CRAN Package Check Results for Package qtlnet

Last updated on 2017-07-22 14:46:51.

Check Details

Version: 1.3.6
Check: DESCRIPTION meta-information
Result: NOTE
    Malformed Description field: should contain one or more complete sentences.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64, r-oldrel-osx-x86_64

Version: 1.3.6
Check: dependencies in R code
Result: NOTE
    Packages in Depends field not imported from:
     ‘graph’ ‘igraph’ ‘pcalg’ ‘qtl’ ‘sem’
     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-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64, r-oldrel-osx-x86_64

Version: 1.3.6
Check: S3 generic/method consistency
Result: NOTE
    Found the following apparent S3 methods exported but not registered:
     c.qtlnet subset.qtlnet
    See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
    manual.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64

Version: 1.3.6
Check: R code for possible problems
Result: NOTE
    adjust.pheno: no visible global function definition for ‘find.pheno’
    approximate.UDG : pvalue: no visible global function definition for
     ‘pt’
    approximate.UDG: no visible global function definition for ‘cor’
    approximate.UDG: no visible global function definition for ‘combn’
    bic.qtlnet: no visible global function definition for ‘calc.genoprob’
    cov.formula: no visible global function definition for ‘as.formula’
    create.cov.matrix: no visible global function definition for ‘formula’
    create.cov.matrix: no visible global function definition for
     ‘model.matrix’
    dist.qtlnet: no visible global function definition for ‘plot’
    dist.qtlnet: no visible global function definition for ‘abline’
    edgematch.qtlnet: no visible global function definition for ‘plot’
    edgematch.qtlnet: no visible global function definition for ‘abline’
    edgematch.qtlnet: no visible global function definition for ‘points’
    est.qtlnet: no visible global function definition for ‘calc.genoprob’
    est.qtlnet: no visible global function definition for ‘makeqtl’
    est.qtlnet: no visible global function definition for ‘formula’
    est.qtlnet: no visible global function definition for ‘fitqtl’
    est.qtlnet: no visible global function definition for ‘coef’
    est.qtlnet: no visible global function definition for ‘lm’
    generate.data.graph.a : gibbs.graph.a: no visible global function
     definition for ‘rnorm’
    generate.data.graph.b : gibbs.graph.b: no visible global function
     definition for ‘rnorm’
    generate.data.graph.c : gibbs.graph.c: no visible global function
     definition for ‘rnorm’
    generate.qtl.markers: no visible global function definition for
     ‘makeqtl’
    generate.qtl.markers: no visible global function definition for
     ‘find.marker’
    geno.effect: no visible global function definition for ‘rnorm’
    get.graph.edges: no visible global function definition for
     ‘list.edge.attributes’
    get.graph.edges: no visible global function definition for
     ‘get.edgelist’
    get.graph.edges: no visible global function definition for
     ‘get.edge.attribute’
    get.graph.vertices: no visible global function definition for
     ‘list.vertex.attributes’
    get.graph.vertices: no visible global function definition for
     ‘get.vertex.attribute’
    get.model.average: no visible binding for global variable
     ‘weighted.mean’
    igraph.qdg: no visible global function definition for ‘pchisq’
    igraph.qtlnet: no visible global function definition for
     ‘igraph.options’
    igraph.qtlnet: no visible global function definition for
     ‘graph.data.frame’
    loci.qtlnet: no visible global function definition for ‘calc.genoprob’
    lod.score: no visible global function definition for ‘compareVersion’
    lod.score: no visible global function definition for ‘qtlversion’
    lod.score : myfitqtl: no visible global function definition for
     ‘fitqtl’
    lod.score: no visible global function definition for ‘find.pheno’
    log.likelihood.s: no visible global function definition for
     ‘find.pheno’
    log.likelihood.s: no visible global function definition for ‘lm’
    log.likelihood.s: no visible global function definition for ‘logLik’
    log.likelihood.s: no visible global function definition for ‘AIC’
    match.parents: no visible global function definition for ‘nind’
    mcmc.qtlnet: no visible global function definition for ‘calc.genoprob’
    mcmc.qtlnet: no visible global function definition for ‘plot’
    mcmc.qtlnet: no visible global function definition for ‘points’
    mcmc.qtlnet: no visible global function definition for ‘runif’
    mds.qtlnet: no visible global function definition for ‘dist’
    mds.qtlnet: no visible global function definition for ‘cmdscale’
    mds.qtlnet: no visible global function definition for ‘plot’
    mds.qtlnet: no visible global function definition for ‘points’
    newfun: no visible global function definition for ‘plot’
    newfun: no visible global function definition for ‘points’
    newfun: no visible global function definition for ‘abline’
    parallel.error: no visible global function definition for ‘write.table’
    parallel.message: no visible global function definition for
     ‘write.table’
    parents.qtlnet: no visible global function definition for ‘combn’
    plot.qtlnet: no visible global function definition for ‘tkplot’
    plotbic.qtlnet : plotfn: no visible global function definition for
     ‘lines’
    plotbic.qtlnet : splotfn: no visible global function definition for
     ‘lines’
    plotbic.qtlnet : splotfn: no visible global function definition for
     ‘lowess’
    plotbic.qtlnet: no visible global function definition for ‘plot’
    plotbic.qtlnet: no visible global function definition for ‘title’
    propose.new.node.edge: no visible global function definition for
     ‘runif’
    pull.loci: no visible global function definition for ‘create.map’
    qdg: no visible global function definition for ‘cor’
    qdg: no visible global function definition for ‘skeleton’
    qdg: no visible binding for global variable ‘gaussCItest’
    qdg: no visible global function definition for ‘argmax.geno’
    qdg.sem : score.sem.models: no visible global function definition for
     ‘nind’
    qdg.sem : score.sem.models: no visible global function definition for
     ‘lm’
    qdg.sem : score.sem.models: no visible global function definition for
     ‘as.formula’
    qdg.sem : score.sem.models: no visible global function definition for
     ‘cov’
    qdg.sem : score.sem.models: no visible global function definition for
     ‘sem’
    qtlnet.phase1: no visible global function definition for
     ‘calc.genoprob’
    qtlnet.phase1: no visible global function definition for ‘write.table’
    s.formula: no visible global function definition for ‘as.formula’
    s.formula: no visible global function definition for ‘model.matrix’
    scan.genome: no visible global function definition for ‘makeqtl’
    scan.genome: no visible global function definition for ‘lm’
    scan.genome: no visible global function definition for ‘AIC’
    scan.genome: no visible global function definition for ‘update’
    scanone.summary: no visible global function definition for ‘scanone’
    summary.qtlnet: no visible global function definition for
     ‘weighted.mean’
    write.qtlnet: no visible global function definition for ‘write.table’
    Undefined global functions or variables:
     AIC abline argmax.geno as.formula calc.genoprob cmdscale coef combn
     compareVersion cor cov create.map dist find.marker find.pheno fitqtl
     formula gaussCItest get.edge.attribute get.edgelist
     get.vertex.attribute graph.data.frame igraph.options lines
     list.edge.attributes list.vertex.attributes lm logLik lowess makeqtl
     model.matrix nind pchisq plot points pt qtlversion rnorm runif
     scanone sem skeleton title tkplot update weighted.mean write.table
    Consider adding
     importFrom("graphics", "abline", "lines", "plot", "points", "title")
     importFrom("stats", "AIC", "as.formula", "cmdscale", "coef", "cor",
     "cov", "dist", "formula", "lm", "logLik", "lowess",
     "model.matrix", "pchisq", "pt", "rnorm", "runif", "update",
     "weighted.mean")
     importFrom("utils", "combn", "compareVersion", "write.table")
    to your NAMESPACE file.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64, r-oldrel-osx-x86_64

Version: 1.3.6
Check: package dependencies
Result: ERROR
    Packages required but not available: ‘graph’ ‘pcalg’
    
    See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
    manual.
Flavor: r-release-osx-x86_64