CRAN Package Check Results for Package qtlbim

Last updated on 2014-10-10 15:49:16.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 2.0.7 5.97 113.92 119.88 NOTE
r-devel-linux-x86_64-debian-gcc 2.0.7 8.23 113.04 121.28 NOTE
r-devel-linux-x86_64-fedora-clang 2.0.7 268.31 NOTE
r-devel-linux-x86_64-fedora-gcc 2.0.7 261.92 NOTE
r-devel-osx-x86_64-clang 2.0.7 177.16 NOTE
r-devel-windows-ix86+x86_64 2.0.7 28.00 195.00 223.00 NOTE
r-patched-linux-x86_64 2.0.7 8.44 139.92 148.36 NOTE
r-patched-solaris-sparc 2.0.7 1483.10 NOTE
r-patched-solaris-x86 2.0.7 290.30 NOTE
r-release-linux-ix86 2.0.7 9.83 150.80 160.63 NOTE
r-release-linux-x86_64 2.0.7 8.47 132.29 140.76 NOTE
r-release-osx-x86_64-mavericks 2.0.7 NOTE
r-release-osx-x86_64-snowleopard 2.0.7 NOTE
r-release-windows-ix86+x86_64 2.0.7 29.00 200.00 229.00 NOTE
r-oldrel-windows-ix86+x86_64 2.0.7 30.00 206.00 236.00 NOTE

Check Details

Version: 2.0.7
Check: dependencies in R code
Result: NOTE
    'library' or 'require' calls to packages already attached by Depends:
     ‘MASS’ ‘coda’ ‘lattice’ ‘tools’
     Please remove these calls from your code.
    Packages in Depends field not imported from:
     ‘MASS’ ‘coda’ ‘lattice’ ‘qtl’ ‘tools’
     These packages need to be imported from (in the NAMESPACE file)
     for when this namespace is loaded but not attached.
    See the information on DESCRIPTION files in the chapter ‘Creating R
    packages’ of 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-devel-osx-x86_64-clang, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86

Version: 2.0.7
Check: R code for possible problems
Result: NOTE
    make.main: no visible global function definition for ‘nchr’
    make.main: no visible global function definition for ‘drop.markers’
    make.main: no visible global function definition for ‘nind’
    make.main: no visible global function definition for ‘nmar’
    plot.qb.close: no visible global function definition for ‘bwplot’
    plot.qb.condloci: no visible global function definition for
     ‘densityplot’
    plot.qb.covar: no visible global function definition for
     ‘trellis.par.set’
    plot.qb.covar: no visible global function definition for ‘col.whitebg’
    plot.qb.covar: no visible global function definition for ‘xyplot’
    plot.qb.covar : <anonymous>: no visible global function definition for
     ‘panel.abline’
    plot.qb.covar : <anonymous>: no visible global function definition for
     ‘panel.xyplot’
    plot.qb.epistasis: no visible global function definition for
     ‘trellis.par.set’
    plot.qb.epistasis: no visible global function definition for
     ‘col.whitebg’
    plot.qb.epistasis: no visible global function definition for ‘bwplot’
    plot.qb.epistasis : <anonymous>: no visible global function definition
     for ‘panel.abline’
    plot.qb.epistasis : <anonymous>: no visible global function definition
     for ‘panel.stripplot’
    plot.qb.epistasis : <anonymous>: no visible global function definition
     for ‘panel.bwplot’
    plot.qb.epistasis : <anonymous>: no visible global function definition
     for ‘panel.lines’
    plot.qb.meancomp: no visible global function definition for
     ‘trellis.par.set’
    plot.qb.meancomp: no visible global function definition for
     ‘col.whitebg’
    plot.qb.meancomp: no visible global function definition for ‘splom’
    plot.qb.meancomp : <anonymous>: no visible global function definition
     for ‘panel.abline’
    plot.qb.meancomp : <anonymous>: no visible global function definition
     for ‘panel.splom’
    plot.qb.meancomp : <anonymous>: no visible global function definition
     for ‘panel.xyplot’
    plot.qb.meancomp : <anonymous>: no visible global function definition
     for ‘diag.panel.splom’
    plot.qb.meancomp: no visible global function definition for
     ‘densityplot’
    plot.qb.multloci: no visible global function definition for
     ‘trellis.par.set’
    plot.qb.multloci: no visible global function definition for
     ‘col.whitebg’
    plot.qb.multloci : mydensityplot: no visible global function definition
     for ‘densityplot’
    plot.qb.multloci : mydensityplot : <anonymous>: no visible global
     function definition for ‘trellis.par.get’
    plot.qb.multloci : mydensityplot : <anonymous>: no visible global
     function definition for ‘current.panel.limits’
    plot.qb.multloci : mydensityplot : <anonymous>: no visible global
     function definition for ‘panel.lines’
    plot.qb.multloci : mydensityplot : <anonymous>: no visible global
     function definition for ‘panel.xyplot’
    plot.qb.multloci : mydensityplot : <anonymous>: no visible global
     function definition for ‘panel.abline’
    plot.qb.multloci : mydensityplot : <anonymous>: no visible global
     function definition for ‘panel.rug’
    plot.qb.multloci : mydensityplot : <anonymous>: no visible global
     function definition for ‘panel.superpose’
    plot.qb.multloci: no visible global function definition for
     ‘densityplot’
    plot.qb.multloci : <anonymous>: no visible global function definition
     for ‘panel.densityplot’
    plot.qb.multloci : <anonymous>: no visible global function definition
     for ‘panel.rug’
    plot.qb.multloci: no visible global function definition for ‘barchart’
    plot.qb.multloci: no visible global function definition for ‘xyplot’
    plot.qb.multloci : <anonymous>: no visible global function definition
     for ‘panel.abline’
    plot.qb.multloci : <anonymous>: no visible global function definition
     for ‘panel.points’
    plot.qb.multloci : <anonymous>: no visible global function definition
     for ‘panel.superpose’
    plot.qb.multloci : <anonymous> : <anonymous>: no visible global
     function definition for ‘panel.lines’
    plot.qb.scantwo: no visible global function definition for ‘qtlversion’
    plot.qb.slicetwo: no visible global function definition for
     ‘find.marker’
    plot.qb.slicetwo: no visible global function definition for ‘sim.geno’
    plot.qb.slicetwo: no visible global function definition for
     ‘effectplot’
    plot.qb.varcomp: no visible global function definition for
     ‘trellis.par.set’
    plot.qb.varcomp: no visible global function definition for
     ‘col.whitebg’
    plot.qb.varcomp: no visible global function definition for ‘splom’
    plot.qb.varcomp : <anonymous>: no visible global function definition
     for ‘panel.abline’
    plot.qb.varcomp : <anonymous>: no visible global function definition
     for ‘panel.splom’
    plot.qb.varcomp : <anonymous>: no visible global function definition
     for ‘panel.xyplot’
    plot.qb.varcomp : <anonymous>: no visible global function definition
     for ‘diag.panel.splom’
    plot.qb.varcomp: no visible global function definition for
     ‘densityplot’
    pull.grid: no visible global function definition for ‘pull.map’
    pull.loci : tmpfn: no visible global function definition for
     ‘create.map’
    qb.chrom: no visible global function definition for ‘pull.map’
    qb.coda: no visible global function definition for ‘mcmc’
    qb.condloci: no visible global function definition for ‘lda’
    qb.confound: no visible global function definition for ‘nind’
    qb.data: no visible global function definition for ‘find.pheno’
    qb.data: no visible global function definition for ‘nind’
    qb.epimodes : chrsplit: no visible global function definition for ‘lda’
    qb.genoprob: no visible binding for global variable ‘calc.genoprob’
    qb.genoprob: no visible global function definition for ‘pull.map’
    qb.genoprob: no visible global function definition for ‘jittermap’
    qb.genoprob: no visible global function definition for ‘calc.genoprob’
    qb.genoprob.defaults: no visible binding for global variable
     ‘calc.genoprob’
    qb.hpdone: no visible global function definition for ‘pull.map’
    qb.humanGenoProb: no visible global function definition for ‘nchr’
    qb.humanGenoProb: no visible global function definition for ‘nind’
    qb.humanGenoProb: no visible global function definition for ‘nmar’
    qb.legacy: no visible global function definition for ‘clean’
    qb.loci: no visible global function definition for ‘pull.map’
    qb.mainmodes : chrsplit: no visible global function definition for
     ‘lda’
    qb.mcmc: no visible global function definition for ‘nind’
    qb.mcmc: no visible global function definition for ‘nchr’
    qb.model: no visible global function definition for ‘nchr’
    qb.multloci: no visible global function definition for ‘pull.map’
    qb.outbredF2: no visible global function definition for ‘read.cross’
    qb.pairloci: no visible global function definition for ‘pull.map’
    qb.pairs: no visible global function definition for ‘pull.map’
    qb.pattern: no visible global function definition for ‘pull.map’
    qb.recover: no visible global function definition for ‘find.pheno’
    qb.reorder: no visible global function definition for ‘pull.map’
    qb.save: no visible global function definition for ‘clean’
    qb.scantwo: no visible global function definition for ‘pull.map’
    qb.sim.cross: no visible global function definition for ‘mvrnorm’
    qb.sweave: no visible global function definition for ‘clean’
    qb.valid.phenoData: no visible global function definition for ‘nind’
    select.cc: no visible global function definition for ‘nchr’
    select.cc: no visible global function definition for ‘nind’
    step.fitqtl: no visible global function definition for ‘qtlversion’
    step.fitqtl : myfitqtl: no visible global function definition for
     ‘fitqtl’
    subset.qb: no visible global function definition for ‘pull.map’
    summary.qb.scantwo: no visible global function definition for
     ‘qtlversion’
    
    Found the following assignments to the global environment:
    File ‘qtlbim/R/sweave.R’:
     assign(".qb.name", .qb.name, ".GlobalEnv")
     assign(".qb.cross", cross, ".GlobalEnv")
     assign(".qb.pheno", pheno.col, ".GlobalEnv")
     assign(".qb.niter", n.iter, ".GlobalEnv")
     assign(".qb.draws", n.draws, ".GlobalEnv")
     assign(".qb.threshold", c(upper = upper.threshold), ".GlobalEnv")
     assign(".qb.scan.type", scan.type, ".GlobalEnv")
     assign(".qb.hpd.level", hpd.level, ".GlobalEnv")
     assign(".qb.PDFDir", PDFDir, ".GlobalEnv")
     assign(".qb.SweaveFile", SweaveFile, ".GlobalEnv")
     assign(".qb.SweaveExtra", SweaveExtra, ".GlobalEnv")
     assign(".qb.remove", remove.qb, ".GlobalEnv")
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-osx-x86_64-clang

Version: 2.0.7
Check: compiled code
Result: NOTE
    File ‘qtlbim/libs/qtlbim.so’:
     Found ‘rand’, possibly from ‘rand’ (C)
     Objects: ‘MultipleTraitsMCMC.o’, ‘SingleTraitMCMC.o’, ‘StatUtils.o’
     Found ‘srand’, possibly from ‘srand’ (C)
     Objects: ‘MultipleTraitsMCMC.o’, ‘SingleTraitMCMC.o’
    
    Compiled code should not call entry points which might terminate R nor
    write to stdout/stderr instead of to the console, nor the C RNG.
    
    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, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 2.0.7
Check: R code for possible problems
Result: NOTE
    make.main: no visible global function definition for ‘nchr’
    make.main: no visible global function definition for ‘drop.markers’
    make.main: no visible global function definition for ‘nind’
    make.main: no visible global function definition for ‘nmar’
    plot.qb.close: no visible global function definition for ‘bwplot’
    plot.qb.condloci: no visible global function definition for
     ‘densityplot’
    plot.qb.covar: no visible global function definition for
     ‘trellis.par.set’
    plot.qb.covar: no visible global function definition for ‘col.whitebg’
    plot.qb.covar: no visible global function definition for ‘xyplot’
    plot.qb.covar : <anonymous>: no visible global function definition for
     ‘panel.abline’
    plot.qb.covar : <anonymous>: no visible global function definition for
     ‘panel.xyplot’
    plot.qb.epistasis: no visible global function definition for
     ‘trellis.par.set’
    plot.qb.epistasis: no visible global function definition for
     ‘col.whitebg’
    plot.qb.epistasis: no visible global function definition for ‘bwplot’
    plot.qb.epistasis : <anonymous>: no visible global function definition
     for ‘panel.abline’
    plot.qb.epistasis : <anonymous>: no visible global function definition
     for ‘panel.stripplot’
    plot.qb.epistasis : <anonymous>: no visible global function definition
     for ‘panel.bwplot’
    plot.qb.epistasis : <anonymous>: no visible global function definition
     for ‘panel.lines’
    plot.qb.meancomp: no visible global function definition for
     ‘trellis.par.set’
    plot.qb.meancomp: no visible global function definition for
     ‘col.whitebg’
    plot.qb.meancomp: no visible global function definition for ‘splom’
    plot.qb.meancomp : <anonymous>: no visible global function definition
     for ‘panel.abline’
    plot.qb.meancomp : <anonymous>: no visible global function definition
     for ‘panel.splom’
    plot.qb.meancomp : <anonymous>: no visible global function definition
     for ‘panel.xyplot’
    plot.qb.meancomp : <anonymous>: no visible global function definition
     for ‘diag.panel.splom’
    plot.qb.meancomp: no visible global function definition for
     ‘densityplot’
    plot.qb.multloci: no visible global function definition for
     ‘trellis.par.set’
    plot.qb.multloci: no visible global function definition for
     ‘col.whitebg’
    plot.qb.multloci : mydensityplot: no visible global function definition
     for ‘densityplot’
    plot.qb.multloci : mydensityplot : <anonymous>: no visible global
     function definition for ‘trellis.par.get’
    plot.qb.multloci : mydensityplot : <anonymous>: no visible global
     function definition for ‘current.panel.limits’
    plot.qb.multloci : mydensityplot : <anonymous>: no visible global
     function definition for ‘panel.lines’
    plot.qb.multloci : mydensityplot : <anonymous>: no visible global
     function definition for ‘panel.xyplot’
    plot.qb.multloci : mydensityplot : <anonymous>: no visible global
     function definition for ‘panel.abline’
    plot.qb.multloci : mydensityplot : <anonymous>: no visible global
     function definition for ‘panel.rug’
    plot.qb.multloci : mydensityplot : <anonymous>: no visible global
     function definition for ‘panel.superpose’
    plot.qb.multloci: no visible global function definition for
     ‘densityplot’
    plot.qb.multloci : <anonymous>: no visible global function definition
     for ‘panel.densityplot’
    plot.qb.multloci : <anonymous>: no visible global function definition
     for ‘panel.rug’
    plot.qb.multloci: no visible global function definition for ‘barchart’
    plot.qb.multloci: no visible global function definition for ‘xyplot’
    plot.qb.multloci : <anonymous>: no visible global function definition
     for ‘panel.abline’
    plot.qb.multloci : <anonymous>: no visible global function definition
     for ‘panel.points’
    plot.qb.multloci : <anonymous>: no visible global function definition
     for ‘panel.superpose’
    plot.qb.multloci : <anonymous> : <anonymous>: no visible global
     function definition for ‘panel.lines’
    plot.qb.scantwo: no visible global function definition for ‘qtlversion’
    plot.qb.slicetwo: no visible global function definition for
     ‘find.marker’
    plot.qb.slicetwo: no visible global function definition for ‘sim.geno’
    plot.qb.slicetwo: no visible global function definition for
     ‘effectplot’
    plot.qb.varcomp: no visible global function definition for
     ‘trellis.par.set’
    plot.qb.varcomp: no visible global function definition for
     ‘col.whitebg’
    plot.qb.varcomp: no visible global function definition for ‘splom’
    plot.qb.varcomp : <anonymous>: no visible global function definition
     for ‘panel.abline’
    plot.qb.varcomp : <anonymous>: no visible global function definition
     for ‘panel.splom’
    plot.qb.varcomp : <anonymous>: no visible global function definition
     for ‘panel.xyplot’
    plot.qb.varcomp : <anonymous>: no visible global function definition
     for ‘diag.panel.splom’
    plot.qb.varcomp: no visible global function definition for
     ‘densityplot’
    pull.grid: no visible global function definition for ‘pull.map’
    pull.loci : tmpfn: no visible global function definition for
     ‘create.map’
    qb.chrom: no visible global function definition for ‘pull.map’
    qb.coda: no visible global function definition for ‘mcmc’
    qb.condloci: no visible global function definition for ‘lda’
    qb.confound: no visible global function definition for ‘nind’
    qb.data: no visible global function definition for ‘find.pheno’
    qb.data: no visible global function definition for ‘nind’
    qb.epimodes : chrsplit: no visible global function definition for ‘lda’
    qb.genoprob: no visible binding for global variable ‘calc.genoprob’
    qb.genoprob: no visible global function definition for ‘pull.map’
    qb.genoprob: no visible global function definition for ‘jittermap’
    qb.genoprob: no visible global function definition for ‘calc.genoprob’
    qb.genoprob.defaults: no visible binding for global variable
     ‘calc.genoprob’
    qb.hpdone: no visible global function definition for ‘pull.map’
    qb.humanGenoProb: no visible global function definition for ‘nchr’
    qb.humanGenoProb: no visible global function definition for ‘nind’
    qb.humanGenoProb: no visible global function definition for ‘nmar’
    qb.legacy: no visible global function definition for ‘clean’
    qb.loci: no visible global function definition for ‘pull.map’
    qb.mainmodes : chrsplit: no visible global function definition for
     ‘lda’
    qb.mcmc: no visible global function definition for ‘nind’
    qb.mcmc: no visible global function definition for ‘nchr’
    qb.model: no visible global function definition for ‘nchr’
    qb.multloci: no visible global function definition for ‘pull.map’
    qb.outbredF2: no visible global function definition for ‘read.cross’
    qb.pairloci: no visible global function definition for ‘pull.map’
    qb.pairs: no visible global function definition for ‘pull.map’
    qb.pattern: no visible global function definition for ‘pull.map’
    qb.recover: no visible global function definition for ‘find.pheno’
    qb.reorder: no visible global function definition for ‘pull.map’
    qb.save: no visible global function definition for ‘clean’
    qb.scantwo: no visible global function definition for ‘pull.map’
    qb.sim.cross: no visible global function definition for ‘mvrnorm’
    qb.sweave: no visible global function definition for ‘clean’
    qb.valid.phenoData: no visible global function definition for ‘nind’
    select.cc: no visible global function definition for ‘nchr’
    select.cc: no visible global function definition for ‘nind’
    step.fitqtl: no visible global function definition for ‘qtlversion’
    step.fitqtl : myfitqtl: no visible global function definition for
     ‘fitqtl’
    subset.qb: no visible global function definition for ‘pull.map’
    summary.qb.scantwo: no visible global function definition for
     ‘qtlversion’
Flavors: r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64

Version: 2.0.7
Check: compiled code
Result: NOTE
    File ‘qtlbim/libs/qtlbim.so’:
     Found ‘_rand’, possibly from ‘rand’ (C)
     Objects: ‘MultipleTraitsMCMC.o’, ‘SingleTraitMCMC.o’, ‘StatUtils.o’
     Found ‘_srand’, possibly from ‘srand’ (C)
     Objects: ‘MultipleTraitsMCMC.o’, ‘SingleTraitMCMC.o’
    
    Compiled code should not call entry points which might terminate R nor
    write to stdout/stderr instead of to the console, nor the C RNG.
    
    See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Flavor: r-devel-osx-x86_64-clang

Version: 2.0.7
Check: compiled code
Result: NOTE
    File 'qtlbim/libs/i386/qtlbim.dll':
     Found 'rand', possibly from 'rand' (C)
     Objects: 'MultipleTraitsMCMC.o', 'SingleTraitMCMC.o', 'StatUtils.o'
     Found 'srand', possibly from 'srand' (C)
     Objects: 'MultipleTraitsMCMC.o', 'SingleTraitMCMC.o'
    File 'qtlbim/libs/x64/qtlbim.dll':
     Found 'rand', possibly from 'rand' (C)
     Objects: 'MultipleTraitsMCMC.o', 'SingleTraitMCMC.o', 'StatUtils.o'
     Found 'srand', possibly from 'srand' (C)
     Objects: 'MultipleTraitsMCMC.o', 'SingleTraitMCMC.o'
    
    Compiled code should not call entry points which might terminate R nor
    write to stdout/stderr instead of to the console, nor the C RNG.
    
    See 'Writing portable packages' in the 'Writing R Extensions' manual.
Flavor: r-devel-windows-ix86+x86_64

Version: 2.0.7
Check: R code for possible problems
Result: NOTE
    Found the following assignments to the global environment:
    File ‘qtlbim/R/sweave.R’:
     assign(".qb.name", .qb.name, ".GlobalEnv")
     assign(".qb.cross", cross, ".GlobalEnv")
     assign(".qb.pheno", pheno.col, ".GlobalEnv")
     assign(".qb.niter", n.iter, ".GlobalEnv")
     assign(".qb.draws", n.draws, ".GlobalEnv")
     assign(".qb.threshold", c(upper = upper.threshold), ".GlobalEnv")
     assign(".qb.scan.type", scan.type, ".GlobalEnv")
     assign(".qb.hpd.level", hpd.level, ".GlobalEnv")
     assign(".qb.PDFDir", PDFDir, ".GlobalEnv")
     assign(".qb.SweaveFile", SweaveFile, ".GlobalEnv")
     assign(".qb.SweaveExtra", SweaveExtra, ".GlobalEnv")
     assign(".qb.remove", remove.qb, ".GlobalEnv")
Flavors: r-patched-linux-x86_64, r-release-linux-ix86, r-release-linux-x86_64

Version: 2.0.7
Check: dependencies in R code
Result: NOTE
    'library' or 'require' calls to packages already attached by Depends:
     ‘MASS’ ‘coda’ ‘lattice’ ‘tools’
     Please remove these calls from your code.
    Packages in Depends field not imported from:
     ‘MASS’ ‘coda’ ‘lattice’ ‘qtl’
     These packages need to be imported from (in the NAMESPACE file)
     for when this namespace is loaded but not attached.
    See the information on DESCRIPTION files in the chapter ‘Creating R
    packages’ of the ‘Writing R Extensions’ manual.
Flavors: r-release-linux-ix86, r-release-linux-x86_64, r-release-osx-x86_64-mavericks, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 2.0.7
Check: dependencies in R code
Result: NOTE
    'library' or 'require' calls to packages already attached by Depends:
     'MASS' 'coda' 'lattice' 'tools'
     Please remove these calls from your code.
    See the information on DESCRIPTION files in the chapter 'Creating R
    packages' of the 'Writing R Extensions' manual.
Flavor: r-release-osx-x86_64-snowleopard