CRAN Package Check Results for Package isa2

Last updated on 2016-09-28 03:47:08.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.3.4 1.23 27.84 29.07 ERROR
r-devel-linux-x86_64-debian-gcc 0.3.4 1.28 27.90 29.18 NOTE
r-devel-linux-x86_64-fedora-clang 0.3.4 53.52 NOTE
r-devel-linux-x86_64-fedora-gcc 0.3.4 50.95 NOTE
r-devel-macos-x86_64-clang 0.3.4 41.67 NOTE
r-devel-windows-ix86+x86_64 0.3.4 9.00 83.00 92.00 NOTE
r-patched-linux-x86_64 0.3.4 1.29 28.60 29.89 NOTE
r-patched-solaris-sparc 0.3.4 349.90 NOTE
r-patched-solaris-x86 0.3.4 69.10 NOTE
r-release-linux-x86_64 0.3.4 1.30 27.54 28.83 NOTE
r-release-osx-x86_64-mavericks 0.3.4 NOTE
r-release-windows-ix86+x86_64 0.3.4 9.00 68.00 77.00 NOTE
r-oldrel-windows-ix86+x86_64 0.3.4 12.00 90.00 102.00 OK

Check Details

Version: 0.3.4
Check: R code for possible problems
Result: NOTE
    images: no visible global function definition for ‘colorRampPalette’
    isa.biclust: no visible global function definition for ‘new’
    isa.in.silico: no visible global function definition for ‘rnorm’
    isa.iterate.default: no visible global function definition for ‘tail’
    isa.sweep.default: no visible global function definition for ‘cor’
    isa.unique.default: no visible global function definition for ‘cor’
    ppa.in.silico: no visible global function definition for ‘rnorm’
    ppa.unique.default: no visible global function definition for ‘cor’
    sweep.graph.default : <anonymous>: no visible global function
     definition for ‘tail’
    Undefined global functions or variables:
     colorRampPalette cor new rnorm tail
    Consider adding
     importFrom("grDevices", "colorRampPalette")
     importFrom("methods", "new")
     importFrom("stats", "cor", "rnorm")
     importFrom("utils", "tail")
    to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
    contains 'methods').
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-macos-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: 0.3.4
Check: examples
Result: ERROR
    Running examples in ‘isa2-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: isa.sweep
    > ### Title: Create a hierarchical structure of ISA biclusters
    > ### Aliases: isa.sweep isa.sweep,matrix-method sweep.graph
    > ### sweep.graph,list-method
    > ### Keywords: cluster
    >
    > ### ** Examples
    >
    > ## In-silico data
    > set.seed(1)
    > insili <- isa.in.silico()
    Creating in-silico data set
    DONE
    >
    > ## Do ISA with a bunch of row thresholds while keeping the column
    > ## threshold fixed. This is quite an artificial example...
    > isares <- isa(insili[[1]], thr.row=c(0.5,1,2), thr.col=0)
    Performing complete ISA work flow
    ISA normalization
    DONE
    Generating seeds
    DONE
    Doing ISA iteration
    DONE
    Doing ISA iteration
    DONE
    Doing ISA iteration
    DONE
    Creating unique module set
    DONE
    Creating unique module set
    DONE
    Creating unique module set
    DONE
    Filtering ISA result for robustness...
    Calculating ISA robustness
    DONE
    ISA normalization
    DONE
    Doing ISA iteration
    DONE
    Calculating ISA robustness
    DONE
    DONE.
    Filtering ISA result for robustness...
    Calculating ISA robustness
    DONE
    ISA normalization
    DONE
    Doing ISA iteration
    DONE
    Calculating ISA robustness
    DONE
    DONE.
    Filtering ISA result for robustness...
    Calculating ISA robustness
    DONE
    ISA normalization
    DONE
    Doing ISA iteration
    DONE
    Calculating ISA robustness
    DONE
    DONE.
    Creating unique module set
    DONE
    DONE
    >
    > ## Create a nice tree from the modules, we need the normed data for this
    > nm <- isa.normalize(insili[[1]])
    ISA normalization
    DONE
    > isa.tree <- isa.sweep(insili[[1]], nm, isares)
    Performing an ISA sweep
    Doing ISA iteration
    DONE
    Creating unique module set
    DONE
    Calculating ISA robustness
    DONE
    Doing ISA iteration
    DONE
    Creating unique module set
    DONE
    Calculating ISA robustness
    DONE
    DONE
    > network <- sweep.graph(isa.tree)
    Loading required namespace: igraph
    Error in if (vr[1] == vr[2]) { : missing value where TRUE/FALSE needed
    Calls: sweep.graph ... sweep.graph.default -> lapply -> FUN -> <Anonymous> -> .layout.norm.col
    Execution halted
Flavor: r-devel-linux-x86_64-debian-clang