline’
    PGC: no visible global function definition for ‘lines’
    VIFGC : Clust: no visible global function definition for ‘as.dist’
    VIFGC : Clust: no visible global function definition for ‘cmdscale’
    VIFGC : ClustN: no visible global function definition for ‘kmeans’
    VIFGC : GC_VIF_nlm: no visible global function definition for ‘ks.test’
    VIFGC : GC_VIF_nlm: no visible global function definition for ‘qchisq’
    VIFGC : GC_VIF_nlm: no visible global function definition for ‘median’
    VIFGC : GC_VIF: no visible global function definition for ‘ks.test’
    VIFGC : GC_VIF: no visible global function definition for ‘qchisq’
    VIFGC : GC_VIF: no visible global function definition for ‘median’
    VIFGC: no visible global function definition for ‘qchisq’
    VIFGC: no visible global function definition for ‘median’
    VIFGC: no visible global function definition for ‘ppoints’
    VIFGC: no visible global function definition for ‘optimize’
    VIFGC: no visible global function definition for ‘nlm’
    VIFGC: no visible global function definition for ‘abline’
    VIFGC: no visible global function definition for ‘lines’
    VIFGC_ovdom : Clust: no visible global function definition for
     ‘as.dist’
    VIFGC_ovdom : Clust: no visible global function definition for
     ‘cmdscale’
    VIFGC_ovdom : ClustN: no visible global function definition for
     ‘kmeans’
    VIFGC_ovdom : GC_VIF_nlm: no visible global function definition for
     ‘ks.test’
    VIFGC_ovdom : GC_VIF_nlm: no visible global function definition for
     ‘qchisq’
    VIFGC_ovdom : GC_VIF_nlm: no visible global function definition for
     ‘median’
    VIFGC_ovdom : GC_VIF: no visible global function definition for
     ‘ks.test’
    VIFGC_ovdom : GC_VIF: no visible global function definition for
     ‘qchisq’
    VIFGC_ovdom : GC_VIF: no visible global function definition for
     ‘median’
    VIFGC_ovdom: no visible global function definition for ‘qchisq’
    VIFGC_ovdom: no visible global function definition for ‘ppoints’
    VIFGC_ovdom: no visible global function definition for ‘optimize’
    VIFGC_ovdom: no visible global function definition for ‘median’
    VIFGC_ovdom: no visible global function definition for ‘nlm’
    VIFGC_ovdom: no visible global function definition for ‘abline’
    Xcheck: no visible global function definition for ‘is’
    Xfix: no visible global function definition for ‘is’
    Xfix.internal: no visible global function definition for ‘is’
    add.phdata: no visible global function definition for ‘is’
    add.plot: no visible global function definition for ‘is’
    add.plot: no visible global function definition for ‘points’
    add.plot: no visible global function definition for ‘image’
    arrange_probabel_phe: no visible global function definition for
     ‘read.table’
    arrange_probabel_phe: no visible global function definition for
     ‘databel’
    arrange_probabel_phe: no visible global function definition for
     ‘write.table’
    as.character.gwaa.data: no visible global function definition for ‘is’
    as.character.snp.data: no visible global function definition for ‘is’
    as.double.gwaa.data: no visible global function definition for ‘is’
    as.double.snp.data: no visible global function definition for ‘is’
    as.genotype.gwaa.data: no visible global function definition for ‘is’
    as.genotype.snp.data: no visible global function definition for ‘is’
    as.genotype.snp.data: no visible global function definition for
     ‘genotype’
    as.hsgeno.gwaa.data: no visible global function definition for ‘is’
    as.hsgeno.snp.data: no visible global function definition for ‘is’
    as.raw.snp.data: no visible global function definition for ‘is’
    as.raw.snp.mx: no visible global function definition for ‘is’
    autosomal: no visible global function definition for ‘is’
    blurGenotype: no visible global function definition for ‘is’
    catable: no visible global function definition for ‘quantile’
    catable: no visible global function definition for ‘is’
    ccfast: no visible global function definition for ‘is’
    ccfast: no visible global function definition for ‘flush.console’
    ccfast: no visible global function definition for ‘pchisq’
    ccfast: no visible global function definition for ‘new’
    ccfast.new: no visible global function definition for ‘is’
    check.marker: no visible global function definition for ‘is’
    check.marker.internal: no visible global function definition for ‘is’
    check.marker.internal: no visible global function definition for
     ‘flush.console’
    check.marker.internal: no visible global function definition for
     ‘qvalue’
    check.marker.internal: no visible global function definition for ‘sd’
    check.marker.internal: no visible global function definition for
     ‘pchisq’
    check.trait: no visible global function definition for ‘is’
    checkphengen: no visible global function definition for ‘is’
    cocohet: no visible global function definition for ‘is’
    cocohet: no visible global function definition for ‘pchisq’
    convert.snp.affymetrix: no visible global function definition for ‘is’
    convert.snp.mach: no visible global function definition for
     ‘read.table’
    convert.snp.mach: no visible global function definition for ‘new’
    descriptives.marker: no visible global function definition for ‘is’
    descriptives.marker: no visible global function definition for ‘sd’
    descriptives.marker: no visible global function definition for
     ‘write.table’
    descriptives.scan: no visible global function definition for ‘is’
    descriptives.scan: no visible global function definition for
     ‘write.table’
    descriptives.trait: no visible global function definition for ‘is’
    descriptives.trait: no visible global function definition for ‘sd’
    descriptives.trait: no visible global function definition for ‘t.test’
    descriptives.trait: no visible global function definition for
     ‘kruskal.test’
    descriptives.trait: no visible global function definition for
     ‘fisher.test’
    descriptives.trait: no visible global function definition for
     ‘write.table’
    dprfast: no visible global function definition for ‘is’
    drop.out.points: no visible global function definition for ‘var’
    dump.piece: no visible global function definition for ‘write.table’
    egscore: no visible global function definition for ‘is’
    egscore: no visible global function definition for ‘as’
    egscore: no visible global function definition for ‘model.frame’
    egscore: no visible binding for global variable ‘na.omit’
    egscore: no visible global function definition for ‘model.response’
    egscore: no visible global function definition for ‘model.matrix’
    egscore: no visible global function definition for ‘glm.fit’
    egscore: no visible global function definition for ‘lm’
    egscore: no visible global function definition for ‘flush.console’
    egscore: no visible global function definition for ‘pchisq’
    egscore: no visible global function definition for ‘new’
    egscore.old: no visible global function definition for ‘is’
    egscore.old: no visible global function definition for ‘as’
    egscore.old: no visible global function definition for ‘model.frame’
    egscore.old: no visible binding for global variable ‘na.omit’
    egscore.old: no visible global function definition for ‘model.response’
    egscore.old: no visible global function definition for ‘model.matrix’
    egscore.old: no visible global function definition for ‘glm.fit’
    egscore.old: no visible global function definition for ‘lm’
    egscore.old: no visible global function definition for ‘flush.console’
    egscore.old: no visible global function definition for ‘pchisq’
    estLambdaKS: no visible global function definition for ‘optimize’
    estlambda: no visible global function definition for ‘qchisq’
    estlambda: no visible global function definition for ‘ppoints’
    estlambda: no visible global function definition for ‘lm’
    estlambda: no visible global function definition for ‘median’
    estlambda: no visible global function definition for ‘par’
    estlambda: no visible global function definition for ‘abline’
    export.impute: no visible global function definition for ‘is’
    export.impute: no visible global function definition for ‘write.table’
    export.merlin: no visible global function definition for ‘is’
    export.merlin: no visible global function definition for ‘new’
    export.merlin: no visible global function definition for ‘write.table’
    export.plink: no visible global function definition for ‘write.table’
    extract.annotation.impute: no visible global function definition for
     ‘extract_text_file_columns’
    extract.annotation.mach: no visible global function definition for
     ‘extract_text_file_columns’
    fcc: no visible global function definition for ‘is’
    fcc.new: no visible global function definition for ‘is’
    findRelatives: no visible global function definition for ‘is’
    findRelatives: no visible global function definition for
     ‘txtProgressBar’
    findRelatives: no visible global function definition for
     ‘setTxtProgressBar’
    formetascore: no visible global function definition for ‘is’
    formetascore: no visible global function definition for ‘as’
    formetascore: no visible global function definition for ‘model.frame’
    formetascore: no visible binding for global variable ‘na.omit’
    generateOffspring : genSOG: no visible global function definition for
     ‘runif’
    generateOffspring : infer: no visible global function definition for
     ‘rbinom’
    generateOffspring: no visible global function definition for ‘rbinom’
    get.snp.distr.plot: no visible global function definition for ‘na.omit’
    get.snp.distr.plot: no visible global function definition for ‘bitmap’
    get.snp.distr.plot: no visible global function definition for ‘par’
    get.snp.distr.plot: no visible global function definition for
     ‘bartlett.test’
    get.snp.distr.plot: no visible global function definition for ‘boxplot’
    get.snp.distr.plot: no visible global function definition for ‘plot’
    get.snp.distr.plot: no visible global function definition for ‘density’
    get.snp.distr.plot: no visible global function definition for ‘dev.off’
    grammar: no visible global function definition for ‘pchisq’
    grammar.old: no visible global function definition for ‘is’
    grammar.old: no visible global function definition for ‘flush.console’
    grammar.old: no visible global function definition for ‘pchisq’
    hom: no visible global function definition for ‘is’
    hom.old: no visible global function definition for ‘is’
    ibs: no visible global function definition for ‘is’
    ibs.old: no visible global function definition for ‘is’
    imphetcheck: no visible global function definition for ‘is’
    impute2databel: no visible global function definition for
     ‘get_temporary_file_name’
    impute2databel: no visible global function definition for
     ‘text2databel’
    impute2databel: no visible global function definition for
     ‘get_dimnames’
    impute2databel: no visible global function definition for ‘apply2dfo’
    impute2databel: no visible global function definition for ‘databel’
    impute2databel: no visible global function definition for
     ‘set_dimnames<-’
    impute2databel: no visible global function definition for ‘disconnect’
    impute2mach: no visible global function definition for ‘write.table’
    impute2mach: no visible global function definition for ‘get_dimnames’
    impute2mach: no visible global function definition for ‘as’
    impute2mach: no visible global function definition for ‘disconnect’
    load.gwaa.data: no visible global function definition for ‘read.table’
    load.gwaa.data: no visible global function definition for ‘new’
    lossFunctionLambdaKS: no visible global function definition for
     ‘ks.test’
    mach2databel: no visible global function definition for
     ‘get_temporary_file_name’
    mach2databel: no visible global function definition for ‘text2databel’
    mach2databel: no visible global function definition for ‘get_dimnames’
    makeTransitionMatrix: no visible global function definition for ‘is’
    merge.gwaa.data: no visible global function definition for ‘is’
    merge.gwaa.data: no visible global function definition for ‘new’
    merge.snp.data: no visible global function definition for ‘is’
    merge.snp.data: no visible global function definition for ‘write.table’
    merge.snp.data: no visible global function definition for ‘new’
    minimac2databel: no visible global function definition for
     ‘get_temporary_file_name’
    minimac2databel: no visible global function definition for
     ‘text2databel’
    minimac2databel: no visible global function definition for
     ‘get_dimnames’
    mlreg: no visible global function definition for ‘is’
    mlreg: no visible global function definition for ‘model.matrix’
    mlreg: no visible global function definition for ‘model.extract’
    mlreg: no visible global function definition for ‘pchisq’
    mlreg: no visible global function definition for ‘new’
    mlreg.p: no visible global function definition for ‘is’
    mlreg.p: no visible global function definition for ‘model.matrix’
    mlreg.p: no visible global function definition for ‘model.extract’
    mlreg.p: no visible global function definition for ‘pchisq’
    mmscore: no visible global function definition for ‘is’
    mmscore: no visible global function definition for ‘flush.console’
    mmscore: no visible global function definition for ‘pchisq’
    mmscore: no visible global function definition for ‘new’
    palinear2LiLog: no visible global function definition for ‘read.table’
    palinear2LiLog: no visible global function definition for ‘write.table’
    patch_strand: no visible global function definition for ‘new’
    perid.summary: no visible global function definition for ‘is’
    plot.check.marker: no visible global function definition for ‘is’
    plot.check.marker: no visible global function definition for ‘plot’
    plot.check.marker: no visible global function definition for ‘text’
    plot.check.marker: no visible global function definition for ‘lines’
    plot.check.marker: no visible global function definition for ‘points’
    plot.check.marker: no visible global function definition for ‘abline’
    plot.check.marker: no visible global function definition for ‘rug’
    plot.scan.gwaa: no visible global function definition for ‘is’
    plot.scan.gwaa: no visible global function definition for ‘plot’
    plot.scan.gwaa: no visible global function definition for ‘points’
    plot.scan.gwaa: no visible global function definition for ‘axis’
    plot.scan.gwaa.2D: no visible global function definition for ‘image’
    polygenic: no visible global function definition for ‘is’
    polygenic: no visible global function definition for ‘gaussian’
    polygenic: no visible global function definition for ‘binomial’
    polygenic: no visible global function definition for ‘as’
    polygenic: no visible global function definition for ‘model.frame’
    polygenic: no visible binding for global variable ‘na.omit’
    polygenic: no visible global function definition for ‘as.formula’
    polygenic: no visible global function definition for ‘model.response’
    polygenic: no visible global function definition for ‘sd’
    polygenic: no visible global function definition for ‘model.matrix’
    polygenic: no visible global function definition for ‘glm’
    polygenic: no visible global function definition for ‘var’
    polygenic: no visible global function definition for ‘ginv’
    polygenic: no visible global function definition for ‘flush.console’
    polygenic: no visible global function definition for ‘nlm’
    polygenic: no visible global function definition for ‘optim’
    polygenic: no visible global function definition for ‘runif’
    polygenic_hglm: no visible global function definition for ‘gaussian’
    polygenic_hglm: no visible global function definition for ‘is’
    polygenic_hglm: no visible global function definition for ‘as.formula’
    polygenic_hglm: no visible global function definition for ‘model.frame’
    polygenic_hglm: no visible binding for global variable ‘na.omit’
    polygenic_hglm: no visible global function definition for
     ‘model.response’
    polygenic_hglm: no visible global function definition for
     ‘model.matrix’
    polygenic_hglm: no visible global function definition for ‘hglm’
    polygenic_hglm: no visible global function definition for ‘ginv’
    qqplot.plot: no visible global function definition for ‘na.omit’
    qqplot.plot: no visible global function definition for ‘rchisq’
    qqplot.plot: no visible global function definition for ‘bitmap’
    qqplot.plot: no visible global function definition for ‘qqplot’
    qqplot.plot: no visible global function definition for ‘abline’
    qqplot.plot: no visible global function definition for ‘dev.off’
    qqplot.plot: no visible global function definition for ‘pchisq’
    qtscore: no visible global function definition for ‘is’
    qtscore: no visible global function definition for ‘as’
    qtscore: no visible global function definition for ‘model.frame’
    qtscore: no visible binding for global variable ‘na.omit’
    qtscore: no visible global function definition for ‘model.response’
    qtscore: no visible global function definition for ‘gaussian’
    qtscore: no visible global function definition for ‘binomial’
    qtscore: no visible global function definition for ‘model.matrix’
    qtscore: no visible global function definition for ‘glm.fit’
    qtscore: no visible global function definition for ‘residuals’
    qtscore: no visible global function definition for ‘txtProgressBar’
    qtscore: no visible global function definition for ‘setTxtProgressBar’
    qtscore: no visible global function definition for ‘pchisq’
    qtscore: no visible global function definition for ‘new’
    r2fast: no visible global function definition for ‘is’
    r2fast.old: no visible global function definition for ‘is’
    reconstructNPs: no visible global function definition for ‘is’
    redundant: no visible global function definition for ‘is’
    refresh.gwaa.data: no visible global function definition for ‘is’
    refresh.gwaa.data: no visible global function definition for ‘new’
    rhofast: no visible global function definition for ‘is’
    rntransform: no visible binding for global variable ‘gaussian’
    rntransform: no visible global function definition for ‘is’
    rntransform: no visible global function definition for ‘as’
    rntransform: no visible global function definition for ‘qnorm’
    save.gwaa.data: no visible global function definition for ‘write.table’
    save.snp.data: no visible global function definition for ‘is’
    scan.glm: no visible global function definition for ‘gaussian’
    scan.glm: no visible global function definition for ‘is’
    scan.glm: no visible global function definition for ‘as.formula’
    scan.glm: no visible global function definition for ‘glm’
    scan.glm: no visible global function definition for ‘anova’
    scan.glm: no visible global function definition for ‘lm’
    scan.glm: no visible global function definition for ‘flush.console’
    scan.glm: no visible global function definition for ‘median’
    scan.glm: no visible global function definition for ‘qchisq’
    scan.glm.2D: no visible global function definition for ‘gaussian’
    scan.glm.2D: no visible global function definition for ‘is’
    scan.glm.2D: no visible global function definition for ‘as.formula’
    scan.glm.2D: no visible global function definition for ‘glm’
    scan.glm.2D: no visible global function definition for ‘anova’
    scan.glm.2D: no visible global function definition for ‘lm’
    scan.glm.2D: no visible global function definition for ‘flush.console’
    scan.glm.2D: no visible global function definition for ‘median’
    scan.glm.2D: no visible global function definition for ‘qchisq’
    scan.haplo: no visible global function definition for ‘is’
    scan.haplo: no visible global function definition for ‘as.formula’
    scan.haplo: no visible global function definition for
     ‘haplo.score.slide’
    scan.haplo: no visible global function definition for ‘flush.console’
    scan.haplo: no visible global function definition for ‘new’
    scan.haplo.2D: no visible global function definition for ‘is’
    scan.haplo.2D: no visible global function definition for ‘as.formula’
    scan.haplo.2D: no visible global function definition for
     ‘haplo.score.slide’
    scan.haplo.2D: no visible global function definition for
     ‘score.sim.control’
    scan.haplo.2D: no visible global function definition for
     ‘flush.console’
    show.ncbi: no visible global function definition for ‘browseURL’
    show.ncbi: no visible global function definition for ‘is’
    snp.data: no visible global function definition for ‘new’
    snp.names: no visible global function definition for ‘is’
    snp.names.gwaa.data: no visible global function definition for ‘is’
    snp.subset: no visible global function definition for ‘is’
    snp.subset.scan.gwaa: no visible global function definition for ‘new’
    summary.snp.data: no visible global function definition for ‘is’
    summary.snp.data: no visible global function definition for ‘pchisq’
    summary.snp.data_old: no visible global function definition for ‘is’
    summary.snp.data_old: no visible global function definition for
     ‘pchisq’
    ztransform: no visible binding for global variable ‘gaussian’
    ztransform: no visible global function definition for ‘is’
    ztransform: no visible global function definition for ‘as’
    ztransform: no visible global function definition for ‘model.frame’
    ztransform: no visible binding for global variable ‘na.pass’
    ztransform: no visible global function definition for ‘complete.cases’
    ztransform: no visible global function definition for ‘model.response’
    ztransform: no visible global function definition for ‘model.matrix’
    ztransform: no visible global function definition for ‘glm.fit’
    ztransform: no visible global function definition for ‘sd’
    [,gwaa.data-ANY-ANY-ANY: no visible global function definition for
     ‘new’
    [,snp.coding-ANY-missing-missing: no visible global function definition
     for ‘new’
    [,snp.data-ANY-ANY-ANY: no visible global function definition for ‘new’
    [,snp.mx-ANY-ANY-ANY: no visible global function definition for ‘new’
    [,snp.strand-ANY-missing-missing: no visible global function definition
     for ‘new’
    coding<-,snp.data: no visible global function definition for ‘new’
    results,scan.gwaa: no visible global function definition for ‘pchisq’
    show,gwaa.data: no visible global function definition for ‘show’
    show,snp.data: no visible global function definition for ‘show’
    Undefined global functions or variables:
     abline anova apply2dfo as as.dist as.formula axis bartlett.test
     binomial bitmap boxplot browseURL cmdscale complete.cases databel
     density dev.off disconnect extract_text_file_columns fisher.test
     flush.console gaussian genotype get_dimnames get_temporary_file_name
     ginv glm glm.fit haplo.score.slide hglm image is kmeans kruskal.test
     ks.test lines lm median model.extract model.frame model.matrix
     model.response na.omit na.pass new nlm optim optimize par pchisq plot
     points ppoints qchisq qnorm qqplot quantile qvalue rbinom rchisq
     read.table residuals rug runif score.sim.control sd setTxtProgressBar
     set_dimnames<- show t.test text text2databel txtProgressBar var
     write.table
    Consider adding
     importFrom("grDevices", "bitmap", "dev.off")
     importFrom("graphics", "abline", "axis", "boxplot", "image", "lines",
     "par", "plot", "points", "rug", "text")
     importFrom("methods", "as", "is", "new", "show")
     importFrom("stats", "anova", "as.dist", "as.formula", "bartlett.test",
     "binomial", "cmdscale", "complete.cases", "density",
     "fisher.test", "gaussian", "glm", "glm.fit", "kmeans",
     "kruskal.test", "ks.test", "lm", "median", "model.extract",
     "model.frame", "model.matrix", "model.response", "na.omit",
     "na.pass", "nlm", "optim", "optimize", "pchisq", "ppoints",
     "qchisq", "qnorm", "qqplot", "quantile", "rbinom", "rchisq",
     "residuals", "runif", "sd", "t.test", "var")
     importFrom("utils", "browseURL", "flush.console", "read.table",
     "setTxtProgressBar", "txtProgressBar", "write.table")
    to your NAMESPACE file (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-macos-x86_64-clang

Version: 1.8-0
Flags: --no-stop-on-test-error
Check: line endings in Makefiles
Result: NOTE
    Found the following Makefile(s) without a final LF:
     inst/unitTests/Makefile
    Some ‘make’ programs ignore lines not ending in LF.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-macos-x86_64-clang

Version: 1.8-0
Flags: --no-stop-on-test-error
Check: compiled code
Result: NOTE
    File ‘GenABEL/libs/GenABEL.so’:
     Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’
    
    It is good practice to register native routines and to disable symbol
    search.
    
    See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-macos-x86_64-clang

Version: 1.8-0
Check: installed package size
Result: NOTE
     installed size is 5.5Mb
     sub-directories of 1Mb or more:
     doc 2.2Mb
     libs 2.3Mb
Flavors: r-devel-windows-ix86+x86_64, r-release-osx-x86_64-mavericks, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 1.8-0
Flags: --no-examples
Check: whether the namespace can be loaded with stated dependencies
Result: NOTE
    Warning: no function found corresponding to methods exports from ‘GenABEL’ for: ‘show’
    
    A namespace must be able to be loaded with just the base namespace
    loaded: otherwise if the namespace gets loaded by a saved object, the
    session will be unable to start.
    
    Probably some imports need to be declared in the NAMESPACE file.
Flavor: r-patched-solaris-sparc

Version: 1.8-0
Flags: --no-examples
Check: dependencies in R code
Result: NOTE
    'library' or 'require' calls in package code:
     ‘DatABEL’ ‘genetics’ ‘haplo.stats’ ‘hglm’ ‘qvalue’
     Please use :: or requireNamespace() instead.
     See section 'Suggested packages' in the 'Writing R Extensions' manual.
    Packages in Depends field not imported from:
     ‘GenABEL.data’ ‘MASS’ ‘methods’
     These packages need to be imported from (in the NAMESPACE file)
     for when this namespace is loaded but not attached.
Flavor: r-patched-solaris-sparc

Version: 1.8-0
Flags: --no-examples
Check: S3 generic/method consistency
Result: NOTE
    Found the following apparent S3 methods exported but not registered:
     as.character.snp.coding as.character.snp.strand merge.gwaa.data
     merge.snp.data summary.snp.data_old
    See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
    manual.
Flavor: r-patched-solaris-sparc

Version: 1.8-0
Flags: --no-examples
Check: R code for possible problems
Result: NOTE
    GASurv: no visible global function definition for ‘is’
    HWE.show: no visible global function definition for ‘is’
    HWE.show: no visible global function definition for ‘pchisq’
    LiLog: no visible global function definition for ‘binomial’
    PGC: no visible global function definition for ‘median’
    PGC: no visible global function definition for ‘qchisq’
    PGC: no visible global function definition for ‘ppoints’
    PGC: no visible global function definition for ‘quantile’
    PGC : f2: no visible global function definition for ‘ks.test’
    PGC : f2: no visible global function definition for ‘median’
    PGC : f2: no visible global function definition for ‘qchisq’
    PGC: no visible global function definition for ‘abline’
    PGC: no visible global function definition for ‘lines’
    VIFGC : Clust: no visible global function definition for ‘as.dist’
    VIFGC : Clust: no visible global function definition for ‘cmdscale’
    VIFGC : ClustN: no visible global function definition for ‘kmeans’
    VIFGC : GC_VIF_nlm: no visible global function definition for ‘ks.test’
    VIFGC : GC_VIF_nlm: no visible global function definition for ‘qchisq’
    VIFGC : GC_VIF_nlm: no visible global function definition for ‘median’
    VIFGC : GC_VIF: no visible global function definition for ‘ks.test’
    VIFGC : GC_VIF: no visible global function definition for ‘qchisq’
    VIFGC : GC_VIF: no visible global function definition for ‘median’
    VIFGC: no visible global function definition for ‘qchisq’
    VIFGC: no visible global function definition for ‘median’
    VIFGC: no visible global function definition for ‘ppoints’
    VIFGC: no visible global function definition for ‘optimize’
    VIFGC: no visible global function definition for ‘nlm’
    VIFGC: no visible global function definition for ‘abline’
    VIFGC: no visible global function definition for ‘lines’
    VIFGC_ovdom : Clust: no visible global function definition for
     ‘as.dist’
    VIFGC_ovdom : Clust: no visible global function definition for
     ‘cmdscale’
    VIFGC_ovdom : ClustN: no visible global function definition for
     ‘kmeans’
    VIFGC_ovdom : GC_VIF_nlm: no visible global function definition for
     ‘ks.test’
    VIFGC_ovdom : GC_VIF_nlm: no visible global function definition for
     ‘qchisq’
    VIFGC_ovdom : GC_VIF_nlm: no visible global function definition for
     ‘median’
    VIFGC_ovdom : GC_VIF: no visible global function definition for
     ‘ks.test’
    VIFGC_ovdom : GC_VIF: no visible global function definition for
     ‘qchisq’
    VIFGC_ovdom : GC_VIF: no visible global function definition for
     ‘median’
    VIFGC_ovdom: no visible global function definition for ‘qchisq’
    VIFGC_ovdom: no visible global function definition for ‘ppoints’
    VIFGC_ovdom: no visible global function definition for ‘optimize’
    VIFGC_ovdom: no visible global function definition for ‘median’
    VIFGC_ovdom: no visible global function definition for ‘nlm’
    VIFGC_ovdom: no visible global function definition for ‘abline’
    Xcheck: no visible global function definition for ‘is’
    Xfix: no visible global function definition for ‘is’
    Xfix.internal: no visible global function definition for ‘is’
    add.phdata: no visible global function definition for ‘is’
    add.plot: no visible global function definition for ‘is’
    add.plot: no visible global function definition for ‘points’
    add.plot: no visible global function definition for ‘image’
    arrange_probabel_phe: no visible global function definition for
     ‘read.table’
    arrange_probabel_phe: no visible global function definition for
     ‘databel’
    arrange_probabel_phe: no visible global function definition for
     ‘write.table’
    as.character.gwaa.data: no visible global function definition for ‘is’
    as.character.snp.data: no visible global function definition for ‘is’
    as.double.gwaa.data: no visible global function definition for ‘is’
    as.double.snp.data: no visible global function definition for ‘is’
    as.genotype.gwaa.data: no visible global function definition for ‘is’
    as.genotype.snp.data: no visible global function definition for ‘is’
    as.genotype.snp.data: no visible global function definition for
     ‘genotype’
    as.hsgeno.gwaa.data: no visible global function definition for ‘is’
    as.hsgeno.snp.data: no visible global function definition for ‘is’
    as.raw.snp.data: no visible global function definition for ‘is’
    as.raw.snp.mx: no visible global function definition for ‘is’
    autosomal: no visible global function definition for ‘is’
    blurGenotype: no visible global function definition for ‘is’
    catable: no visible global function definition for ‘quantile’
    catable: no visible global function definition for ‘is’
    ccfast: no visible global function definition for ‘is’
    ccfast: no visible global function definition for ‘flush.console’
    ccfast: no visible global function definition for ‘pchisq’
    ccfast: no visible global function definition for ‘new’
    ccfast.new: no visible global function definition for ‘is’
    check.marker: no visible global function definition for ‘is’
    check.marker.internal: no visible global function definition for ‘is’
    check.marker.internal: no visible global function definition for
     ‘flush.console’
    check.marker.internal: no visible global function definition for
     ‘qvalue’
    check.marker.internal: no visible global function definition for ‘sd’
    check.marker.internal: no visible global function definition for
     ‘pchisq’
    check.trait: no visible global function definition for ‘is’
    checkphengen: no visible global function definition for ‘is’
    cocohet: no visible global function definition for ‘is’
    cocohet: no visible global function definition for ‘pchisq’
    convert.snp.affymetrix: no visible global function definition for ‘is’
    convert.snp.mach: no visible global function definition for
     ‘read.table’
    convert.snp.mach: no visible global function definition for ‘new’
    descriptives.marker: no visible global function definition for ‘is’
    descriptives.marker: no visible global function definition for ‘sd’
    descriptives.marker: no visible global function definition for
     ‘write.table’
    descriptives.scan: no visible global function definition for ‘is’
    descriptives.scan: no visible global function definition for
     ‘write.table’
    descriptives.trait: no visible global function definition for ‘is’
    descriptives.trait: no visible global function definition for ‘sd’
    descriptives.trait: no visible global function definition for ‘t.test’
    descriptives.trait: no visible global function definition for
     ‘kruskal.test’
    descriptives.trait: no visible global function definition for
     ‘fisher.test’
    descriptives.trait: no visible global function definition for
     ‘write.table’
    dprfast: no visible global function definition for ‘is’
    drop.out.points: no visible global function definition for ‘var’
    dump.piece: no visible global function definition for ‘write.table’
    egscore: no visible global function definition for ‘is’
    egscore: no visible global function definition for ‘as’
    egscore: no visible global function definition for ‘model.frame’
    egscore: no visible binding for global variable ‘na.omit’
    egscore: no visible global function definition for ‘model.response’
    egscore: no visible global function definition for ‘model.matrix’
    egscore: no visible global function definition for ‘glm.fit’
    egscore: no visible global function definition for ‘lm’
    egscore: no visible global function definition for ‘flush.console’
    egscore: no visible global function definition for ‘pchisq’
    egscore: no visible global function definition for ‘new’
    egscore.old: no visible global function definition for ‘is’
    egscore.old: no visible global function definition for ‘as’
    egscore.old: no visible global function definition for ‘model.frame’
    egscore.old: no visible binding for global variable ‘na.omit’
    egscore.old: no visible global function definition for ‘model.response’
    egscore.old: no visible global function definition for ‘model.matrix’
    egscore.old: no visible global function definition for ‘glm.fit’
    egscore.old: no visible global function definition for ‘lm’
    egscore.old: no visible global function definition for ‘flush.console’
    egscore.old: no visible global function definition for ‘pchisq’
    estLambdaKS: no visible global function definition for ‘optimize’
    estlambda: no visible global function definition for ‘qchisq’
    estlambda: no visible global function definition for ‘ppoints’
    estlambda: no visible global function definition for ‘lm’
    estlambda: no visible global function definition for ‘median’
    estlambda: no visible global function definition for ‘par’
    estlambda: no visible global function definition for ‘abline’
    export.impute: no visible global function definition for ‘is’
    export.impute: no visible global function definition for ‘write.table’
    export.merlin: no visible global function definition for ‘is’
    export.merlin: no visible global function definition for ‘new’
    export.merlin: no visible global function definition for ‘write.table’
    export.plink: no visible global function definition for ‘write.table’
    extract.annotation.impute: no visible global function definition for
     ‘extract_text_file_columns’
    extract.annotation.mach: no visible global function definition for
     ‘extract_text_file_columns’
    fcc: no visible global function definition for ‘is’
    fcc.new: no visible global function definition for ‘is’
    findRelatives: no visible global function definition for ‘is’
    findRelatives: no visible global function definition for
     ‘txtProgressBar’
    findRelatives: no visible global function definition for
     ‘setTxtProgressBar’
    formetascore: no visible global function definition for ‘is’
    formetascore: no visible global function definition for ‘as’
    formetascore: no visible global function definition for ‘model.frame’
    formetascore: no visible binding for global variable ‘na.omit’
    generateOffspring : genSOG: no visible global function definition for
     ‘runif’
    generateOffspring : infer: no visible global function definition for
     ‘rbinom’
    generateOffspring: no visible global function definition for ‘rbinom’
    get.snp.distr.plot: no visible global function definition for ‘na.omit’
    get.snp.distr.plot: no visible global function definition for ‘bitmap’
    get.snp.distr.plot: no visible global function definition for ‘par’
    get.snp.distr.plot: no visible global function definition for
     ‘bartlett.test’
    get.snp.distr.plot: no visible global function definition for ‘boxplot’
    get.snp.distr.plot: no visible global function definition for ‘plot’
    get.snp.distr.plot: no visible global function definition for ‘density’
    get.snp.distr.plot: no visible global function definition for ‘dev.off’
    grammar: no visible global function definition for ‘pchisq’
    grammar.old: no visible global function definition for ‘is’
    grammar.old: no visible global function definition for ‘flush.console’
    grammar.old: no visible global function definition for ‘pchisq’
    hom: no visible global function definition for ‘is’
    hom.old: no visible global function definition for ‘is’
    ibs: no visible global function definition for ‘is’
    ibs.old: no visible global function definition for ‘is’
    imphetcheck: no visible global function definition for ‘is’
    impute2databel: no visible global function definition for
     ‘get_temporary_file_name’
    impute2databel: no visible global function definition for
     ‘text2databel’
    impute2databel: no visible global function definition for
     ‘get_dimnames’
    impute2databel: no visible global function definition for ‘apply2dfo’
    impute2databel: no visible global function definition for ‘databel’
    impute2databel: no visible global function definition for
     ‘set_dimnames<-’
    impute2databel: no visible global function definition for ‘disconnect’
    impute2mach: no visible global function definition for ‘write.table’
    impute2mach: no visible global function definition for ‘get_dimnames’
    impute2mach: no visible global function definition for ‘as’
    impute2mach: no visible global function definition for ‘disconnect’
    load.gwaa.data: no visible global function definition for ‘read.table’
    load.gwaa.data: no visible global function definition for ‘new’
    lossFunctionLambdaKS: no visible global function definition for
     ‘ks.test’
    mach2databel: no visible global function definition for
     ‘get_temporary_file_name’
    mach2databel: no visible global function definition for ‘text2databel’
    mach2databel: no visible global function definition for ‘get_dimnames’
    makeTransitionMatrix: no visible global function definition for ‘is’
    merge.gwaa.data: no visible global function definition for ‘is’
    merge.gwaa.data: no visible global function definition for ‘new’
    merge.snp.data: no visible global function definition for ‘is’
    merge.snp.data: no visible global function definition for ‘write.table’
    merge.snp.data: no visible global function definition for ‘new’
    minimac2databel: no visible global function definition for
     ‘get_temporary_file_name’
    minimac2databel: no visible global function definition for
     ‘text2databel’
    minimac2databel: no visible global function definition for
     ‘get_dimnames’
    mlreg: no visible global function definition for ‘is’
    mlreg: no visible global function definition for ‘model.matrix’
    mlreg: no visible global function definition for ‘model.extract’
    mlreg: no visible global function definition for ‘pchisq’
    mlreg: no visible global function definition for ‘new’
    mlreg.p: no visible global function definition for ‘is’
    mlreg.p: no visible global function definition for ‘model.matrix’
    mlreg.p: no visible global function definition for ‘model.extract’
    mlreg.p: no visible global function definition for ‘pchisq’
    mmscore: no visible global function definition for ‘is’
    mmscore: no visible global function definition for ‘flush.console’
    mmscore: no visible global function definition for ‘pchisq’
    mmscore: no visible global function definition for ‘new’
    palinear2LiLog: no visible global function definition for ‘read.table’
    palinear2LiLog: no visible global function definition for ‘write.table’
    patch_strand: no visible global function definition for ‘new’
    perid.summary: no visible global function definition for ‘is’
    plot.check.marker: no visible global function definition for ‘is’
    plot.check.marker: no visible global function definition for ‘plot’
    plot.check.marker: no visible global function definition for ‘text’
    plot.check.marker: no visible global function definition for ‘lines’
    plot.check.marker: no visible global function definition for ‘points’
    plot.check.marker: no visible global function definition for ‘abline’
    plot.check.marker: no visible global function definition for ‘rug’
    plot.scan.gwaa: no visible global function definition for ‘is’
    plot.scan.gwaa: no visible global function definition for ‘plot’
    plot.scan.gwaa: no visible global function definition for ‘points’
    plot.scan.gwaa: no visible global function definition for ‘axis’
    plot.scan.gwaa.2D: no visible global function definition for ‘image’
    polygenic: no visible global function definition for ‘is’
    polygenic: no visible global function definition for ‘gaussian’
    polygenic: no visible global function definition for ‘binomial’
    polygenic: no visible global function definition for ‘as’
    polygenic: no visible global function definition for ‘model.frame’
    polygenic: no visible binding for global variable ‘na.omit’
    polygenic: no visible global function definition for ‘as.formula’
    polygenic: no visible global function definition for ‘model.response’
    polygenic: no visible global function definition for ‘sd’
    polygenic: no visible global function definition for ‘model.matrix’
    polygenic: no visible global function definition for ‘glm’
    polygenic: no visible global function definition for ‘var’
    polygenic: no visible global function definition for ‘ginv’
    polygenic: no visible global function definition for ‘flush.console’
    polygenic: no visible global function definition for ‘nlm’
    polygenic: no visible global function definition for ‘optim’
    polygenic: no visible global function definition for ‘runif’
    polygenic_hglm: no visible global function definition for ‘gaussian’
    polygenic_hglm: no visible global function definition for ‘is’
    polygenic_hglm: no visible global function definition for ‘as.formula’
    polygenic_hglm: no visible global function definition for ‘model.frame’
    polygenic_hglm: no visible binding for global variable ‘na.omit’
    polygenic_hglm: no visible global function definition for
     ‘model.response’
    polygenic_hglm: no visible global function definition for
     ‘model.matrix’
    polygenic_hglm: no visible global function definition for ‘hglm’
    polygenic_hglm: no visible global function definition for ‘ginv’
    qqplot.plot: no visible global function definition for ‘na.omit’
    qqplot.plot: no visible global function definition for ‘rchisq’
    qqplot.plot: no visible global function definition for ‘bitmap’
    qqplot.plot: no visible global function definition for ‘qqplot’
    qqplot.plot: no visible global function definition for ‘abline’
    qqplot.plot: no visible global function definition for ‘dev.off’
    qqplot.plot: no visible global function definition for ‘pchisq’
    qtscore: no visible global function definition for ‘is’
    qtscore: no visible global function definition for ‘as’
    qtscore: no visible global function definition for ‘model.frame’
    qtscore: no visible binding for global variable ‘na.omit’
    qtscore: no visible global function definition for ‘model.response’
    qtscore: no visible global function definition for ‘gaussian’
    qtscore: no visible global function definition for ‘binomial’
    qtscore: no visible global function definition for ‘model.matrix’
    qtscore: no visible global function definition for ‘glm.fit’
    qtscore: no visible global function definition for ‘residuals’
    qtscore: no visible global function definition for ‘txtProgressBar’
    qtscore: no visible global function definition for ‘setTxtProgressBar’
    qtscore: no visible global function definition for ‘pchisq’
    qtscore: no visible global function definition for ‘new’
    r2fast: no visible global function definition for ‘is’
    r2fast.old: no visible global function definition for ‘is’
    reconstructNPs: no visible global function definition for ‘is’
    redundant: no visible global function definition for ‘is’
    refresh.gwaa.data: no visible global function definition for ‘is’
    refresh.gwaa.data: no visible global function definition for ‘new’
    rhofast: no visible global function definition for ‘is’
    rntransform: no visible binding for global variable ‘gaussian’
    rntransform: no visible global function definition for ‘is’
    rntransform: no visible global function definition for ‘as’
    rntransform: no visible global function definition for ‘qnorm’
    save.gwaa.data: no visible global function definition for ‘write.table’
    save.snp.data: no visible global function definition for ‘is’
    scan.glm: no visible global function definition for ‘gaussian’
    scan.glm: no visible global function definition for ‘is’
    scan.glm: no visible global function definition for ‘as.formula’
    scan.glm: no visible global function definition for ‘glm’
    scan.glm: no visible global function definition for ‘anova’
    scan.glm: no visible global function definition for ‘lm’
    scan.glm: no visible global function definition for ‘flush.console’
    scan.glm: no visible global function definition for ‘median’
    scan.glm: no visible global function definition for ‘qchisq’
    scan.glm.2D: no visible global function definition for ‘gaussian’
    scan.glm.2D: no visible global function definition for ‘is’
    scan.glm.2D: no visible global function definition for ‘as.formula’
    scan.glm.2D: no visible global function definition for ‘glm’
    scan.glm.2D: no visible global function definition for ‘anova’
    scan.glm.2D: no visible global function definition for ‘lm’
    scan.glm.2D: no visible global function definition for ‘flush.console’
    scan.glm.2D: no visible global function definition for ‘median’
    scan.glm.2D: no visible global function definition for ‘qchisq’
    scan.haplo: no visible global function definition for ‘is’
    scan.haplo: no visible global function definition for ‘as.formula’
    scan.haplo: no visible global function definition for
     ‘haplo.score.slide’
    scan.haplo: no visible global function definition for ‘flush.console’
    scan.haplo: no visible global function definition for ‘new’
    scan.haplo.2D: no visible global function definition for ‘is’
    scan.haplo.2D: no visible global function definition for ‘as.formula’
    scan.haplo.2D: no visible global function definition for
     ‘haplo.score.slide’
    scan.haplo.2D: no visible global function definition for
     ‘score.sim.control’
    scan.haplo.2D: no visible global function definition for
     ‘flush.console’
    show.ncbi: no visible global function definition for ‘browseURL’
    show.ncbi: no visible global function definition for ‘is’
    snp.data: no visible global function definition for ‘new’
    snp.names: no visible global function definition for ‘is’
    snp.names.gwaa.data: no visible global function definition for ‘is’
    snp.subset: no visible global function definition for ‘is’
    snp.subset.scan.gwaa: no visible global function definition for ‘new’
    summary.snp.data: no visible global function definition for ‘is’
    summary.snp.data: no visible global function definition for ‘pchisq’
    summary.snp.data_old: no visible global function definition for ‘is’
    summary.snp.data_old: no visible global function definition for
     ‘pchisq’
    ztransform: no visible binding for global variable ‘gaussian’
    ztransform: no visible global function definition for ‘is’
    ztransform: no visible global function definition for ‘as’
    ztransform: no visible global function definition for ‘model.frame’
    ztransform: no visible binding for global variable ‘na.pass’
    ztransform: no visible global function definition for ‘complete.cases’
    ztransform: no visible global function definition for ‘model.response’
    ztransform: no visible global function definition for ‘model.matrix’
    ztransform: no visible global function definition for ‘glm.fit’
    ztransform: no visible global function definition for ‘sd’
    [,gwaa.data-ANY-ANY-ANY: no visible global function definition for
     ‘new’
    [,snp.coding-ANY-missing-missing: no visible global function definition
     for ‘new’
    [,snp.data-ANY-ANY-ANY: no visible global function definition for ‘new’
    [,snp.mx-ANY-ANY-ANY: no visible global function definition for ‘new’
    [,snp.strand-ANY-missing-missing: no visible global function definition
     for ‘new’
    coding<-,snp.data: no visible global function definition for ‘new’
    results,scan.gwaa: no visible global function definition for ‘pchisq’
    show,gwaa.data: no visible global function definition for ‘show’
    show,snp.data: no visible global function definition for ‘show’
    Undefined global functions or variables:
     abline anova apply2dfo as as.dist as.formula axis bartlett.test
     binomial bitmap boxplot browseURL cmdscale complete.cases databel
     density dev.off disconnect extract_text_file_columns fisher.test
     flush.console gaussian genotype get_dimnames get_temporary_file_name
     ginv glm glm.fit haplo.score.slide hglm image is kmeans kruskal.test
     ks.test lines lm median model.extract model.frame model.matrix
     model.response na.omit na.pass new nlm optim optimize par pchisq plot
     points ppoints qchisq qnorm qqplot quantile qvalue rbinom rchisq
     read.table residuals rug runif score.sim.control sd setTxtProgressBar
     set_dimnames<- show t.test text text2databel txtProgressBar var
     write.table
    Consider adding
     importFrom("grDevices", "bitmap", "dev.off")
     importFrom("graphics", "abline", "axis", "boxplot", "image", "lines",
     "par", "plot", "points", "rug", "text")
     importFrom("methods", "as", "is", "new", "show")
     importFrom("stats", "anova", "as.dist", "as.formula", "bartlett.test",
     "binomial", "cmdscale", "complete.cases", "density",
     "fisher.test", "gaussian", "glm", "glm.fit", "kmeans",
     "kruskal.test", "ks.test", "lm", "median", "model.extract",
     "model.frame", "model.matrix", "model.response", "na.omit",
     "na.pass", "nlm", "optim", "optimize", "pchisq", "ppoints",
     "qchisq", "qnorm", "qqplot", "quantile", "rbinom", "rchisq",
     "residuals", "runif", "sd", "t.test", "var")
     importFrom("utils", "browseURL", "flush.console", "read.table",
     "setTxtProgressBar", "txtProgressBar", "write.table")
    to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
    contains 'methods').
Flavor: r-patched-solaris-sparc

Version: 1.8-0
Flags: --no-examples
Check: line endings in Makefiles
Result: NOTE
    Found the following Makefile(s) without a final LF:
     inst/unitTests/Makefile
    Some ‘make’ programs ignore lines not ending in LF.
Flavor: r-patched-solaris-sparc

Version: 1.8-0
Check: R code for possible problems
Result: NOTE
    arrange_probabel_phe: no visible global function definition for
     'databel'
    as.genotype.snp.data: no visible global function definition for
     'genotype'
    check.marker.internal: no visible global function definition for
     'qvalue'
    extract.annotation.impute: no visible global function definition for
     'extract_text_file_columns'
    extract.annotation.mach: no visible global function definition for
     'extract_text_file_columns'
    impute2databel: no visible global function definition for
     'get_temporary_file_name'
    impute2databel: no visible global function definition for
     'text2databel'
    impute2databel: no visible global function definition for
     'get_dimnames'
    impute2databel: no visible global function definition for 'apply2dfo'
    impute2databel: no visible global function definition for 'databel'
    impute2databel: no visible global function definition for
     'set_dimnames<-'
    impute2databel: no visible global function definition for 'disconnect'
    impute2mach: no visible global function definition for 'get_dimnames'
    impute2mach: no visible global function definition for 'disconnect'
    mach2databel: no visible global function definition for
     'get_temporary_file_name'
    mach2databel: no visible global function definition for 'text2databel'
    mach2databel: no visible global function definition for 'get_dimnames'
    minimac2databel: no visible global function definition for
     'get_temporary_file_name'
    minimac2databel: no visible global function definition for
     'text2databel'
    minimac2databel: no visible global function definition for
     'get_dimnames'
    polygenic: no visible global function definition for 'ginv'
    polygenic_hglm: no visible global function definition for 'hglm'
    polygenic_hglm: no visible global function definition for 'ginv'
    scan.haplo: no visible global function definition for
     'haplo.score.slide'
    scan.haplo.2D: no visible global function definition for
     'haplo.score.slide'
    scan.haplo.2D: no visible global function definition for
     'score.sim.control'
Flavor: r-oldrel-windows-ix86+x86_64