CRAN Package Check Results for Package isa2

Last updated on 2014-04-18 01:47:47.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.3.3 1.31 27.54 28.85 NOTE
r-devel-linux-x86_64-debian-gcc 0.3.3 1.26 28.76 30.03 NOTE
r-devel-linux-x86_64-fedora-clang 0.3.3 63.20 NOTE
r-devel-linux-x86_64-fedora-gcc 0.3.3 61.28 NOTE
r-devel-macosx-x86_64-clang 0.3.3 51.56 NOTE
r-devel-macosx-x86_64-gcc 0.3.3 ERROR
r-devel-windows-ix86+x86_64 0.3.3 5.00 56.00 61.00 NOTE
r-patched-linux-x86_64 0.3.3 1.35 28.84 30.19 NOTE
r-patched-solaris-sparc 0.3.3 370.00 NOTE
r-patched-solaris-x86 0.3.3 77.80 NOTE
r-release-linux-ix86 0.3.3 3.00 47.00 50.00 NOTE
r-release-linux-x86_64 0.3.3 1.26 27.63 28.89 NOTE
r-release-windows-ix86+x86_64 0.3.3 6.00 55.00 61.00 NOTE
r-oldrel-windows-ix86+x86_64 0.3.3 6.00 59.00 65.00 NOTE

Check Details

Version: 0.3.3
Check: dependencies in R code
Result: NOTE
    Package in Depends field not imported from: ‘methods’
     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-macosx-x86_64-clang, r-devel-macosx-x86_64-gcc, 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-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 0.3.3
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: ‘igraph’
Flavor: r-devel-macosx-x86_64-gcc

Version: 0.3.3
Check: R code for possible problems
Result: NOTE
    sweep.graph.default: no visible global function definition for ‘graph’
    sweep.graph.default: no visible global function definition for ‘V’
    sweep.graph.default: no visible global function definition for ‘V<-’
    sweep.graph.default: no visible global function definition for ‘vcount’
    sweep.graph.default: no visible global function definition for
     ‘decompose.graph’
    sweep.graph.default : <anonymous>: no visible global function
     definition for ‘layout.reingold.tilford’
    sweep.graph.default : <anonymous>: no visible global function
     definition for ‘topological.sort’
    sweep.graph.default : <anonymous>: no visible global function
     definition for ‘V’
    sweep.graph.default : <anonymous>: no visible global function
     definition for ‘layout.norm’
    sweep.graph.default: no visible binding for global variable
     ‘get.vertex.attribute’
    sweep.graph.default: no visible global function definition for ‘E’
    sweep.graph.default: no visible global function definition for ‘E<-’
Flavor: r-devel-macosx-x86_64-gcc

Version: 0.3.3
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 package: igraph
    Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
     there is no package called ‘igraph’
    Error in sweep.graph.default(sweep.result, ...) :
     could not find function "graph"
    Calls: sweep.graph -> sweep.graph -> sweep.graph.default
    Execution halted
Flavor: r-devel-macosx-x86_64-gcc