CRAN Package Check Results for Package muma

Last updated on 2015-08-30 17:48:20.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.4 4.27 42.92 47.19 NOTE
r-devel-linux-x86_64-debian-gcc 1.4 4.20 43.26 47.46 NOTE
r-devel-linux-x86_64-fedora-clang 1.4 101.77 NOTE
r-devel-linux-x86_64-fedora-gcc 1.4 97.00 NOTE
r-devel-osx-x86_64-clang 1.4 83.10 NOTE
r-devel-windows-ix86+x86_64 1.4 21.00 77.00 98.00 NOTE
r-patched-linux-x86_64 1.4 4.56 46.96 51.53 NOTE
r-patched-solaris-sparc 1.4 602.70 NOTE
r-patched-solaris-x86 1.4 142.70 NOTE
r-release-linux-x86_64 1.4 4.55 47.14 51.69 NOTE
r-release-osx-x86_64-mavericks 1.4 NOTE
r-release-windows-ix86+x86_64 1.4 17.00 76.00 93.00 NOTE
r-oldrel-windows-ix86+x86_64 1.4 33.00 116.00 149.00 NOTE

Check Details

Version: 1.4
Check: package dependencies
Result: NOTE
    Depends: includes the non-default packages:
     ‘car’ ‘pdist’ ‘pls’ ‘gplots’ ‘mvtnorm’ ‘robustbase’ ‘gtools’ ‘bitops’
     ‘caTools’ ‘pcaPP’ ‘rrcov’
    Adding so many packages to the search path is excessive and importing
    selectively is preferable.
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

Version: 1.4
Check: dependencies in R code
Result: NOTE
    'library' or 'require' calls to packages already attached by Depends:
     ‘car’ ‘gplots’ ‘pdist’ ‘pls’ ‘rrcov’
     Please remove these calls from your code.
    Packages in Depends field not imported from:
     ‘bitops’ ‘caTools’ ‘car’ ‘gplots’ ‘gtools’ ‘mvtnorm’ ‘pcaPP’ ‘pdist’
     ‘pls’ ‘robustbase’ ‘rrcov’
     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-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

Version: 1.4
Check: R code for possible problems
Result: NOTE
    Plot.pca.loading: no visible global function definition for ‘read.csv’
    Plot.pca.loading: no visible global function definition for ‘dev.new’
    Plot.pca.loading: no visible global function definition for ‘plot’
    Plot.pca.loading: no visible global function definition for ‘axis’
    Plot.pca.loading: no visible global function definition for ‘text’
    Plot.pca.loading: no visible global function definition for
     ‘dev.copy2pdf’
    Plot.pca.pvalues: no visible global function definition for ‘read.csv’
    Plot.pca.pvalues: no visible global function definition for ‘dev.new’
    Plot.pca.pvalues: no visible global function definition for ‘plot’
    Plot.pca.pvalues: no visible global function definition for ‘axis’
    Plot.pca.pvalues: no visible global function definition for ‘text’
    Plot.pca.pvalues: no visible global function definition for
     ‘dev.copy2pdf’
    Plot.pca.score: no visible global function definition for ‘read.csv’
    Plot.pca.score: no visible global function definition for ‘dev.new’
    Plot.pca.score: no visible global function definition for ‘plot’
    Plot.pca.score: no visible global function definition for ‘axis’
    Plot.pca.score: no visible global function definition for ‘dataEllipse’
    Plot.pca.score: no visible global function definition for ‘text’
    Plot.pca.score: no visible global function definition for
     ‘dev.copy2pdf’
    Plot.plsda: no visible global function definition for ‘read.csv’
    Plot.plsda: no visible global function definition for ‘plot’
    Plot.plsda: no visible global function definition for ‘text’
    Plot.plsda: no visible global function definition for ‘axis’
    Plot.plsda: no visible global function definition for ‘dataEllipse’
    Plot.plsda: no visible global function definition for ‘dev.copy2pdf’
    Plot.plsda: no visible global function definition for ‘dev.new’
    box.plot: no visible global function definition for ‘read.csv’
    box.plot: no visible global function definition for ‘pdf’
    box.plot: no visible global function definition for ‘boxplot’
    box.plot: no visible global function definition for ‘dev.off’
    chose.driver: no visible global function definition for ‘read.csv’
    col.pvalues: no visible global function definition for ‘read.csv’
    col.pvalues: no visible global function definition for ‘write.csv’
    explore.data: no visible global function definition for ‘read.csv’
    explore.data: no visible global function definition for ‘write.csv’
    explore.data: no visible global function definition for ‘runif’
    explore.data: no visible binding for global variable ‘sd’
    explore.data: no visible binding for global variable ‘median’
    explore.data: no visible global function definition for ‘prcomp’
    explore.data: no visible global function definition for ‘barplot’
    explore.data: no visible global function definition for ‘dev.copy2pdf’
    explore.data: no visible global function definition for ‘dev.new’
    explore.data: no visible global function definition for ‘T2.test’
    explore.data: no visible global function definition for ‘pf’
    oplsda: no visible global function definition for ‘read.csv’
    oplsda: no visible global function definition for ‘plot’
    oplsda: no visible global function definition for ‘text’
    oplsda: no visible global function definition for ‘axis’
    oplsda: no visible global function definition for ‘dataEllipse’
    oplsda: no visible global function definition for ‘write.csv’
    oplsda: no visible global function definition for ‘dev.copy2pdf’
    oplsda: no visible global function definition for ‘cov’
    oplsda: no visible binding for global variable ‘sd’
    oplsda: no visible global function definition for ‘sd’
    oplsda: no visible global function definition for ‘dev.new’
    oplsda: no visible global function definition for ‘prcomp’
    oplsda: no visible global function definition for ‘pdf’
    oplsda: no visible global function definition for ‘dev.off’
    ostocsy: no visible global function definition for ‘read.csv’
    ostocsy: no visible global function definition for ‘cor’
    ostocsy: no visible global function definition for ‘colorpanel’
    ostocsy: no visible global function definition for ‘image’
    ostocsy: no visible global function definition for ‘axis’
    ostocsy: no visible global function definition for ‘dev.copy2pdf’
    ostocsy: no visible global function definition for ‘write.csv’
    ostocsy: no visible global function definition for ‘dev.new’
    outlier: no visible global function definition for ‘read.csv’
    outlier: no visible global function definition for ‘var’
    outlier: no visible global function definition for ‘pdist’
    outlier: no visible global function definition for ‘write.csv’
    plsda: no visible global function definition for ‘read.csv’
    plsda: no visible global function definition for ‘plsr’
    plsda: no visible global function definition for ‘write.csv’
    plsda: no visible global function definition for ‘plot’
    plsda: no visible global function definition for ‘axis’
    plsda: no visible global function definition for ‘text’
    plsda: no visible global function definition for ‘dev.copy2pdf’
    plsda: no visible global function definition for ‘dev.new’
    pvalues: no visible global function definition for ‘read.csv’
    pvalues: no visible global function definition for ‘p.adjust’
    pvalues: no visible global function definition for ‘write.csv’
    ransy: no visible global function definition for ‘read.csv’
    ransy: no visible global function definition for ‘plot’
    ransy: no visible global function definition for ‘text’
    ransy: no visible global function definition for ‘dev.copy2pdf’
    shapiro: no visible global function definition for ‘read.csv’
    shapiro: no visible global function definition for ‘shapiro.test’
    shapiro: no visible global function definition for ‘write.csv’
    stocsy: no visible global function definition for ‘read.csv’
    stocsy: no visible global function definition for ‘cor’
    stocsy: no visible global function definition for ‘colorpanel’
    stocsy: no visible global function definition for ‘image’
    stocsy: no visible global function definition for ‘axis’
    stocsy: no visible global function definition for ‘dev.copy2pdf’
    stocsy: no visible global function definition for ‘write.csv’
    stocsy: no visible global function definition for ‘dev.new’
    stocsy.1d: no visible global function definition for ‘read.csv’
    stocsy.1d: no visible global function definition for ‘cor’
    stocsy.1d: no visible global function definition for ‘rich.colors’
    stocsy.1d: no visible global function definition for ‘plot’
    stocsy.1d: no visible global function definition for ‘text’
    stocsy.1d: no visible global function definition for ‘dev.copy2pdf’
    univariate: no visible global function definition for ‘read.csv’
    univariate: no visible global function definition for ‘runif’
    univariate: no visible global function definition for ‘write.csv’
    univariate: no visible global function definition for ‘sd’
    volcano: no visible global function definition for ‘read.csv’
    volcano: no visible global function definition for ‘write.csv’
    volcano: no visible global function definition for ‘pdf’
    volcano: no visible global function definition for ‘plot’
    volcano: no visible global function definition for ‘text’
    volcano: no visible global function definition for ‘axis’
    volcano: no visible global function definition for ‘dev.off’
    volcano: no visible global function definition for ‘dev.new’
    welch: no visible global function definition for ‘read.csv’
    welch: no visible global function definition for ‘t.test’
    welch: no visible global function definition for ‘write.csv’
    wmw: no visible global function definition for ‘read.csv’
    wmw: no visible global function definition for ‘wilcox.test’
    wmw: no visible global function definition for ‘write.csv’
    Undefined global functions or variables:
     T2.test axis barplot boxplot colorpanel cor cov dataEllipse
     dev.copy2pdf dev.new dev.off image median p.adjust pdf pdist pf plot
     plsr prcomp read.csv rich.colors runif sd shapiro.test t.test text
     var wilcox.test write.csv
    Consider adding
     importFrom("grDevices", "dev.copy2pdf", "dev.new", "dev.off", "pdf")
     importFrom("graphics", "axis", "barplot", "boxplot", "image", "plot",
     "text")
     importFrom("stats", "cor", "cov", "median", "p.adjust", "pf", "prcomp",
     "runif", "sd", "shapiro.test", "t.test", "var",
     "wilcox.test")
     importFrom("utils", "read.csv", "write.csv")
    to your NAMESPACE.
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

Version: 1.4
Check: Rd line widths
Result: NOTE
    Rd file 'Plot.pca.score.Rd':
     \examples lines wider than 100 characters:
     ylab = ylab, xlim = lim, ylim = lim, pch = 19, sub = paste("Cumulative Proportion of Variance Explained = ",
    
    Rd file 'oplsda.Rd':
     \examples lines wider than 100 characters:
     ylab = ylab, xlim = lim, ylim = lim, pch = 19, sub = paste("Cumulative Proportion of Variance Explained = ",
    
    Rd file 'univariate.Rd':
     \usage lines wider than 90 characters:
     univariate(file, imputation = FALSE, imput, normalize = TRUE, multi.test = TRUE, plot.volcano = FALSE, save.boxplot=TRUE)
    
    Rd file 'volcano.Rd':
     \examples lines wider than 100 characters:
     sep = ""), sub = "(Variables in Blue are significant (Pvalue<0.05) and showed Fold Changes >1.2 or <0.8)")
     j, sep = ""), sub = "(Variables in Blue are significant (Pvalue<0.05) and showed Fold Changes >1.2 or <0.8)")
    
    These lines will be truncated in the PDF 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-release-linux-x86_64

Version: 1.4
Check: R code for possible problems
Result: NOTE
    Plot.pca.score: no visible global function definition for ‘dataEllipse’
    Plot.plsda: no visible global function definition for ‘dataEllipse’
    explore.data: no visible global function definition for ‘T2.test’
    oplsda: no visible global function definition for ‘dataEllipse’
    ostocsy: no visible global function definition for ‘colorpanel’
    outlier: no visible global function definition for ‘pdist’
    plsda: no visible global function definition for ‘plsr’
    stocsy: no visible global function definition for ‘colorpanel’
    stocsy.1d: no visible global function definition for ‘rich.colors’
    Undefined global functions or variables:
     T2.test colorpanel dataEllipse pdist plsr rich.colors
Flavor: r-devel-osx-x86_64-clang

Version: 1.4
Check: R code for possible problems
Result: NOTE
    Plot.pca.score: no visible global function definition for ‘dataEllipse’
    Plot.plsda: no visible global function definition for ‘dataEllipse’
    explore.data: no visible global function definition for ‘T2.test’
    oplsda: no visible global function definition for ‘dataEllipse’
    ostocsy: no visible global function definition for ‘colorpanel’
    outlier: no visible global function definition for ‘pdist’
    plsda: no visible global function definition for ‘plsr’
    stocsy: no visible global function definition for ‘colorpanel’
    stocsy.1d: no visible global function definition for ‘rich.colors’
Flavors: 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