CRAN Package Check Results for Package swamp

Last updated on 2015-08-28 17:49:41.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.2.3 0.70 23.34 24.04 NOTE
r-devel-linux-x86_64-debian-gcc 1.2.3 0.74 22.49 23.22 NOTE
r-devel-linux-x86_64-fedora-clang 1.2.3 47.02 NOTE
r-devel-linux-x86_64-fedora-gcc 1.2.3 43.26 NOTE
r-devel-osx-x86_64-clang 1.2.3 45.59 NOTE
r-devel-windows-ix86+x86_64 1.2.3 5.00 60.00 65.00 NOTE
r-patched-linux-x86_64 1.2.3 0.77 23.49 24.26 NOTE
r-patched-solaris-sparc 1.2.3 295.60 NOTE
r-patched-solaris-x86 1.2.3 62.50 NOTE
r-release-linux-x86_64 1.2.3 0.78 23.61 24.40 NOTE
r-release-osx-x86_64-mavericks 1.2.3 NOTE
r-release-windows-ix86+x86_64 1.2.3 4.00 65.00 69.00 NOTE
r-oldrel-windows-ix86+x86_64 1.2.3 8.00 51.00 59.00 NOTE

Check Details

Version: 1.2.3
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: 1.2.3
Check: dependencies in R code
Result: NOTE
    'library' or 'require' calls to packages already attached by Depends:
     ‘MASS’ ‘amap’ ‘gplots’ ‘impute’
     Please remove these calls from your code.
    Packages in Depends field not imported from:
     ‘MASS’ ‘amap’ ‘gplots’ ‘impute’
     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: 1.2.3
Check: R code for possible problems
Result: NOTE
    adjust.linearmodel: no visible global function definition for ‘lm’
    adjust.linearmodel: no visible global function definition for ‘rlm’
    combat : aprior: no visible global function definition for ‘var’
    combat : bprior: no visible global function definition for ‘var’
    combat : L: no visible global function definition for ‘dnorm’
    combat: no visible binding for global variable ‘var’
    combat: no visible global function definition for ‘par’
    combat: no visible global function definition for ‘density’
    combat: no visible global function definition for ‘plot’
    combat: no visible global function definition for ‘lines’
    combat: no visible global function definition for ‘dnorm’
    combat: no visible global function definition for ‘qqnorm’
    combat: no visible global function definition for ‘qqline’
    combat: no visible global function definition for ‘rgamma’
    combat: no visible global function definition for ‘qqplot’
    combat: no visible global function definition for ‘title’
    confounding: no visible global function definition for ‘heat.colors’
    confounding: no visible global function definition for ‘fisher.test’
    confounding: no visible global function definition for ‘chisq.test’
    confounding: no visible global function definition for ‘lm’
    confounding: no visible global function definition for ‘pf’
    confounding: no visible global function definition for ‘heatmap.2’
    corrected.p: no visible global function definition for ‘p.adjust’
    dense.plot: no visible global function definition for ‘density’
    dense.plot: no visible global function definition for ‘plot’
    dense.plot: no visible global function definition for ‘lines’
    feature.assoc: no visible binding for global variable ‘cor’
    feature.assoc : <anonymous>: no visible global function definition for
     ‘cor.test’
    feature.assoc: no visible global function definition for ‘t.test’
    feature.assoc: no visible global function definition for ‘wilcox.test’
    feature.assoc: no visible global function definition for ‘na.omit’
    feature.assoc: no visible global function definition for ‘lm’
    feature.assoc: no visible global function definition for ‘pf’
    hca.plot: no visible global function definition for ‘palette’
    hca.plot: no visible global function definition for ‘colorpanel’
    hca.plot: no visible global function definition for ‘hcluster’
    hca.plot: no visible global function definition for ‘as.dendrogram’
    hca.plot: no visible global function definition for ‘par’
    hca.plot: no visible global function definition for ‘layout’
    hca.plot: no visible global function definition for ‘plot’
    hca.plot: no visible global function definition for ‘rect’
    hca.plot: no visible global function definition for ‘axis’
    hca.test: no visible global function definition for ‘hcluster’
    hca.test: no visible global function definition for ‘cutree’
    hca.test: no visible global function definition for ‘fisher.test’
    hca.test: no visible global function definition for ‘chisq.test’
    hca.test: no visible global function definition for ‘lm’
    hca.test: no visible global function definition for ‘pf’
    kill.pc: no visible global function definition for ‘impute.knn’
    prince: no visible global function definition for ‘impute.knn’
    prince: no visible global function definition for ‘prcomp’
    prince: no visible global function definition for ‘lm’
    prince: no visible global function definition for ‘pf’
    prince.plot: no visible global function definition for ‘heat.colors’
    prince.plot: no visible global function definition for ‘heatmap.2’
    prince.var.plot: no visible global function definition for ‘impute.knn’
    prince.var.plot: no visible global function definition for ‘prcomp’
    prince.var.plot: no visible binding for global variable ‘median’
    prince.var.plot: no visible global function definition for ‘plot’
    prince.var.plot: no visible global function definition for ‘points’
    prince.var.plot: no visible global function definition for ‘legend’
    quickadjust.ref: no visible binding for global variable ‘median’
    quickadjust.ref: no visible global function definition for ‘median’
    quickadjust.zero: no visible binding for global variable ‘median’
    Undefined global functions or variables:
     as.dendrogram axis chisq.test colorpanel cor cor.test cutree density
     dnorm fisher.test hcluster heat.colors heatmap.2 impute.knn layout
     legend lines lm median na.omit p.adjust palette par pf plot points
     prcomp qqline qqnorm qqplot rect rgamma rlm t.test title var
     wilcox.test
    Consider adding
     importFrom("grDevices", "heat.colors", "palette")
     importFrom("graphics", "axis", "layout", "legend", "lines", "par",
     "plot", "points", "rect", "title")
     importFrom("stats", "as.dendrogram", "chisq.test", "cor", "cor.test",
     "cutree", "density", "dnorm", "fisher.test", "lm", "median",
     "na.omit", "p.adjust", "pf", "prcomp", "qqline", "qqnorm",
     "qqplot", "rgamma", "t.test", "var", "wilcox.test")
    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: 1.2.3
Check: Rd line widths
Result: NOTE
    Rd file 'prince.plot.Rd':
     \examples lines wider than 100 characters:
     ## patient annotations as a data.frame, annotations should be numbers and factors but not characters.
    
    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: 1.2.3
Check: R code for possible problems
Result: NOTE
    adjust.linearmodel: no visible global function definition for ‘rlm’
    confounding: no visible global function definition for ‘heatmap.2’
    hca.plot: no visible global function definition for ‘colorpanel’
    hca.plot: no visible global function definition for ‘hcluster’
    hca.test: no visible global function definition for ‘hcluster’
    kill.pc: no visible global function definition for ‘impute.knn’
    prince: no visible global function definition for ‘impute.knn’
    prince.plot: no visible global function definition for ‘heatmap.2’
    prince.var.plot: no visible global function definition for ‘impute.knn’
    Undefined global functions or variables:
     colorpanel hcluster heatmap.2 impute.knn rlm
Flavor: r-devel-osx-x86_64-clang

Version: 1.2.3
Check: R code for possible problems
Result: NOTE
    adjust.linearmodel: no visible global function definition for ‘rlm’
    confounding: no visible global function definition for ‘heatmap.2’
    hca.plot: no visible global function definition for ‘colorpanel’
    hca.plot: no visible global function definition for ‘hcluster’
    hca.test: no visible global function definition for ‘hcluster’
    kill.pc: no visible global function definition for ‘impute.knn’
    prince: no visible global function definition for ‘impute.knn’
    prince.plot: no visible global function definition for ‘heatmap.2’
    prince.var.plot: no visible global function definition for ‘impute.knn’
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