notebook.community

Edit and run 





In [1]:



    


%matplotlib notebook

from libsignetsim import SbmlDocument, EquilibriumPointCurve
from matplotlib import pyplot as plt



    











In [2]:



    


doc = SbmlDocument()
doc.readSbmlFromFile("sbml_files/tyson2.xml")



    











In [3]:



    


parameter = doc.model.listOfVariables.getBySbmlId('k4prime')



    











In [4]:



    


curve = EquilibriumPointCurve(doc.model)
curve.setParameter(parameter)
curve.setRange(0, 5000)
curve.setDs(0.1)
curve.setMaxSteps(1000)
curve.build()
curve.run()



    


















    






running build
running config_cc
unifing config_cc, config, build_clib, build_ext, build commands --compiler options
running config_fc
unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options
running build_src
build_src
building extension "_auto_model_0_vf" sources
creating auto_temp/src.linux-x86_64-2.7
creating auto_temp/src.linux-x86_64-2.7/auto_temp
swig: /home/labestiol/Env/SigNetSim/libSigNetSim/notebooks/auto_temp/auto_model_0_vf.i
swig -python -I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/numpy/core/include -I/home/labestiol/Env/SigNetSim/libSigNetSim/notebooks -I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/module/include -I/home/labestiol/Env/SigNetSim/libSigNetSim/notebooks/auto_temp -I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/include -o auto_temp/src.linux-x86_64-2.7/auto_temp/auto_model_0_vf_wrap.c -outdir auto_temp/src.linux-x86_64-2.7/auto_temp /home/labestiol/Env/SigNetSim/libSigNetSim/notebooks/auto_temp/auto_model_0_vf.i
build_src: building npy-pkg config files
running build_ext
new_compiler returns distutils.unixccompiler.UnixCCompiler
customize UnixCCompiler
customize UnixCCompiler using build_ext
********************************************************************************
distutils.unixccompiler.UnixCCompiler
linker_exe    = ['x86_64-linux-gnu-gcc', '-pthread']
compiler_so   = ['x86_64-linux-gnu-gcc', '-pthread', '-DNDEBUG', '-g', '-fwrapv', '-O2', '-Wall', '-Wstrict-prototypes', '-fno-strict-aliasing', '-Wdate-time', '-D_FORTIFY_SOURCE=2', '-g', '-fstack-protector-strong', '-Wformat', '-Werror=format-security', '-fPIC']
archiver      = ['x86_64-linux-gnu-gcc-ar', 'rc']
preprocessor  = ['x86_64-linux-gnu-gcc', '-pthread', '-E']
linker_so     = ['x86_64-linux-gnu-gcc', '-pthread', '-shared', '-Wl,-O1', '-Wl,-Bsymbolic-functions', '-Wl,-Bsymbolic-functions', '-Wl,-z,relro', '-fno-strict-aliasing', '-DNDEBUG', '-g', '-fwrapv', '-O2', '-Wall', '-Wstrict-prototypes', '-Wdate-time', '-D_FORTIFY_SOURCE=2', '-g', '-fstack-protector-strong', '-Wformat', '-Werror=format-security', '-Wl,-Bsymbolic-functions', '-Wl,-z,relro', '-Wdate-time', '-D_FORTIFY_SOURCE=2', '-g', '-fstack-protector-strong', '-Wformat', '-Werror=format-security']
compiler_cxx  = ['c++', '-pthread']
ranlib        = None
compiler      = ['x86_64-linux-gnu-gcc', '-pthread', '-DNDEBUG', '-g', '-fwrapv', '-O2', '-Wall', '-Wstrict-prototypes', '-fno-strict-aliasing', '-Wdate-time', '-D_FORTIFY_SOURCE=2', '-g', '-fstack-protector-strong', '-Wformat', '-Werror=format-security']
libraries     = []
library_dirs  = []
include_dirs  = ['/usr/include/python2.7']
********************************************************************************
building '_auto_model_0_vf' extension
compiling C sources
C compiler: x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC

creating auto_temp/auto_temp
creating auto_temp/auto_temp/src.linux-x86_64-2.7
creating auto_temp/auto_temp/src.linux-x86_64-2.7/auto_temp
creating auto_temp/home
creating auto_temp/home/labestiol
creating auto_temp/home/labestiol/Env
creating auto_temp/home/labestiol/Env/SigNetSim
creating auto_temp/home/labestiol/Env/SigNetSim/venv
creating auto_temp/home/labestiol/Env/SigNetSim/venv/local
creating auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib
creating auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7
creating auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages
creating auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool
creating auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont
creating auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto
creating auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src
creating auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/libf2c
creating auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/module
creating auto_temp/home/labestiol/Env/SigNetSim/libSigNetSim
creating auto_temp/home/labestiol/Env/SigNetSim/libSigNetSim/notebooks
creating auto_temp/home/labestiol/Env/SigNetSim/libSigNetSim/notebooks/auto_temp
compile options: '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/numpy/core/include -I/home/labestiol/Env/SigNetSim/libSigNetSim/notebooks -I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/module/include -I/home/labestiol/Env/SigNetSim/libSigNetSim/notebooks/auto_temp -I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/include -I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/numpy/core/include -I/usr/include/python2.7 -c'
extra options: '-w -D__PYTHON__ -std=c99'
x86_64-linux-gnu-gcc: auto_temp/src.linux-x86_64-2.7/auto_temp/auto_model_0_vf_wrap.c
exec_command(['x86_64-linux-gnu-gcc', '-pthread', '-DNDEBUG', '-g', '-fwrapv', '-O2', '-Wall', '-Wstrict-prototypes', '-fno-strict-aliasing', '-Wdate-time', '-D_FORTIFY_SOURCE=2', '-g', '-fstack-protector-strong', '-Wformat', '-Werror=format-security', '-fPIC', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/numpy/core/include', '-I/home/labestiol/Env/SigNetSim/libSigNetSim/notebooks', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/module/include', '-I/home/labestiol/Env/SigNetSim/libSigNetSim/notebooks/auto_temp', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/include', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/numpy/core/include', '-I/usr/include/python2.7', '-c', 'auto_temp/src.linux-x86_64-2.7/auto_temp/auto_model_0_vf_wrap.c', '-o', 'auto_temp/auto_temp/src.linux-x86_64-2.7/auto_temp/auto_model_0_vf_wrap.o', '-MMD', '-MF', 'auto_temp/auto_temp/src.linux-x86_64-2.7/auto_temp/auto_model_0_vf_wrap.o.d', '-w', '-D__PYTHON__', '-std=c99'],)
Retaining cwd: /home/labestiol/Env/SigNetSim/libSigNetSim/notebooks
_preserve_environment([])
_update_environment(...)
_update_environment(...)
x86_64-linux-gnu-gcc: /home/labestiol/Env/SigNetSim/libSigNetSim/notebooks/auto_temp/model_0_vf.c
exec_command(['x86_64-linux-gnu-gcc', '-pthread', '-DNDEBUG', '-g', '-fwrapv', '-O2', '-Wall', '-Wstrict-prototypes', '-fno-strict-aliasing', '-Wdate-time', '-D_FORTIFY_SOURCE=2', '-g', '-fstack-protector-strong', '-Wformat', '-Werror=format-security', '-fPIC', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/numpy/core/include', '-I/home/labestiol/Env/SigNetSim/libSigNetSim/notebooks', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/module/include', '-I/home/labestiol/Env/SigNetSim/libSigNetSim/notebooks/auto_temp', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/include', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/numpy/core/include', '-I/usr/include/python2.7', '-c', '/home/labestiol/Env/SigNetSim/libSigNetSim/notebooks/auto_temp/model_0_vf.c', '-o', 'auto_temp/home/labestiol/Env/SigNetSim/libSigNetSim/notebooks/auto_temp/model_0_vf.o', '-MMD', '-MF', 'auto_temp/home/labestiol/Env/SigNetSim/libSigNetSim/notebooks/auto_temp/model_0_vf.o.d', '-w', '-D__PYTHON__', '-std=c99'],)
Retaining cwd: /home/labestiol/Env/SigNetSim/libSigNetSim/notebooks
_preserve_environment([])
_update_environment(...)
_update_environment(...)
x86_64-linux-gnu-gcc: /home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/module/../src/libf2c/i_nint.c
exec_command(['x86_64-linux-gnu-gcc', '-pthread', '-DNDEBUG', '-g', '-fwrapv', '-O2', '-Wall', '-Wstrict-prototypes', '-fno-strict-aliasing', '-Wdate-time', '-D_FORTIFY_SOURCE=2', '-g', '-fstack-protector-strong', '-Wformat', '-Werror=format-security', '-fPIC', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/numpy/core/include', '-I/home/labestiol/Env/SigNetSim/libSigNetSim/notebooks', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/module/include', '-I/home/labestiol/Env/SigNetSim/libSigNetSim/notebooks/auto_temp', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/include', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/numpy/core/include', '-I/usr/include/python2.7', '-c', '/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/module/../src/libf2c/i_nint.c', '-o', 'auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/libf2c/i_nint.o', '-MMD', '-MF', 'auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/libf2c/i_nint.o.d', '-w', '-D__PYTHON__', '-std=c99'],)
Retaining cwd: /home/labestiol/Env/SigNetSim/libSigNetSim/notebooks
_preserve_environment([])
_update_environment(...)
_update_environment(...)
x86_64-linux-gnu-gcc: /home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/module/../src/libf2c/d_imag.c
exec_command(['x86_64-linux-gnu-gcc', '-pthread', '-DNDEBUG', '-g', '-fwrapv', '-O2', '-Wall', '-Wstrict-prototypes', '-fno-strict-aliasing', '-Wdate-time', '-D_FORTIFY_SOURCE=2', '-g', '-fstack-protector-strong', '-Wformat', '-Werror=format-security', '-fPIC', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/numpy/core/include', '-I/home/labestiol/Env/SigNetSim/libSigNetSim/notebooks', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/module/include', '-I/home/labestiol/Env/SigNetSim/libSigNetSim/notebooks/auto_temp', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/include', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/numpy/core/include', '-I/usr/include/python2.7', '-c', '/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/module/../src/libf2c/d_imag.c', '-o', 'auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/libf2c/d_imag.o', '-MMD', '-MF', 'auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/libf2c/d_imag.o.d', '-w', '-D__PYTHON__', '-std=c99'],)
Retaining cwd: /home/labestiol/Env/SigNetSim/libSigNetSim/notebooks
_preserve_environment([])
_update_environment(...)
_update_environment(...)
x86_64-linux-gnu-gcc: /home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/module/../src/libf2c/r_lg10.c
exec_command(['x86_64-linux-gnu-gcc', '-pthread', '-DNDEBUG', '-g', '-fwrapv', '-O2', '-Wall', '-Wstrict-prototypes', '-fno-strict-aliasing', '-Wdate-time', '-D_FORTIFY_SOURCE=2', '-g', '-fstack-protector-strong', '-Wformat', '-Werror=format-security', '-fPIC', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/numpy/core/include', '-I/home/labestiol/Env/SigNetSim/libSigNetSim/notebooks', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/module/include', '-I/home/labestiol/Env/SigNetSim/libSigNetSim/notebooks/auto_temp', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/include', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/numpy/core/include', '-I/usr/include/python2.7', '-c', '/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/module/../src/libf2c/r_lg10.c', '-o', 'auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/libf2c/r_lg10.o', '-MMD', '-MF', 'auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/libf2c/r_lg10.o.d', '-w', '-D__PYTHON__', '-std=c99'],)
Retaining cwd: /home/labestiol/Env/SigNetSim/libSigNetSim/notebooks
_preserve_environment([])
_update_environment(...)
_update_environment(...)
x86_64-linux-gnu-gcc: /home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/module/../src/reduce.c
exec_command(['x86_64-linux-gnu-gcc', '-pthread', '-DNDEBUG', '-g', '-fwrapv', '-O2', '-Wall', '-Wstrict-prototypes', '-fno-strict-aliasing', '-Wdate-time', '-D_FORTIFY_SOURCE=2', '-g', '-fstack-protector-strong', '-Wformat', '-Werror=format-security', '-fPIC', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/numpy/core/include', '-I/home/labestiol/Env/SigNetSim/libSigNetSim/notebooks', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/module/include', '-I/home/labestiol/Env/SigNetSim/libSigNetSim/notebooks/auto_temp', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/include', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/numpy/core/include', '-I/usr/include/python2.7', '-c', '/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/module/../src/reduce.c', '-o', 'auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/reduce.o', '-MMD', '-MF', 'auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/reduce.o.d', '-w', '-D__PYTHON__', '-std=c99'],)
Retaining cwd: /home/labestiol/Env/SigNetSim/libSigNetSim/notebooks
_preserve_environment([])
_update_environment(...)
_update_environment(...)
x86_64-linux-gnu-gcc: /home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/module/../src/eispack.c
exec_command(['x86_64-linux-gnu-gcc', '-pthread', '-DNDEBUG', '-g', '-fwrapv', '-O2', '-Wall', '-Wstrict-prototypes', '-fno-strict-aliasing', '-Wdate-time', '-D_FORTIFY_SOURCE=2', '-g', '-fstack-protector-strong', '-Wformat', '-Werror=format-security', '-fPIC', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/numpy/core/include', '-I/home/labestiol/Env/SigNetSim/libSigNetSim/notebooks', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/module/include', '-I/home/labestiol/Env/SigNetSim/libSigNetSim/notebooks/auto_temp', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/include', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/numpy/core/include', '-I/usr/include/python2.7', '-c', '/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/module/../src/eispack.c', '-o', 'auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/eispack.o', '-MMD', '-MF', 'auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/eispack.o.d', '-w', '-D__PYTHON__', '-std=c99'],)
Retaining cwd: /home/labestiol/Env/SigNetSim/libSigNetSim/notebooks
_preserve_environment([])
_update_environment(...)
_update_environment(...)
x86_64-linux-gnu-gcc: /home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/module/../src/setubv.c
exec_command(['x86_64-linux-gnu-gcc', '-pthread', '-DNDEBUG', '-g', '-fwrapv', '-O2', '-Wall', '-Wstrict-prototypes', '-fno-strict-aliasing', '-Wdate-time', '-D_FORTIFY_SOURCE=2', '-g', '-fstack-protector-strong', '-Wformat', '-Werror=format-security', '-fPIC', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/numpy/core/include', '-I/home/labestiol/Env/SigNetSim/libSigNetSim/notebooks', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/module/include', '-I/home/labestiol/Env/SigNetSim/libSigNetSim/notebooks/auto_temp', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/include', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/numpy/core/include', '-I/usr/include/python2.7', '-c', '/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/module/../src/setubv.c', '-o', 'auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/setubv.o', '-MMD', '-MF', 'auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/setubv.o.d', '-w', '-D__PYTHON__', '-std=c99'],)
Retaining cwd: /home/labestiol/Env/SigNetSim/libSigNetSim/notebooks
_preserve_environment([])
_update_environment(...)
_update_environment(...)
x86_64-linux-gnu-gcc: /home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/module/../src/auto.c
exec_command(['x86_64-linux-gnu-gcc', '-pthread', '-DNDEBUG', '-g', '-fwrapv', '-O2', '-Wall', '-Wstrict-prototypes', '-fno-strict-aliasing', '-Wdate-time', '-D_FORTIFY_SOURCE=2', '-g', '-fstack-protector-strong', '-Wformat', '-Werror=format-security', '-fPIC', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/numpy/core/include', '-I/home/labestiol/Env/SigNetSim/libSigNetSim/notebooks', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/module/include', '-I/home/labestiol/Env/SigNetSim/libSigNetSim/notebooks/auto_temp', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/include', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/numpy/core/include', '-I/usr/include/python2.7', '-c', '/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/module/../src/auto.c', '-o', 'auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/auto.o', '-MMD', '-MF', 'auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/auto.o.d', '-w', '-D__PYTHON__', '-std=c99'],)
Retaining cwd: /home/labestiol/Env/SigNetSim/libSigNetSim/notebooks
_preserve_environment([])
_update_environment(...)
_update_environment(...)
x86_64-linux-gnu-gcc: /home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/module/../src/libf2c/z_log.c
exec_command(['x86_64-linux-gnu-gcc', '-pthread', '-DNDEBUG', '-g', '-fwrapv', '-O2', '-Wall', '-Wstrict-prototypes', '-fno-strict-aliasing', '-Wdate-time', '-D_FORTIFY_SOURCE=2', '-g', '-fstack-protector-strong', '-Wformat', '-Werror=format-security', '-fPIC', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/numpy/core/include', '-I/home/labestiol/Env/SigNetSim/libSigNetSim/notebooks', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/module/include', '-I/home/labestiol/Env/SigNetSim/libSigNetSim/notebooks/auto_temp', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/include', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/numpy/core/include', '-I/usr/include/python2.7', '-c', '/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/module/../src/libf2c/z_log.c', '-o', 'auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/libf2c/z_log.o', '-MMD', '-MF', 'auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/libf2c/z_log.o.d', '-w', '-D__PYTHON__', '-std=c99'],)
Retaining cwd: /home/labestiol/Env/SigNetSim/libSigNetSim/notebooks
_preserve_environment([])
_update_environment(...)
_update_environment(...)
x86_64-linux-gnu-gcc: /home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/module/../src/autlib1.c
exec_command(['x86_64-linux-gnu-gcc', '-pthread', '-DNDEBUG', '-g', '-fwrapv', '-O2', '-Wall', '-Wstrict-prototypes', '-fno-strict-aliasing', '-Wdate-time', '-D_FORTIFY_SOURCE=2', '-g', '-fstack-protector-strong', '-Wformat', '-Werror=format-security', '-fPIC', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/numpy/core/include', '-I/home/labestiol/Env/SigNetSim/libSigNetSim/notebooks', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/module/include', '-I/home/labestiol/Env/SigNetSim/libSigNetSim/notebooks/auto_temp', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/include', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/numpy/core/include', '-I/usr/include/python2.7', '-c', '/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/module/../src/autlib1.c', '-o', 'auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/autlib1.o', '-MMD', '-MF', 'auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/autlib1.o.d', '-w', '-D__PYTHON__', '-std=c99'],)
Retaining cwd: /home/labestiol/Env/SigNetSim/libSigNetSim/notebooks
_preserve_environment([])
_update_environment(...)
_update_environment(...)
x86_64-linux-gnu-gcc: /home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/module/../src/libf2c/d_sign.c
exec_command(['x86_64-linux-gnu-gcc', '-pthread', '-DNDEBUG', '-g', '-fwrapv', '-O2', '-Wall', '-Wstrict-prototypes', '-fno-strict-aliasing', '-Wdate-time', '-D_FORTIFY_SOURCE=2', '-g', '-fstack-protector-strong', '-Wformat', '-Werror=format-security', '-fPIC', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/numpy/core/include', '-I/home/labestiol/Env/SigNetSim/libSigNetSim/notebooks', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/module/include', '-I/home/labestiol/Env/SigNetSim/libSigNetSim/notebooks/auto_temp', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/include', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/numpy/core/include', '-I/usr/include/python2.7', '-c', '/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/module/../src/libf2c/d_sign.c', '-o', 'auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/libf2c/d_sign.o', '-MMD', '-MF', 'auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/libf2c/d_sign.o.d', '-w', '-D__PYTHON__', '-std=c99'],)
Retaining cwd: /home/labestiol/Env/SigNetSim/libSigNetSim/notebooks
_preserve_environment([])
_update_environment(...)
_update_environment(...)
x86_64-linux-gnu-gcc: /home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/module/automod.c
exec_command(['x86_64-linux-gnu-gcc', '-pthread', '-DNDEBUG', '-g', '-fwrapv', '-O2', '-Wall', '-Wstrict-prototypes', '-fno-strict-aliasing', '-Wdate-time', '-D_FORTIFY_SOURCE=2', '-g', '-fstack-protector-strong', '-Wformat', '-Werror=format-security', '-fPIC', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/numpy/core/include', '-I/home/labestiol/Env/SigNetSim/libSigNetSim/notebooks', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/module/include', '-I/home/labestiol/Env/SigNetSim/libSigNetSim/notebooks/auto_temp', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/include', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/numpy/core/include', '-I/usr/include/python2.7', '-c', '/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/module/automod.c', '-o', 'auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/module/automod.o', '-MMD', '-MF', 'auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/module/automod.o.d', '-w', '-D__PYTHON__', '-std=c99'],)
Retaining cwd: /home/labestiol/Env/SigNetSim/libSigNetSim/notebooks
_preserve_environment([])
_update_environment(...)
_update_environment(...)
x86_64-linux-gnu-gcc: /home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/module/interface.c
exec_command(['x86_64-linux-gnu-gcc', '-pthread', '-DNDEBUG', '-g', '-fwrapv', '-O2', '-Wall', '-Wstrict-prototypes', '-fno-strict-aliasing', '-Wdate-time', '-D_FORTIFY_SOURCE=2', '-g', '-fstack-protector-strong', '-Wformat', '-Werror=format-security', '-fPIC', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/numpy/core/include', '-I/home/labestiol/Env/SigNetSim/libSigNetSim/notebooks', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/module/include', '-I/home/labestiol/Env/SigNetSim/libSigNetSim/notebooks/auto_temp', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/include', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/numpy/core/include', '-I/usr/include/python2.7', '-c', '/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/module/interface.c', '-o', 'auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/module/interface.o', '-MMD', '-MF', 'auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/module/interface.o.d', '-w', '-D__PYTHON__', '-std=c99'],)
Retaining cwd: /home/labestiol/Env/SigNetSim/libSigNetSim/notebooks
_preserve_environment([])
_update_environment(...)
_update_environment(...)
x86_64-linux-gnu-gcc: /home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/module/../src/dmatrix.c
exec_command(['x86_64-linux-gnu-gcc', '-pthread', '-DNDEBUG', '-g', '-fwrapv', '-O2', '-Wall', '-Wstrict-prototypes', '-fno-strict-aliasing', '-Wdate-time', '-D_FORTIFY_SOURCE=2', '-g', '-fstack-protector-strong', '-Wformat', '-Werror=format-security', '-fPIC', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/numpy/core/include', '-I/home/labestiol/Env/SigNetSim/libSigNetSim/notebooks', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/module/include', '-I/home/labestiol/Env/SigNetSim/libSigNetSim/notebooks/auto_temp', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/include', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/numpy/core/include', '-I/usr/include/python2.7', '-c', '/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/module/../src/dmatrix.c', '-o', 'auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/dmatrix.o', '-MMD', '-MF', 'auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/dmatrix.o.d', '-w', '-D__PYTHON__', '-std=c99'],)
Retaining cwd: /home/labestiol/Env/SigNetSim/libSigNetSim/notebooks
_preserve_environment([])
_update_environment(...)
_update_environment(...)
x86_64-linux-gnu-gcc: /home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/module/../src/libf2c/pow_dd.c
exec_command(['x86_64-linux-gnu-gcc', '-pthread', '-DNDEBUG', '-g', '-fwrapv', '-O2', '-Wall', '-Wstrict-prototypes', '-fno-strict-aliasing', '-Wdate-time', '-D_FORTIFY_SOURCE=2', '-g', '-fstack-protector-strong', '-Wformat', '-Werror=format-security', '-fPIC', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/numpy/core/include', '-I/home/labestiol/Env/SigNetSim/libSigNetSim/notebooks', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/module/include', '-I/home/labestiol/Env/SigNetSim/libSigNetSim/notebooks/auto_temp', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/include', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/numpy/core/include', '-I/usr/include/python2.7', '-c', '/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/module/../src/libf2c/pow_dd.c', '-o', 'auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/libf2c/pow_dd.o', '-MMD', '-MF', 'auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/libf2c/pow_dd.o.d', '-w', '-D__PYTHON__', '-std=c99'],)
Retaining cwd: /home/labestiol/Env/SigNetSim/libSigNetSim/notebooks
_preserve_environment([])
_update_environment(...)
_update_environment(...)
x86_64-linux-gnu-gcc: /home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/module/../src/libf2c/d_lg10.c
exec_command(['x86_64-linux-gnu-gcc', '-pthread', '-DNDEBUG', '-g', '-fwrapv', '-O2', '-Wall', '-Wstrict-prototypes', '-fno-strict-aliasing', '-Wdate-time', '-D_FORTIFY_SOURCE=2', '-g', '-fstack-protector-strong', '-Wformat', '-Werror=format-security', '-fPIC', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/numpy/core/include', '-I/home/labestiol/Env/SigNetSim/libSigNetSim/notebooks', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/module/include', '-I/home/labestiol/Env/SigNetSim/libSigNetSim/notebooks/auto_temp', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/include', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/numpy/core/include', '-I/usr/include/python2.7', '-c', '/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/module/../src/libf2c/d_lg10.c', '-o', 'auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/libf2c/d_lg10.o', '-MMD', '-MF', 'auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/libf2c/d_lg10.o.d', '-w', '-D__PYTHON__', '-std=c99'],)
Retaining cwd: /home/labestiol/Env/SigNetSim/libSigNetSim/notebooks
_preserve_environment([])
_update_environment(...)
_update_environment(...)
x86_64-linux-gnu-gcc: /home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/module/../src/libf2c/z_exp.c
exec_command(['x86_64-linux-gnu-gcc', '-pthread', '-DNDEBUG', '-g', '-fwrapv', '-O2', '-Wall', '-Wstrict-prototypes', '-fno-strict-aliasing', '-Wdate-time', '-D_FORTIFY_SOURCE=2', '-g', '-fstack-protector-strong', '-Wformat', '-Werror=format-security', '-fPIC', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/numpy/core/include', '-I/home/labestiol/Env/SigNetSim/libSigNetSim/notebooks', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/module/include', '-I/home/labestiol/Env/SigNetSim/libSigNetSim/notebooks/auto_temp', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/include', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/numpy/core/include', '-I/usr/include/python2.7', '-c', '/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/module/../src/libf2c/z_exp.c', '-o', 'auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/libf2c/z_exp.o', '-MMD', '-MF', 'auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/libf2c/z_exp.o.d', '-w', '-D__PYTHON__', '-std=c99'],)
Retaining cwd: /home/labestiol/Env/SigNetSim/libSigNetSim/notebooks
_preserve_environment([])
_update_environment(...)
_update_environment(...)
x86_64-linux-gnu-gcc: /home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/module/../src/libf2c/pow_ii.c
exec_command(['x86_64-linux-gnu-gcc', '-pthread', '-DNDEBUG', '-g', '-fwrapv', '-O2', '-Wall', '-Wstrict-prototypes', '-fno-strict-aliasing', '-Wdate-time', '-D_FORTIFY_SOURCE=2', '-g', '-fstack-protector-strong', '-Wformat', '-Werror=format-security', '-fPIC', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/numpy/core/include', '-I/home/labestiol/Env/SigNetSim/libSigNetSim/notebooks', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/module/include', '-I/home/labestiol/Env/SigNetSim/libSigNetSim/notebooks/auto_temp', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/include', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/numpy/core/include', '-I/usr/include/python2.7', '-c', '/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/module/../src/libf2c/pow_ii.c', '-o', 'auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/libf2c/pow_ii.o', '-MMD', '-MF', 'auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/libf2c/pow_ii.o.d', '-w', '-D__PYTHON__', '-std=c99'],)
Retaining cwd: /home/labestiol/Env/SigNetSim/libSigNetSim/notebooks
_preserve_environment([])
_update_environment(...)
_update_environment(...)
x86_64-linux-gnu-gcc: /home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/module/../src/libf2c/z_abs.c
exec_command(['x86_64-linux-gnu-gcc', '-pthread', '-DNDEBUG', '-g', '-fwrapv', '-O2', '-Wall', '-Wstrict-prototypes', '-fno-strict-aliasing', '-Wdate-time', '-D_FORTIFY_SOURCE=2', '-g', '-fstack-protector-strong', '-Wformat', '-Werror=format-security', '-fPIC', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/numpy/core/include', '-I/home/labestiol/Env/SigNetSim/libSigNetSim/notebooks', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/module/include', '-I/home/labestiol/Env/SigNetSim/libSigNetSim/notebooks/auto_temp', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/include', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/numpy/core/include', '-I/usr/include/python2.7', '-c', '/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/module/../src/libf2c/z_abs.c', '-o', 'auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/libf2c/z_abs.o', '-MMD', '-MF', 'auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/libf2c/z_abs.o.d', '-w', '-D__PYTHON__', '-std=c99'],)
Retaining cwd: /home/labestiol/Env/SigNetSim/libSigNetSim/notebooks
_preserve_environment([])
_update_environment(...)
_update_environment(...)
x86_64-linux-gnu-gcc: /home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/module/../src/autlib2.c
exec_command(['x86_64-linux-gnu-gcc', '-pthread', '-DNDEBUG', '-g', '-fwrapv', '-O2', '-Wall', '-Wstrict-prototypes', '-fno-strict-aliasing', '-Wdate-time', '-D_FORTIFY_SOURCE=2', '-g', '-fstack-protector-strong', '-Wformat', '-Werror=format-security', '-fPIC', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/numpy/core/include', '-I/home/labestiol/Env/SigNetSim/libSigNetSim/notebooks', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/module/include', '-I/home/labestiol/Env/SigNetSim/libSigNetSim/notebooks/auto_temp', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/include', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/numpy/core/include', '-I/usr/include/python2.7', '-c', '/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/module/../src/autlib2.c', '-o', 'auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/autlib2.o', '-MMD', '-MF', 'auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/autlib2.o.d', '-w', '-D__PYTHON__', '-std=c99'],)
Retaining cwd: /home/labestiol/Env/SigNetSim/libSigNetSim/notebooks
_preserve_environment([])
_update_environment(...)
_update_environment(...)
x86_64-linux-gnu-gcc: /home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/module/../src/autlib5.c
exec_command(['x86_64-linux-gnu-gcc', '-pthread', '-DNDEBUG', '-g', '-fwrapv', '-O2', '-Wall', '-Wstrict-prototypes', '-fno-strict-aliasing', '-Wdate-time', '-D_FORTIFY_SOURCE=2', '-g', '-fstack-protector-strong', '-Wformat', '-Werror=format-security', '-fPIC', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/numpy/core/include', '-I/home/labestiol/Env/SigNetSim/libSigNetSim/notebooks', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/module/include', '-I/home/labestiol/Env/SigNetSim/libSigNetSim/notebooks/auto_temp', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/include', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/numpy/core/include', '-I/usr/include/python2.7', '-c', '/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/module/../src/autlib5.c', '-o', 'auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/autlib5.o', '-MMD', '-MF', 'auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/autlib5.o.d', '-w', '-D__PYTHON__', '-std=c99'],)
Retaining cwd: /home/labestiol/Env/SigNetSim/libSigNetSim/notebooks
_preserve_environment([])
_update_environment(...)
_update_environment(...)
x86_64-linux-gnu-gcc: /home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/module/../src/autlib3.c
exec_command(['x86_64-linux-gnu-gcc', '-pthread', '-DNDEBUG', '-g', '-fwrapv', '-O2', '-Wall', '-Wstrict-prototypes', '-fno-strict-aliasing', '-Wdate-time', '-D_FORTIFY_SOURCE=2', '-g', '-fstack-protector-strong', '-Wformat', '-Werror=format-security', '-fPIC', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/numpy/core/include', '-I/home/labestiol/Env/SigNetSim/libSigNetSim/notebooks', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/module/include', '-I/home/labestiol/Env/SigNetSim/libSigNetSim/notebooks/auto_temp', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/include', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/numpy/core/include', '-I/usr/include/python2.7', '-c', '/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/module/../src/autlib3.c', '-o', 'auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/autlib3.o', '-MMD', '-MF', 'auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/autlib3.o.d', '-w', '-D__PYTHON__', '-std=c99'],)
Retaining cwd: /home/labestiol/Env/SigNetSim/libSigNetSim/notebooks
_preserve_environment([])
_update_environment(...)
_update_environment(...)
x86_64-linux-gnu-gcc: /home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/module/../src/libf2c/pow_di.c
exec_command(['x86_64-linux-gnu-gcc', '-pthread', '-DNDEBUG', '-g', '-fwrapv', '-O2', '-Wall', '-Wstrict-prototypes', '-fno-strict-aliasing', '-Wdate-time', '-D_FORTIFY_SOURCE=2', '-g', '-fstack-protector-strong', '-Wformat', '-Werror=format-security', '-fPIC', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/numpy/core/include', '-I/home/labestiol/Env/SigNetSim/libSigNetSim/notebooks', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/module/include', '-I/home/labestiol/Env/SigNetSim/libSigNetSim/notebooks/auto_temp', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/include', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/numpy/core/include', '-I/usr/include/python2.7', '-c', '/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/module/../src/libf2c/pow_di.c', '-o', 'auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/libf2c/pow_di.o', '-MMD', '-MF', 'auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/libf2c/pow_di.o.d', '-w', '-D__PYTHON__', '-std=c99'],)
Retaining cwd: /home/labestiol/Env/SigNetSim/libSigNetSim/notebooks
_preserve_environment([])
_update_environment(...)
_update_environment(...)
x86_64-linux-gnu-gcc: /home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/module/../src/libf2c/i_dnnt.c
exec_command(['x86_64-linux-gnu-gcc', '-pthread', '-DNDEBUG', '-g', '-fwrapv', '-O2', '-Wall', '-Wstrict-prototypes', '-fno-strict-aliasing', '-Wdate-time', '-D_FORTIFY_SOURCE=2', '-g', '-fstack-protector-strong', '-Wformat', '-Werror=format-security', '-fPIC', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/numpy/core/include', '-I/home/labestiol/Env/SigNetSim/libSigNetSim/notebooks', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/module/include', '-I/home/labestiol/Env/SigNetSim/libSigNetSim/notebooks/auto_temp', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/include', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/numpy/core/include', '-I/usr/include/python2.7', '-c', '/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/module/../src/libf2c/i_dnnt.c', '-o', 'auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/libf2c/i_dnnt.o', '-MMD', '-MF', 'auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/libf2c/i_dnnt.o.d', '-w', '-D__PYTHON__', '-std=c99'],)
Retaining cwd: /home/labestiol/Env/SigNetSim/libSigNetSim/notebooks
_preserve_environment([])
_update_environment(...)
_update_environment(...)
x86_64-linux-gnu-gcc: /home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/module/../src/libf2c/cabs.c
exec_command(['x86_64-linux-gnu-gcc', '-pthread', '-DNDEBUG', '-g', '-fwrapv', '-O2', '-Wall', '-Wstrict-prototypes', '-fno-strict-aliasing', '-Wdate-time', '-D_FORTIFY_SOURCE=2', '-g', '-fstack-protector-strong', '-Wformat', '-Werror=format-security', '-fPIC', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/numpy/core/include', '-I/home/labestiol/Env/SigNetSim/libSigNetSim/notebooks', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/module/include', '-I/home/labestiol/Env/SigNetSim/libSigNetSim/notebooks/auto_temp', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/include', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/numpy/core/include', '-I/usr/include/python2.7', '-c', '/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/module/../src/libf2c/cabs.c', '-o', 'auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/libf2c/cabs.o', '-MMD', '-MF', 'auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/libf2c/cabs.o.d', '-w', '-D__PYTHON__', '-std=c99'],)
Retaining cwd: /home/labestiol/Env/SigNetSim/libSigNetSim/notebooks
_preserve_environment([])
_update_environment(...)
_update_environment(...)
x86_64-linux-gnu-gcc: /home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/module/../src/fcon.c
exec_command(['x86_64-linux-gnu-gcc', '-pthread', '-DNDEBUG', '-g', '-fwrapv', '-O2', '-Wall', '-Wstrict-prototypes', '-fno-strict-aliasing', '-Wdate-time', '-D_FORTIFY_SOURCE=2', '-g', '-fstack-protector-strong', '-Wformat', '-Werror=format-security', '-fPIC', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/numpy/core/include', '-I/home/labestiol/Env/SigNetSim/libSigNetSim/notebooks', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/module/include', '-I/home/labestiol/Env/SigNetSim/libSigNetSim/notebooks/auto_temp', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/include', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/numpy/core/include', '-I/usr/include/python2.7', '-c', '/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/module/../src/fcon.c', '-o', 'auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/fcon.o', '-MMD', '-MF', 'auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/fcon.o.d', '-w', '-D__PYTHON__', '-std=c99'],)
Retaining cwd: /home/labestiol/Env/SigNetSim/libSigNetSim/notebooks
_preserve_environment([])
_update_environment(...)
_update_environment(...)
x86_64-linux-gnu-gcc: /home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/module/../src/autlib4.c
exec_command(['x86_64-linux-gnu-gcc', '-pthread', '-DNDEBUG', '-g', '-fwrapv', '-O2', '-Wall', '-Wstrict-prototypes', '-fno-strict-aliasing', '-Wdate-time', '-D_FORTIFY_SOURCE=2', '-g', '-fstack-protector-strong', '-Wformat', '-Werror=format-security', '-fPIC', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/numpy/core/include', '-I/home/labestiol/Env/SigNetSim/libSigNetSim/notebooks', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/module/include', '-I/home/labestiol/Env/SigNetSim/libSigNetSim/notebooks/auto_temp', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/include', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/numpy/core/include', '-I/usr/include/python2.7', '-c', '/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/module/../src/autlib4.c', '-o', 'auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/autlib4.o', '-MMD', '-MF', 'auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/autlib4.o.d', '-w', '-D__PYTHON__', '-std=c99'],)
Retaining cwd: /home/labestiol/Env/SigNetSim/libSigNetSim/notebooks
_preserve_environment([])
_update_environment(...)
_update_environment(...)
x86_64-linux-gnu-gcc: /home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/module/../src/conpar.c
exec_command(['x86_64-linux-gnu-gcc', '-pthread', '-DNDEBUG', '-g', '-fwrapv', '-O2', '-Wall', '-Wstrict-prototypes', '-fno-strict-aliasing', '-Wdate-time', '-D_FORTIFY_SOURCE=2', '-g', '-fstack-protector-strong', '-Wformat', '-Werror=format-security', '-fPIC', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/numpy/core/include', '-I/home/labestiol/Env/SigNetSim/libSigNetSim/notebooks', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/module/include', '-I/home/labestiol/Env/SigNetSim/libSigNetSim/notebooks/auto_temp', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/include', '-I/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/numpy/core/include', '-I/usr/include/python2.7', '-c', '/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/module/../src/conpar.c', '-o', 'auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/conpar.o', '-MMD', '-MF', 'auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/conpar.o.d', '-w', '-D__PYTHON__', '-std=c99'],)
Retaining cwd: /home/labestiol/Env/SigNetSim/libSigNetSim/notebooks
_preserve_environment([])
_update_environment(...)
_update_environment(...)
x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security auto_temp/auto_temp/src.linux-x86_64-2.7/auto_temp/auto_model_0_vf_wrap.o auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/auto.o auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/autlib1.o auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/autlib2.o auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/autlib3.o auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/autlib4.o auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/autlib5.o auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/eispack.o auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/conpar.o auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/setubv.o auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/reduce.o auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/dmatrix.o auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/fcon.o auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/libf2c/cabs.o auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/libf2c/d_lg10.o auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/libf2c/i_nint.o auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/libf2c/pow_di.o auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/libf2c/r_lg10.o auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/libf2c/z_exp.o auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/libf2c/d_imag.o auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/libf2c/d_sign.o auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/libf2c/i_dnnt.o auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/libf2c/pow_dd.o auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/libf2c/pow_ii.o auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/libf2c/z_abs.o auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/libf2c/z_log.o auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/module/automod.o auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/module/interface.o auto_temp/home/labestiol/Env/SigNetSim/libSigNetSim/notebooks/auto_temp/model_0_vf.o -L./ -o ./_auto_model_0_vf.so -w
exec_command(['x86_64-linux-gnu-gcc', '-pthread', '-shared', '-Wl,-O1', '-Wl,-Bsymbolic-functions', '-Wl,-Bsymbolic-functions', '-Wl,-z,relro', '-fno-strict-aliasing', '-DNDEBUG', '-g', '-fwrapv', '-O2', '-Wall', '-Wstrict-prototypes', '-Wdate-time', '-D_FORTIFY_SOURCE=2', '-g', '-fstack-protector-strong', '-Wformat', '-Werror=format-security', '-Wl,-Bsymbolic-functions', '-Wl,-z,relro', '-Wdate-time', '-D_FORTIFY_SOURCE=2', '-g', '-fstack-protector-strong', '-Wformat', '-Werror=format-security', 'auto_temp/auto_temp/src.linux-x86_64-2.7/auto_temp/auto_model_0_vf_wrap.o', 'auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/auto.o', 'auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/autlib1.o', 'auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/autlib2.o', 'auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/autlib3.o', 'auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/autlib4.o', 'auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/autlib5.o', 'auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/eispack.o', 'auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/conpar.o', 'auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/setubv.o', 'auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/reduce.o', 'auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/dmatrix.o', 'auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/fcon.o', 'auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/libf2c/cabs.o', 'auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/libf2c/d_lg10.o', 'auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/libf2c/i_nint.o', 'auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/libf2c/pow_di.o', 'auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/libf2c/r_lg10.o', 'auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/libf2c/z_exp.o', 'auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/libf2c/d_imag.o', 'auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/libf2c/d_sign.o', 'auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/libf2c/i_dnnt.o', 'auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/libf2c/pow_dd.o', 'auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/libf2c/pow_ii.o', 'auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/libf2c/z_abs.o', 'auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/src/libf2c/z_log.o', 'auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/module/automod.o', 'auto_temp/home/labestiol/Env/SigNetSim/venv/local/lib/python2.7/site-packages/PyDSTool/PyCont/auto/module/interface.o', 'auto_temp/home/labestiol/Env/SigNetSim/libSigNetSim/notebooks/auto_temp/model_0_vf.o', '-L./', '-o', './_auto_model_0_vf.so', '-w'],)
Retaining cwd: /home/labestiol/Env/SigNetSim/libSigNetSim/notebooks
_preserve_environment([])
_update_environment(...)
_update_environment(...)
Warning: setSize is either not a valid parameter or immutable.

















In [5]:



    


variable_1 = doc.model.listOfVariables.getBySbmlId('cyclin_cdk_p')
variable_2 = doc.model.listOfVariables.getBySbmlId('cyclin_cdk')



    











In [6]:



    


figure = plt.figure(figsize=(12, 6))
plot = figure.add_subplot(211)
plot.set_title(variable_1.getName())
curve.plotCurve(plot, variable_1)
if curve.hasHopfBifurcations():
    curve.plotLimitCycles(plot, variable_1)

plot = figure.add_subplot(212)
plot.set_title(variable_2.getName())
curve.plotCurve(plot, variable_2)
if curve.hasHopfBifurcations():
    curve.plotLimitCycles(plot, variable_2)



    


















    




















    























In [ ]:

Content source: vincent-noel/libSigNetSim

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