CellNOptR

Package: CellNOptR
Type: Package
Title: Training of boolean logic models of signalling networks using
prior knowledge networks and perturbation data.
Version: 1.18.0
Date: 2014-03-13
Author: T.Cokelaer, F.Eduati, A.MacNamara, S.Schrier, C.Terfve
Maintainer: T.Cokelaer <cokelaer@ebi.ac.uk>
Depends: R (>= 2.15.0), RBGL, graph, methods, hash, ggplot2, RCurl,
Rgraphviz, XML
Suggests: RUnit, BiocGenerics, igraph
biocViews: CellBasedAssays, CellBiology, Proteomics, TimeCourse
Description: This package does optimisation of boolean logic networks of signalling pathways based on a previous knowledge network and a set of data upon perturbation of the nodes in the network.
License: GPL-3
LazyLoad: yes
SystemRequirements: Graphviz version >= 2.2
NeedsCompilation: yes
Packaged: 2016-05-04 04:18:04 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'CellNOptR' ...
** libs
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I./include  -fpic  -g -O2  -c getFit.c -o getFit.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I./include  -fpic  -g -O2  -c simulatorT1.c -o simulatorT1.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I./include  -fpic  -g -O2  -c simulatorTN.c -o simulatorTN.o
gcc -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o CellNOptR.so getFit.o simulatorT1.o simulatorTN.o -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/CellNOptR/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'CellNOptR'
    finding HTML links ... done
    CNORbool                                html  
    CNORwrap                                html  
    CNOdata                                 html  
    CNOlist-class                           html  
    CNOlist-methods                         html  
    CNOlistDREAM                            html  
    CNOlistToy                              html  
    CNOlistToy2                             html  
    CNOlistToyMMB                           html  
    CellNOptR-package                       html  
    DreamModel                              html  
    ToyModel                                html  
    ToyModel2                               html  
    buildBitString                          html  
    cSimulator                              html  
    checkSignals                            html  
    compressModel                           html  
    computeScoreT1                          html  
    computeScoreTN                          html  
    cutAndPlot                              html  
    cutAndPlotResultsT1                     html  
    cutAndPlotResultsTN                     html  
    cutCNOlist                              html  
    cutModel                                html  
    cutNONC                                 html  
    cutSimList                              html  
    defaultParameters                       html  
    exhaustive                              html  
    expandGates                             html  
    findNONC                                html  
    gaBinaryT1                              html  
    gaBinaryT2                              html  
    gaBinaryTN                              html  
    getFit                                  html  
    graph2sif                               html  
    indexFinder                             html  
    internals                               html  
    makeCNOlist                             html  
    mapBack                                 html  
    model2igraph                            html  
    model2sif                               html  
    normaliseCNOlist                        html  
    plot-methods                            html  
    plotCNOlist                             html  
    plotCNOlist2                            html  
    plotCNOlistLarge                        html  
    plotCNOlistLargePDF                     html  
    plotCNOlistPDF                          html  
    plotFit                                 html  
    plotModel                               html  
    plotOptimResults                        html  
    plotOptimResultsPDF                     html  
    plotOptimResultsPan                     html  
    prep4sim                                html  
    preprocessing                           html  
    randomizeCNOlist                        html  
    readMIDAS                               html  
    readSBMLQual                            html  
    readSIF                                 html  
    residualError                           html  
    sif2graph                               html  
    simulateT1                              html  
    simulateTN                              html  
    simulatorT0                             html  
    simulatorT1                             html  
    simulatorT2                             html  
    simulatorTN                             html  
    writeDot                                html  
    writeMIDAS                              html  
    writeNetwork                            html  
    writeReport                             html  
    writeSIF                                html  
    writeScaffold                           html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (CellNOptR)
Making 'packages.html' ... done