Last data update: 2014.03.03


Package: CNORode
Type: Package
Title: ODE add-on to CellNOptR
Version: 1.14.0
Date: 2014-01-10
Author: David Henriques, Thomas Cokelaer
Maintainer: David Henriques <>
biocViews: CellBasedAssays, CellBiology, Proteomics, Bioinformatics,
Description: ODE add-on to CellNOptR
License: GPL-2
LazyLoad: yes
Depends: CellNOptR (>= 1.5.14), genalg
Enhances: MEIGOR
NeedsCompilation: yes
Packaged: 2016-05-04 04:45:08 UTC; biocbuild

● BiocViews: Bioinformatics, CellBasedAssays, CellBiology, Proteomics, TimeCourse
147 images, 22 functions, 0 datasets
Reverse Depends: 1

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'CNORode' ...
** libs
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I./include  -fpic  -g -O2  -c cvodea.c -o cvodea.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I./include  -fpic  -g -O2  -c cvodea_io.c -o cvodea_io.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I./include  -fpic  -g -O2  -c cvodes.c -o cvodes.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I./include  -fpic  -g -O2  -c cvodes_band.c -o cvodes_band.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I./include  -fpic  -g -O2  -c cvodes_bandpre.c -o cvodes_bandpre.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I./include  -fpic  -g -O2  -c cvodes_bbdpre.c -o cvodes_bbdpre.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I./include  -fpic  -g -O2  -c cvodes_dense.c -o cvodes_dense.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I./include  -fpic  -g -O2  -c cvodes_diag.c -o cvodes_diag.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I./include  -fpic  -g -O2  -c cvodes_direct.c -o cvodes_direct.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I./include  -fpic  -g -O2  -c cvodes_io.c -o cvodes_io.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I./include  -fpic  -g -O2  -c cvodes_spbcgs.c -o cvodes_spbcgs.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I./include  -fpic  -g -O2  -c cvodes_spgmr.c -o cvodes_spgmr.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I./include  -fpic  -g -O2  -c cvodes_spils.c -o cvodes_spils.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I./include  -fpic  -g -O2  -c cvodes_sptfqmr.c -o cvodes_sptfqmr.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I./include  -fpic  -g -O2  -c decimal2binary.c -o decimal2binary.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I./include  -fpic  -g -O2  -c findStates.c -o findStates.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I./include  -fpic  -g -O2  -c fnvector_serial.c -o fnvector_serial.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I./include  -fpic  -g -O2  -c getAdjacencyMatrix.c -o getAdjacencyMatrix.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I./include  -fpic  -g -O2  -c getNumBits.c -o getNumBits.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I./include  -fpic  -g -O2  -c getNumInputs.c -o getNumInputs.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I./include  -fpic  -g -O2  -c getStateIndex.c -o getStateIndex.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I./include  -fpic  -g -O2  -c getTruthTables.c -o getTruthTables.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I./include  -fpic  -g -O2  -c get_count_bits.c -o get_count_bits.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I./include  -fpic  -g -O2  -c get_input_index.c -o get_input_index.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I./include  -fpic  -g -O2  -c get_support_truth_tables.c -o get_support_truth_tables.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I./include  -fpic  -g -O2  -c get_truth_tables_index.c -o get_truth_tables_index.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I./include  -fpic  -g -O2  -c hill_function.c -o hill_function.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I./include  -fpic  -g -O2  -c linear_transfer_function.c -o linear_transfer_function.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I./include  -fpic  -g -O2  -c normHill.c -o normHill.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I./include  -fpic  -g -O2  -c nvector_serial.c -o nvector_serial.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I./include  -fpic  -g -O2  -c printAdjMat.c -o printAdjMat.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I./include  -fpic  -g -O2  -c printInterMat.c -o printInterMat.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I./include  -fpic  -g -O2  -c printNminiTerms.c -o printNminiTerms.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I./include  -fpic  -g -O2  -c printTruthTables.c -o printTruthTables.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I./include  -fpic  -g -O2  -c rhsODE.c -o rhsODE.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I./include  -fpic  -g -O2  -c sim_logic_ode.c -o sim_logic_ode.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I./include  -fpic  -g -O2  -c simulateODE.c -o simulateODE.o
simulateODE.c: In function 'simulateODE':
simulateODE.c:150:11: warning: implicit declaration of function 'CVDense' [-Wimplicit-function-declaration]
    flag = CVDense(cvode_mem, neq);
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I./include  -fpic  -g -O2  -c sundials_band.c -o sundials_band.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I./include  -fpic  -g -O2  -c sundials_dense.c -o sundials_dense.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I./include  -fpic  -g -O2  -c sundials_direct.c -o sundials_direct.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I./include  -fpic  -g -O2  -c sundials_iterative.c -o sundials_iterative.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I./include  -fpic  -g -O2  -c sundials_math.c -o sundials_math.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I./include  -fpic  -g -O2  -c sundials_nvector.c -o sundials_nvector.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I./include  -fpic  -g -O2  -c sundials_spbcgs.c -o sundials_spbcgs.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I./include  -fpic  -g -O2  -c sundials_spgmr.c -o sundials_spgmr.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -I./include  -fpic  -g -O2  -c sundials_sptfqmr.c -o sundials_sptfqmr.o
gcc -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o cvodea.o cvodea_io.o cvodes.o cvodes_band.o cvodes_bandpre.o cvodes_bbdpre.o cvodes_dense.o cvodes_diag.o cvodes_direct.o cvodes_io.o cvodes_spbcgs.o cvodes_spgmr.o cvodes_spils.o cvodes_sptfqmr.o decimal2binary.o findStates.o fnvector_serial.o getAdjacencyMatrix.o getNumBits.o getNumInputs.o getStateIndex.o getTruthTables.o get_count_bits.o get_input_index.o get_support_truth_tables.o get_truth_tables_index.o hill_function.o linear_transfer_function.o normHill.o nvector_serial.o printAdjMat.o printInterMat.o printNminiTerms.o printTruthTables.o rhsODE.o sim_logic_ode.o simulateODE.o sundials_band.o sundials_dense.o sundials_direct.o sundials_iterative.o sundials_math.o sundials_nvector.o sundials_spbcgs.o sundials_spgmr.o sundials_sptfqmr.o -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/CNORode/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'CNORode'
    finding HTML links ... done
    CNORode-package                         html  
    finding level-2 HTML links ... done

    cnolistCNORodeExample                   html  
    createLBodeContPars                     html  
    defaultParametersGA                     html  
    defaultParametersSSm                    html  
    getLBodeContObjFunction                 html  
    getLBodeDataSim                         html  
    getLBodeMINLPObjFunction                html  
    getLBodeModelSim                        html  
    getLBodeSimFunction                     html  
    getStates                               html  
    incidence2Adjacency                     html  
    indices                                 html  
    minlpLBodeSSm                           html  
    model                                   html  
    parEstimationLBode                      html  
    parEstimationLBodeGA                    html  
    parEstimationLBodeSSm                   html  
    plotLBodeFitness                        html  
    plotLBodeModelSim                       html  
    simdata2cnolist                         html  
    simulate                                html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (CNORode)
Making 'packages.html' ... done