CRAN Package Check Results for Package BoolNet

Last updated on 2014-04-24 11:48:42.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.63 2.52 59.14 61.66 OK
r-devel-linux-x86_64-debian-gcc 1.63 6.17 60.06 66.23 OK
r-devel-linux-x86_64-fedora-clang 1.63 107.62 OK
r-devel-linux-x86_64-fedora-gcc 1.63 111.09 OK
r-devel-osx-x86_64-clang 1.63 101.98 OK
r-devel-osx-x86_64-gcc 1.63 ERROR
r-devel-windows-ix86+x86_64 1.63 17.00 91.00 108.00 OK
r-patched-linux-x86_64 1.63 6.12 59.54 65.66 OK
r-patched-solaris-sparc 1.63 723.70 OK
r-patched-solaris-x86 1.63 125.90 OK
r-release-linux-ix86 1.63 10.00 166.00 176.00 OK
r-release-linux-x86_64 1.63 6.34 59.31 65.65 OK
r-release-osx-x86_64-mavericks 1.63 WARN
r-release-osx-x86_64-snowleopard 1.63 OK
r-release-windows-ix86+x86_64 1.63 20.00 91.00 111.00 OK
r-oldrel-windows-ix86+x86_64 1.63 18.00 97.00 115.00 OK

Check Details

Version: 1.63
Check: package dependencies
Result: NOTE
    Packages suggested but not available for checking: ‘igraph’ ‘XML’
Flavor: r-devel-osx-x86_64-gcc

Version: 1.63
Check: R code for possible problems
Result: NOTE
    loadBioTapestry: no visible global function definition for ‘xmlRoot’
    loadBioTapestry: no visible global function definition for
     ‘xmlTreeParse’
    loadSBML: no visible global function definition for ‘xmlRoot’
    loadSBML: no visible global function definition for ‘xmlParse’
    loadSBML: no visible global function definition for ‘getNodeSet’
    loadSBML: no visible global function definition for ‘removeNodes’
    loadSBML: no visible global function definition for ‘xmlName’
    loadSBML: no visible global function definition for ‘xmlAttrs’
    loadSBML: no visible global function definition for ‘xmlNamespaces’
    parseAllGenes: no visible global function definition for ‘xmlApply’
    parseAllLinks: no visible global function definition for ‘xmlChildren’
    parseAllLinks: no visible global function definition for ‘xmlAttrs’
    parseGeneAttrs: no visible global function definition for ‘xmlApply’
    parseGeneAttrs : <anonymous>: no visible global function definition for
     ‘xmlAttrs’
    parseGeneAttrs : <anonymous>: no visible global function definition for
     ‘xmlName’
    parseGeneAttrs : <anonymous>: no visible global function definition for
     ‘xmlChildren’
    parseMathML: no visible global function definition for ‘xmlName’
    parseMathML: no visible global function definition for ‘xmlChildren’
    parseMathML: no visible global function definition for ‘xmlValue’
    parseMathML: no visible global function definition for ‘xmlAttrs’
    parseSBMLFunctionTerms: no visible global function definition for
     ‘xmlApply’
    parseSBMLFunctionTerms : <anonymous>: no visible global function
     definition for ‘xmlAttrs’
    parseSBMLFunctionTerms : <anonymous>: no visible global function
     definition for ‘xmlName’
    parseSBMLSpecies: no visible global function definition for
     ‘xmlChildren’
    parseSBMLSpecies: no visible global function definition for ‘xmlAttrs’
    parseSBMLTransitions: no visible global function definition for
     ‘xmlApply’
    parseSBMLTransitions : <anonymous>: no visible global function
     definition for ‘xmlChildren’
    parseSBMLTransitions : <anonymous>: no visible global function
     definition for ‘xmlAttrs’
    plotAttractors: no visible binding for global variable ‘layout.circle’
    plotAttractors : <anonymous>: no visible global function definition for
     ‘graph.data.frame’
    plotNetworkWiring: no visible binding for global variable
     ‘layout.fruchterman.reingold’
    plotNetworkWiring: no visible global function definition for
     ‘graph.data.frame’
    plotNetworkWiring: no visible global function definition for
     ‘set.vertex.attribute’
    plotPBNTransitions: no visible binding for global variable
     ‘layout.fruchterman.reingold’
    plotPBNTransitions: no visible global function definition for
     ‘graph.data.frame’
    plotPBNTransitions: no visible global function definition for
     ‘set.edge.attribute’
    plotSequence: no visible global function definition for
     ‘graph.data.frame’
    plotStateGraph: no visible binding for global variable
     ‘layout.fruchterman.reingold’
    plotStateGraph: no visible global function definition for
     ‘graph.edgelist’
    plotStateGraph: no visible global function definition for
     ‘set.vertex.attribute’
    plotStateGraph: no visible global function definition for
     ‘set.edge.attribute’
    plotStateGraph: no visible global function definition for
     ‘piecewise.layout’
    testIndegree: no visible global function definition for ‘degree’
    xmlFindNode: no visible global function definition for ‘xmlSApply’
    xmlFindNode: no visible binding for global variable ‘xmlName’
    xmlFindNode: no visible global function definition for ‘xmlChildren’
Flavor: r-devel-osx-x86_64-gcc

Version: 1.63
Check: Rd cross-references
Result: NOTE
    Package unavailable to check Rd xrefs: ‘igraph’
Flavor: r-devel-osx-x86_64-gcc

Version: 1.63
Check: examples
Result: ERROR
    Running examples in ‘BoolNet-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: loadBioTapestry
    > ### Title: Import a network from BioTapestry
    > ### Aliases: loadBioTapestry
    > ### Keywords: BioTapestry import
    >
    > ### ** Examples
    >
    > # import the example BioTapestry file
    > # included in the package vignette
    > exampleFile <- system.file("doc/example.btp",
    + package="BoolNet")
    > net <- loadBioTapestry(exampleFile)
    Loading required package: XML
    Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
     there is no package called ‘XML’
    Error in loadBioTapestry(exampleFile) :
     Please install the XML package before using this function!
    Execution halted
Flavor: r-devel-osx-x86_64-gcc

Version: 1.63
Check: PDF version of manual
Result: WARNING
    LaTeX errors when creating PDF version.
    This typically indicates Rd problems.
    LaTeX errors found:
    ! LaTeX Error: File `upquote.sty' not found.
    
    Type X to quit or <RETURN> to proceed,
    or enter new name. (Default extension: sty)
    
    b0ac80e/Rd2.tex:8: ==> Fatal error occurred, no output PDF file produced!
Flavor: r-release-osx-x86_64-mavericks