CRAN Package Check Results for Package RJaCGH

Last updated on 2015-06-30 15:47:22.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 2.0.3 2.53 64.32 66.85 NOTE
r-devel-linux-x86_64-debian-gcc 2.0.3 4.16 64.71 68.86 NOTE
r-devel-linux-x86_64-fedora-clang 2.0.3 121.60 NOTE
r-devel-linux-x86_64-fedora-gcc 2.0.3 120.93 NOTE
r-devel-osx-x86_64-clang 2.0.3 94.08 NOTE
r-devel-windows-ix86+x86_64 2.0.3 17.00 191.00 208.00 NOTE
r-patched-linux-x86_64 2.0.3 4.29 64.69 68.98 NOTE
r-patched-solaris-sparc 2.0.3 727.20 NOTE
r-patched-solaris-x86 2.0.3 149.60 NOTE
r-release-linux-x86_64 2.0.3 4.24 67.12 71.35 NOTE
r-release-osx-x86_64-mavericks 2.0.3 NOTE
r-release-windows-ix86+x86_64 2.0.3 10.00 186.00 196.00 NOTE
r-oldrel-windows-ix86+x86_64 2.0.3 16.00 188.00 204.00 NOTE

Check Details

Version: 2.0.3
Check: DESCRIPTION meta-information
Result: NOTE
    Malformed Title field: should not end in a period.
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, r-release-linux-x86_64, r-release-osx-x86_64-mavericks, r-release-windows-ix86+x86_64

Version: 2.0.3
Check: S3 generic/method consistency
Result: NOTE
    Found the following apparent S3 methods exported but not registered:
     plot.Q.NH
    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-devel-osx-x86_64-clang, r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-x86_64

Version: 2.0.3
Check: R code for possible problems
Result: NOTE
    MetropolisSweep.C: no visible global function definition for ‘median’
    MetropolisSweep.C: no visible global function definition for ‘sd’
    RJMCMC.NH.HMM.Metropolis: no visible global function definition for
     ‘median’
    RJaCGH: no visible global function definition for ‘na.omit’
    genomePlot: no visible global function definition for ‘colors’
    genomePlot: no visible global function definition for ‘par’
    genomePlot: no visible global function definition for ‘layout’
    genomePlot: no visible global function definition for ‘plot’
    genomePlot: no visible global function definition for ‘axis’
    genomePlot: no visible global function definition for ‘lines’
    genomePlot: no visible global function definition for ‘points’
    genomePlot: no visible global function definition for ‘legend’
    get.jump: no visible global function definition for ‘runif’
    get.jump: no visible global function definition for ‘rgamma’
    internal.plot.obs.pred: no visible global function definition for
     ‘plot’
    internal.plot.obs.pred: no visible global function definition for
     ‘polygon’
    internal.plot.obs.pred: no visible global function definition for
     ‘text’
    internal.plot.obs.pred: no visible global function definition for
     ‘points’
    internal.plot.obs.pred: no visible global function definition for
     ‘abline’
    internal.plot.obs.pred: no visible global function definition for
     ‘lines’
    internal.plot.obs.pred: no visible global function definition for ‘par’
    internal.plot.obs.pred: no visible global function definition for
     ‘axis’
    internal.plot.obs.pred: no visible global function definition for
     ‘mtext’
    normal.HMM.likelihood.NH.filter: no visible global function definition
     for ‘dnorm’
    plot.Q.NH: no visible global function definition for ‘plot’
    plot.Q.NH: no visible global function definition for ‘abline’
    plot.Q.NH: no visible global function definition for ‘lines’
    plot.Q.NH: no visible global function definition for ‘rug’
    plot.RJaCGH: no visible global function definition for ‘par’
    plot.RJaCGH.Chrom: no visible global function definition for ‘par’
    plot.RJaCGH.Genome: no visible global function definition for ‘par’
    plot.RJaCGH.Genome: no visible global function definition for ‘layout’
    plot.RJaCGH.Genome: no visible global function definition for ‘barplot’
    plot.RJaCGH.Genome: no visible global function definition for ‘plot’
    plot.RJaCGH.Genome: no visible global function definition for ‘density’
    plot.RJaCGH.Genome: no visible global function definition for ‘sd’
    plot.RJaCGH.Genome: no visible global function definition for ‘lines’
    plot.pREC_S : f2: no visible global function definition for ‘xtabs’
    plot.pREC_S: no visible global function definition for ‘par’
    plot.pREC_S: no visible global function definition for ‘layout’
    plot.pREC_S: no visible global function definition for ‘as.dendrogram’
    plot.pREC_S: no visible global function definition for ‘hclust’
    plot.pREC_S: no visible global function definition for ‘as.dist’
    plot.pREC_S: no visible global function definition for
     ‘order.dendrogram’
    plot.pREC_S: no visible global function definition for ‘plot’
    plot.pREC_S: no visible global function definition for ‘plot.new’
    plot.pREC_S: no visible global function definition for ‘quantile’
    plot.pREC_S: no visible global function definition for ‘image’
    plot.pREC_S: no visible global function definition for ‘axis’
    plot.pREC_S: no visible global function definition for ‘box’
    plot.pREC_S: no visible global function definition for ‘text’
    relabel.core: no visible binding for global variable ‘median’
    relabel.core: no visible global function definition for ‘pnorm’
    simulateRJaCGH: no visible global function definition for ‘rnorm’
    summary.iRJaCGH: no visible binding for global variable ‘density’
    summary.iRJaCGH: no visible binding for global variable ‘quantile’
    tempdir2: no visible global function definition for ‘runif’
    tempfile00: no visible global function definition for ‘runif’
    trace.plot: no visible global function definition for ‘par’
    trace.plot: no visible global function definition for ‘matplot’
    trace.plot: no visible global function definition for ‘mtext’
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang

Version: 2.0.3
Check: Rd \usage sections
Result: NOTE
    S3 methods shown with full name in documentation object 'plot.Q.NH':
     ‘plot.Q.NH’
    
    The \usage entries for S3 methods should use the \method markup and not
    their full name.
    See chapter ‘Writing R documentation files’ 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-devel-osx-x86_64-clang, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-sparc, 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