CRAN Package Check Results for Package BiomarkeR

Last updated on 2014-07-31 01:47:43.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.3 1.19 27.76 28.95 NOTE
r-devel-linux-x86_64-debian-gcc 1.3 1.18 27.64 28.82 NOTE
r-devel-linux-x86_64-fedora-clang 1.3 62.22 NOTE
r-devel-linux-x86_64-fedora-gcc 1.3 60.45 NOTE
r-devel-osx-x86_64-clang 1.3 58.29 NOTE
r-devel-windows-ix86+x86_64 1.3 5.00 44.00 49.00 NOTE
r-patched-linux-x86_64 1.3 1.57 27.62 29.20 NOTE
r-patched-solaris-sparc 1.3 357.90 ERROR
r-patched-solaris-x86 1.3 88.00 NOTE
r-release-linux-ix86 1.3 1.58 37.07 38.65 NOTE
r-release-linux-x86_64 1.3 1.53 31.69 33.22 NOTE
r-release-osx-x86_64-mavericks 1.3 NOTE
r-release-windows-ix86+x86_64 1.3 7.00 64.00 71.00 NOTE
r-oldrel-windows-ix86+x86_64 1.3 8.00 85.00 93.00 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: 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