CRAN Package Check Results for Package BiomarkeR

Last updated on 2014-09-18 21:46:40.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.3 1.22 32.18 33.41 NOTE
r-devel-linux-x86_64-debian-gcc 1.3 1.22 28.59 29.81 NOTE
r-devel-linux-x86_64-fedora-clang 1.3 64.42 NOTE
r-devel-linux-x86_64-fedora-gcc 1.3 73.77 NOTE
r-devel-osx-x86_64-clang 1.3 54.25 NOTE
r-devel-windows-ix86+x86_64 1.3 6.00 48.00 54.00 NOTE
r-patched-linux-x86_64 1.3 1.32 30.89 32.21 NOTE
r-patched-solaris-sparc 1.3 347.60 ERROR
r-patched-solaris-x86 1.3 87.50 NOTE
r-release-linux-ix86 1.3 1.71 39.94 41.64 NOTE
r-release-linux-x86_64 1.3 1.41 31.38 32.78 NOTE
r-release-osx-x86_64-mavericks 1.3 NOTE
r-release-windows-ix86+x86_64 1.3 6.00 50.00 56.00 NOTE
r-oldrel-windows-ix86+x86_64 1.3 7.00 66.00 73.00 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: R code for possible problems
Result: NOTE
    .calculateRatios: no visible global function definition for ‘na.keep’
    .createGraph: no visible global function definition for ‘V’
    .createGraph: no visible global function definition for ‘V<-’
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

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: 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-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: 1.3
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: examples
Result: ERROR
    Running examples in ‘BiomarkeR-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: BiomarkeR-package
    > ### Title: Paired and Unpaired Biomarker Identifier including a method to
    > ### infer networks.
    > ### Aliases: BiomarkeR-package BiomarkeR
    > ### Keywords: ts univar
    >
    > ### ** Examples
    >
    > data(BIdata)
    > pbi.scores <- pBI(dataset=pbi.data, classlabels=pbi.class, referenceclasslabel="rest", ids=pbi.id, useMedian = TRUE, lambda = 100, plotScores = TRUE, numTopRankedToPlot = 5)
    > g <- pBIGraph(dataset=pbi.data, classlabels=pbi.class, referenceclasslabel="rest", ids=pbi.id, useMedian = TRUE, lambda = 100, threshold = "q90", plotGraph = FALSE, edge.file = NULL)
    
     *** caught segfault ***
    address 82800000, cause 'memory not mapped'
    
    Traceback:
     1: base::.Call(.NAME, ...)
     2: .Call("R_igraph_graph_adjacency", adjmatrix, as.numeric(mode), PACKAGE = "igraph")
     3: graph.adjacency.dense(adjmatrix, mode = mode, weighted = weighted, diag = diag)
     4: igraph::graph.adjacency(adjmat, mode = "undirected")
     5: .getGraph(nodes, significant)
     6: .createGraph(biscores, nodes = rownames(dataset), threshold, edge.file, plotGraph)
     7: pBIGraph(dataset = pbi.data, classlabels = pbi.class, referenceclasslabel = "rest", ids = pbi.id, useMedian = TRUE, lambda = 100, threshold = "q90", plotGraph = FALSE, edge.file = NULL)
    aborting ...
Flavor: r-patched-solaris-sparc

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