rBiopaxParser

Package: rBiopaxParser
Type: Package
Title: Parses BioPax files and represents them in R
Version: 2.10.0
Date: 2014-03-25
Author: Frank Kramer
Maintainer: Frank Kramer <dev@frankkramer.de>
Description: Parses BioPAX files and represents them in R, at the moment BioPAX level 2 and level 3 are supported.
License: GPL (>= 2)
Depends: R (>= 3.0.0), data.table
Imports: XML
Suggests: Rgraphviz, RCurl, graph, RUnit, BiocGenerics, nem, RBGL
URL: https://github.com/frankkramer/rBiopaxParser
biocViews: DataRepresentation
NeedsCompilation: no
Packaged: 2016-05-04 04:50:57 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'rBiopaxParser' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'rBiopaxParser'
    finding HTML links ... done
    CLASS_INHERITANCE_BP2                   html  
    CLASS_INHERITANCE_BP3                   html  
    CLASS_PROPERTIES_BP2                    html  
    CLASS_PROPERTIES_BP3                    html  
    DATABASE_BIOPAX                         html  
    addBiochemicalReaction                  html  
    addBiopaxInstance                       html  
    addBiopaxInstances                      html  
    addControl                              html  
    addPathway                              html  
    addPathwayComponents                    html  
    addPhysicalEntity                       html  
    addPhysicalEntityParticipant            html  
    addPropertiesToBiopaxInstance           html  
    addhash                                 html  
    addns                                   html  
    biopax                                  html  
    calcGraphOverlap                        html  
    checkValidity                           html  
    colorGraphNodes                         html  
    combineNodes                            html  
    createBiopax                            html  
    diffGraphs                              html  
    downloadBiopaxData                      html  
    generateNewUniqueID                     html  
    getClassProperties                      html  
    getInstanceClass                        html  
    getInstanceProperty                     html  
    getNeighborhood                         html  
    getReferencedIDs                        html  
    getReferencingIDs                       html  
    getSubClasses                           html  
    getSuperClasses                         html  
    getXrefAnnotations                      html  
    hasProperty                             html  
    internal_NrOfXMLNodes                   html  
    internal_XMLInstance2DF                 html  
    internal_checkArguments                 html  
    internal_generateXMLfromBiopax          html  
    internal_getBiopaxModelAsDataFrame      html  
    internal_propertyListToDF               html  
    internal_resolvePhysicalEntityParticipant
                                            html  
    intersectGraphs                         html  
    isOfClass                               html  
    isOfNamespace                           html  
    layoutRegulatoryGraph                   html  
    listComplexComponents                   html  
    listInstances                           html  
    listInteractionComponents               html  
    listPathwayComponents                   html  
    listPathways                            html  
    mergePathways                           html  
    pathway2AdjacancyMatrix                 html  
    pathway2Geneset                         html  
    pathway2RegulatoryGraph                 html  
    plotRegulatoryGraph                     html  
    print.biopax                            html  
    rBiopaxParser-package                   html  
    readBiopax                              html  
    removeInstance                          html  
    removeNodes                             html  
    removeProperties                        html  
    selectInstances                         html  
    splitComplex                            html  
    striphash                               html  
    stripns                                 html  
    transitiveClosure                       html  
    transitiveReduction                     html  
    unfactorize                             html  
    uniteGraphs                             html  
    writeBiopax                             html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (rBiopaxParser)
Making 'packages.html' ... done