CRAN Package Check Results for Package BiomarkeR

Last updated on 2014-07-24 22:48:34.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.3 1.18 27.55 28.73 NOTE
r-devel-linux-x86_64-debian-gcc 1.3 1.18 27.20 28.38 NOTE
r-devel-linux-x86_64-fedora-clang 1.3 64.05 NOTE
r-devel-linux-x86_64-fedora-gcc 1.3 61.74 NOTE
r-devel-osx-x86_64-clang 1.3 57.65 NOTE
r-devel-windows-ix86+x86_64 1.3 5.00 45.00 50.00 NOTE
r-patched-linux-x86_64 1.3 1.34 27.30 28.64 NOTE
r-patched-solaris-sparc 1.3 367.80 NOTE
r-patched-solaris-x86 1.3 82.00 NOTE
r-release-linux-ix86 1.3 1.65 37.33 38.98 NOTE
r-release-linux-x86_64 1.3 1.31 28.87 30.18 NOTE
r-release-osx-x86_64-mavericks 1.3 NOTE
r-release-windows-ix86+x86_64 1.3 5.00 44.00 49.00 NOTE
r-oldrel-windows-ix86+x86_64 1.3 6.00 63.00 69.00 NOTE

Check Details

Version: 1.3
Check: dependencies in R code
Result: NOTE
    Packages in Depends field not imported from:
     ‘Hmisc’ ‘igraph’
     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, 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: 1.3
Check: Rd files
Result: NOTE
    prepare_Rd: BIdata.RData.Rd:27-28: Dropping empty section \details
    prepare_Rd: BIdata.RData.Rd:29-30: Dropping empty section \source
    prepare_Rd: BIdata.RData.Rd:31-32: Dropping empty section \references
    prepare_Rd: pBI.Rd:52-53: Dropping empty section \note
    prepare_Rd: pBIGraph.Rd:57-58: Dropping empty section \note
    prepare_Rd: pBIGraph.Rd:52-53: Dropping empty section \references
    prepare_Rd: uBI.Rd:53-54: Dropping empty section \note
    prepare_Rd: uBIGraph.Rd:54-55: Dropping empty section \note
    prepare_Rd: uBIGraph.Rd:49-50: Dropping empty section \references
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-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: 1.3
Check: for old-style vignette sources
Result: NOTE
    Vignette sources only in ‘inst/doc’:
     ‘BiomarkeR.Rnw’
    A ‘vignettes’ directory is required as from R 3.1.0
    and these will not be indexed nor checked
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-ix86, r-release-linux-x86_64, r-release-osx-x86_64-mavericks, r-release-windows-ix86+x86_64

Version: 1.3
Check: Rd line widths
Result: NOTE
    Rd file 'BiomarkeR-package.Rd':
     \examples lines wider than 100 characters:
     pbi.scores <- pBI(dataset=pbi.data, classlabels=pbi.class, referenceclasslabel="rest", ids=pbi.id, useMedian = TRUE, lambda = 100, plot ... [TRUNCATED]
     g <- pBIGraph(dataset=pbi.data, classlabels=pbi.class, referenceclasslabel="rest", ids=pbi.id, useMedian = TRUE, lambda = 100, threshol ... [TRUNCATED]
     ubi.scores <- uBI(dataset=ubi.data, classlabels=ubi.class, referenceclasslabel="control", useMedian = TRUE, lambda = 100, plotScores = ... [TRUNCATED]
    
    Rd file 'pBI.Rd':
     \usage lines wider than 90 characters:
     pBI(dataset, classlabels, referenceclasslabel, ids, useMedian = TRUE, lambda = 100, plotScores = TRUE, numTopRankedToPlot = 10, bars.co ... [TRUNCATED]
     \examples lines wider than 100 characters:
     pbi.scores <- pBI(dataset=pbi.data, classlabels=pbi.class, referenceclasslabel="rest", ids=pbi.id, useMedian = TRUE, lambda = 100, plot ... [TRUNCATED]
    
    Rd file 'pBIGraph.Rd':
     \usage lines wider than 90 characters:
     pBIGraph(dataset, classlabels, referenceclasslabel, ids, useMedian = TRUE, lambda = 100, threshold = "q90", plotGraph = FALSE, edge.fil ... [TRUNCATED]
     \examples lines wider than 100 characters:
     g <- pBIGraph(dataset=pbi.data, classlabels=pbi.class, referenceclasslabel="rest", ids=pbi.id, useMedian = TRUE, lambda = 100, threshol ... [TRUNCATED]
    
    Rd file 'uBI.Rd':
     \usage lines wider than 90 characters:
     uBI(dataset, classlabels, referenceclasslabel, useMedian = TRUE, lambda = 100, plotScores = TRUE, numTopRankedToPlot = 10, bars.cols = ... [TRUNCATED]
     \examples lines wider than 100 characters:
     ubi.scores <- uBI(dataset=ubi.data, classlabels=ubi.class, referenceclasslabel="control", useMedian = TRUE, lambda = 100, plotScores = ... [TRUNCATED]
    
    Rd file 'uBIGraph.Rd':
     \usage lines wider than 90 characters:
     uBIGraph(dataset, classlabels, referenceclasslabel, useMedian = TRUE, lambda = 100, threshold = "q90", plotGraph = FALSE, edge.file = N ... [TRUNCATED]
     \examples lines wider than 100 characters:
     g <- uBIGraph(dataset=ubi.data, classlabels=ubi.class, referenceclasslabel="control", useMedian = TRUE, lambda = 100, threshold = "q90" ... [TRUNCATED]
    
    These lines will be truncated in the PDF manual.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 1.3
Check: for old-style vignette sources
Result: NOTE
    Vignette sources only in 'inst/doc':
     'BiomarkeR.Rnw'
    A 'vignettes' directory will be required as from R 3.1.0
Flavor: r-oldrel-windows-ix86+x86_64