Last data update: 2014.03.03
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CNORode
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 <davidpcnet@hotmail.com>
biocViews: CellBasedAssays, CellBiology, Proteomics, Bioinformatics,
TimeCourse
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
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 CNORode.so 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
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