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sys-bio / tellurium

Python Environment for Modeling and Simulating Biological Systems
http://tellurium.analogmachine.org/
Apache License 2.0
107 stars 36 forks source link

import error; macOS 10.14; Anaconda #442

Open rheiland opened 4 years ago

rheiland commented 4 years ago

First, Happy New Year!

I had tellurium installed and wanted to upgrade to 2.2. Following your FAQ, I:

 conda install python=3.6.9
then:
 pip uninstall tellurium
 pip uninstall libroadrunner
 pip install --no-cache-dir option tellurium

When I attempt to import it, I get:

$ ipython
Python 3.6.9 |Anaconda, Inc.| (default, Jul 30 2019, 13:42:17) 
Type 'copyright', 'credits' or 'license' for more information
IPython 7.11.1 -- An enhanced Interactive Python. Type '?' for help.

In [1]: import tellurium as te                                                                                                                  
---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
<ipython-input-1-a1d15ad2750a> in <module>
----> 1 import tellurium as te

~/anaconda3/lib/python3.6/site-packages/tellurium/__init__.py in <module>
    109 
    110 # Bifurcations
--> 111 from .analysis.bifurcation import (
    112     plotBifurcation,
    113 )

~/anaconda3/lib/python3.6/site-packages/tellurium/analysis/bifurcation.py in <module>
      5 
      6 import os.path
----> 7 from rrplugins import Plugin
      8 from roadrunner import RoadRunner
      9 

~/anaconda3/lib/python3.6/site-packages/rrplugins/__init__.py in <module>
----> 1 from rrplugins.telplugins import *
      2 from rrplugins.telplugins_c_api import *
      3 
      4 __version__ = '1.2.2'

~/anaconda3/lib/python3.6/site-packages/rrplugins/telplugins.py in <module>
      4 # An example is given at the end of the code.
      5 
----> 6 import rrplugins.telplugins_c_api as tpc
      7 import matplotlib.pyplot as plt
      8 import numpy as np

~/anaconda3/lib/python3.6/site-packages/rrplugins/telplugins_c_api.py in <module>
   1633         return None
   1634 
-> 1635 rrpLib.tpSetLogLevel.restype = c_bool
   1636 rrpLib.tpSetLogLevel.argtypes = [c_char_p]
   1637 def setLogLevel(lvl):

~/anaconda3/lib/python3.6/ctypes/__init__.py in __getattr__(self, name)
    359         if name.startswith('__') and name.endswith('__'):
    360             raise AttributeError(name)
--> 361         func = self.__getitem__(name)
    362         setattr(self, name, func)
    363         return func

~/anaconda3/lib/python3.6/ctypes/__init__.py in __getitem__(self, name_or_ordinal)
    364 
    365     def __getitem__(self, name_or_ordinal):
--> 366         func = self._FuncPtr((name_or_ordinal, self))
    367         if not isinstance(name_or_ordinal, int):
    368             func.__name__ = name_or_ordinal

AttributeError: dlsym(0x7f8554e91b20, tpSetLogLevel): symbol not found
hsauro commented 4 years ago

I'm not sure what that is doing, we've not had any problems installing tellurium on mac os with python 3.6.

What does --no-cache-dir option do? Normally we just use pip install tellurium

Herbert

On Sat, Jan 4, 2020 at 8:06 AM Randy Heiland notifications@github.com wrote:

First, Happy New Year!

I had tellurium installed and wanted to upgrade to 2.2. Following your FAQ, I:

conda install python=3.6.9 then: pip uninstall tellurium pip uninstall libroadrunner pip install --no-cache-dir option tellurium

When I attempt to import it, I get:

$ ipython Python 3.6.9 |Anaconda, Inc.| (default, Jul 30 2019, 13:42:17) Type 'copyright', 'credits' or 'license' for more information IPython 7.11.1 -- An enhanced Interactive Python. Type '?' for help.

In [1]: import tellurium as te

AttributeError Traceback (most recent call last)

in ----> 1 import tellurium as te ~/anaconda3/lib/python3.6/site-packages/tellurium/__init__.py in 109 110 # Bifurcations --> 111 from .analysis.bifurcation import ( 112 plotBifurcation, 113 ) ~/anaconda3/lib/python3.6/site-packages/tellurium/analysis/bifurcation.py in 5 6 import os.path ----> 7 from rrplugins import Plugin 8 from roadrunner import RoadRunner 9 ~/anaconda3/lib/python3.6/site-packages/rrplugins/__init__.py in ----> 1 from rrplugins.telplugins import * 2 from rrplugins.telplugins_c_api import * 3 4 __version__ = '1.2.2' ~/anaconda3/lib/python3.6/site-packages/rrplugins/telplugins.py in 4 # An example is given at the end of the code. 5 ----> 6 import rrplugins.telplugins_c_api as tpc 7 import matplotlib.pyplot as plt 8 import numpy as np ~/anaconda3/lib/python3.6/site-packages/rrplugins/telplugins_c_api.py in 1633 return None 1634 -> 1635 rrpLib.tpSetLogLevel.restype = c_bool 1636 rrpLib.tpSetLogLevel.argtypes = [c_char_p] 1637 def setLogLevel(lvl): ~/anaconda3/lib/python3.6/ctypes/__init__.py in __getattr__(self, name) 359 if name.startswith('__') and name.endswith('__'): 360 raise AttributeError(name) --> 361 func = self.__getitem__(name) 362 setattr(self, name, func) 363 return func ~/anaconda3/lib/python3.6/ctypes/__init__.py in __getitem__(self, name_or_ordinal) 364 365 def __getitem__(self, name_or_ordinal): --> 366 func = self._FuncPtr((name_or_ordinal, self)) 367 if not isinstance(name_or_ordinal, int): 368 func.__name__ = name_or_ordinal AttributeError: dlsym(0x7f8554e91b20, tpSetLogLevel): symbol not found — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub , or unsubscribe .

-- Herbert Sauro, Professor University of Washington, Bioengineering 206-685-2119, www.sys-bio.org hsauro@uw.edu Books: http://books.analogmachine.org/

rheiland commented 4 years ago

Yes, I'd first tried just pip install tellurium but it attempted to reinstalled my previous/cached version, so I tracked down this option to prevent that. I just now attempted a re-install, but get the same:

~$ pip install tellurium
Requirement already satisfied: tellurium in ./anaconda3/lib/python3.6/site-packages (2.1.5)
Requirement already satisfied: tecombine>=0.2.2 in ./anaconda3/lib/python3.6/site-packages (from tellurium) (0.2.2.1)
Requirement already satisfied: jupyter-core>=4.3.0 in ./anaconda3/lib/python3.6/site-packages (from tellurium) (4.6.1)
Requirement already satisfied: tesedml>=0.4.3 in ./anaconda3/lib/python3.6/site-packages (from tellurium) (0.4.3)
Requirement already satisfied: tenuml>=1.1.1 in ./anaconda3/lib/python3.6/site-packages (from tellurium) (1.1.1)
Requirement already satisfied: phrasedml>=1.0.9 in ./anaconda3/lib/python3.6/site-packages (from tellurium) (1.0.9)
Requirement already satisfied: antimony>=2.9.3 in ./anaconda3/lib/python3.6/site-packages (from tellurium) (2.11.0)
Requirement already satisfied: pandas>=0.20.2 in ./anaconda3/lib/python3.6/site-packages (from tellurium) (0.25.3)
Requirement already satisfied: tesbml>=5.15.0.1 in ./anaconda3/lib/python3.6/site-packages (from tellurium) (5.15.0.1)
Requirement already satisfied: appdirs>=1.4.3 in ./anaconda3/lib/python3.6/site-packages (from tellurium) (1.4.3)
Requirement already satisfied: matplotlib>=2.0.2 in ./anaconda3/lib/python3.6/site-packages (from tellurium) (3.1.2)
Requirement already satisfied: rrplugins>=1.1.8 in ./anaconda3/lib/python3.6/site-packages (from tellurium) (1.2.2)
Requirement already satisfied: requests in ./anaconda3/lib/python3.6/site-packages (from tellurium) (2.22.0)
Requirement already satisfied: jupyter-client>=5.1.0 in ./anaconda3/lib/python3.6/site-packages (from tellurium) (5.3.4)
Requirement already satisfied: pytest in ./anaconda3/lib/python3.6/site-packages (from tellurium) (5.3.2)
Requirement already satisfied: numpy>=1.11.0 in ./anaconda3/lib/python3.6/site-packages (from tellurium) (1.18.0)
Requirement already satisfied: plotly>=2.0.12 in ./anaconda3/lib/python3.6/site-packages (from tellurium) (4.4.1)
Requirement already satisfied: ipython in ./anaconda3/lib/python3.6/site-packages (from tellurium) (7.11.1)
Requirement already satisfied: jinja2>=2.9.6 in ./anaconda3/lib/python3.6/site-packages (from tellurium) (2.10.3)
Requirement already satisfied: ipykernel>=4.6.1 in ./anaconda3/lib/python3.6/site-packages (from tellurium) (5.1.3)
Requirement already satisfied: libroadrunner>=1.4.24 in ./anaconda3/lib/python3.6/site-packages (from tellurium) (1.5.4)
Requirement already satisfied: scipy>=0.19.0 in ./anaconda3/lib/python3.6/site-packages (from tellurium) (1.4.1)
Requirement already satisfied: sbml2matlab>=0.9.1 in ./anaconda3/lib/python3.6/site-packages (from tellurium) (0.9.1)
Requirement already satisfied: traitlets in ./anaconda3/lib/python3.6/site-packages (from jupyter-core>=4.3.0->tellurium) (4.3.3)
Requirement already satisfied: pytz>=2017.2 in ./anaconda3/lib/python3.6/site-packages (from pandas>=0.20.2->tellurium) (2019.3)
Requirement already satisfied: python-dateutil>=2.6.1 in ./anaconda3/lib/python3.6/site-packages (from pandas>=0.20.2->tellurium) (2.8.1)
Requirement already satisfied: kiwisolver>=1.0.1 in ./anaconda3/lib/python3.6/site-packages (from matplotlib>=2.0.2->tellurium) (1.1.0)
Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in ./anaconda3/lib/python3.6/site-packages (from matplotlib>=2.0.2->tellurium) (2.4.6)
Requirement already satisfied: cycler>=0.10 in ./anaconda3/lib/python3.6/site-packages (from matplotlib>=2.0.2->tellurium) (0.10.0)
Requirement already satisfied: certifi>=2017.4.17 in ./anaconda3/lib/python3.6/site-packages (from requests->tellurium) (2019.11.28)
Requirement already satisfied: idna<2.9,>=2.5 in ./anaconda3/lib/python3.6/site-packages (from requests->tellurium) (2.8)
Requirement already satisfied: chardet<3.1.0,>=3.0.2 in ./anaconda3/lib/python3.6/site-packages (from requests->tellurium) (3.0.4)
Requirement already satisfied: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in ./anaconda3/lib/python3.6/site-packages (from requests->tellurium) (1.25.7)
Requirement already satisfied: pyzmq>=13 in ./anaconda3/lib/python3.6/site-packages (from jupyter-client>=5.1.0->tellurium) (18.1.1)
Requirement already satisfied: tornado>=4.1 in ./anaconda3/lib/python3.6/site-packages (from jupyter-client>=5.1.0->tellurium) (6.0.3)
Requirement already satisfied: packaging in ./anaconda3/lib/python3.6/site-packages (from pytest->tellurium) (19.2)
Requirement already satisfied: attrs>=17.4.0 in ./anaconda3/lib/python3.6/site-packages (from pytest->tellurium) (19.3.0)
Requirement already satisfied: py>=1.5.0 in ./anaconda3/lib/python3.6/site-packages (from pytest->tellurium) (1.8.1)
Requirement already satisfied: importlib-metadata>=0.12; python_version < "3.8" in ./anaconda3/lib/python3.6/site-packages (from pytest->tellurium) (1.3.0)
Requirement already satisfied: more-itertools>=4.0.0 in ./anaconda3/lib/python3.6/site-packages (from pytest->tellurium) (8.0.2)
Requirement already satisfied: wcwidth in ./anaconda3/lib/python3.6/site-packages (from pytest->tellurium) (0.1.8)
Requirement already satisfied: pluggy<1.0,>=0.12 in ./anaconda3/lib/python3.6/site-packages (from pytest->tellurium) (0.13.1)
Requirement already satisfied: six in ./anaconda3/lib/python3.6/site-packages (from plotly>=2.0.12->tellurium) (1.13.0)
Requirement already satisfied: retrying>=1.3.3 in ./anaconda3/lib/python3.6/site-packages (from plotly>=2.0.12->tellurium) (1.3.3)
Requirement already satisfied: setuptools>=18.5 in ./anaconda3/lib/python3.6/site-packages (from ipython->tellurium) (44.0.0)
Requirement already satisfied: pickleshare in ./anaconda3/lib/python3.6/site-packages (from ipython->tellurium) (0.7.5)
Requirement already satisfied: appnope; sys_platform == "darwin" in ./anaconda3/lib/python3.6/site-packages (from ipython->tellurium) (0.1.0)
Requirement already satisfied: pexpect; sys_platform != "win32" in ./anaconda3/lib/python3.6/site-packages (from ipython->tellurium) (4.7.0)
Requirement already satisfied: pygments in ./anaconda3/lib/python3.6/site-packages (from ipython->tellurium) (2.5.2)
Requirement already satisfied: decorator in ./anaconda3/lib/python3.6/site-packages (from ipython->tellurium) (4.4.1)
Requirement already satisfied: prompt-toolkit!=3.0.0,!=3.0.1,<3.1.0,>=2.0.0 in ./anaconda3/lib/python3.6/site-packages (from ipython->tellurium) (3.0.2)
Requirement already satisfied: jedi>=0.10 in ./anaconda3/lib/python3.6/site-packages (from ipython->tellurium) (0.15.2)
Requirement already satisfied: backcall in ./anaconda3/lib/python3.6/site-packages (from ipython->tellurium) (0.1.0)
Requirement already satisfied: MarkupSafe>=0.23 in ./anaconda3/lib/python3.6/site-packages (from jinja2>=2.9.6->tellurium) (1.1.1)
Requirement already satisfied: ipython-genutils in ./anaconda3/lib/python3.6/site-packages (from traitlets->jupyter-core>=4.3.0->tellurium) (0.2.0)
Requirement already satisfied: zipp>=0.5 in ./anaconda3/lib/python3.6/site-packages (from importlib-metadata>=0.12; python_version < "3.8"->pytest->tellurium) (0.6.0)
Requirement already satisfied: ptyprocess>=0.5 in ./anaconda3/lib/python3.6/site-packages (from pexpect; sys_platform != "win32"->ipython->tellurium) (0.6.0)
Requirement already satisfied: parso>=0.5.2 in ./anaconda3/lib/python3.6/site-packages (from jedi>=0.10->ipython->tellurium) (0.5.2)
~$ python
Python 3.6.9 |Anaconda, Inc.| (default, Jul 30 2019, 13:42:17) 
[GCC 4.2.1 Compatible Clang 4.0.1 (tags/RELEASE_401/final)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import tellurium
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Users/heiland/anaconda3/lib/python3.6/site-packages/tellurium/__init__.py", line 111, in <module>
    from .analysis.bifurcation import (
  File "/Users/heiland/anaconda3/lib/python3.6/site-packages/tellurium/analysis/bifurcation.py", line 7, in <module>
    from rrplugins import Plugin
  File "/Users/heiland/anaconda3/lib/python3.6/site-packages/rrplugins/__init__.py", line 1, in <module>
    from rrplugins.telplugins import *
  File "/Users/heiland/anaconda3/lib/python3.6/site-packages/rrplugins/telplugins.py", line 6, in <module>
    import rrplugins.telplugins_c_api as tpc
  File "/Users/heiland/anaconda3/lib/python3.6/site-packages/rrplugins/telplugins_c_api.py", line 1635, in <module>
    rrpLib.tpSetLogLevel.restype = c_bool
  File "/Users/heiland/anaconda3/lib/python3.6/ctypes/__init__.py", line 361, in __getattr__
    func = self.__getitem__(name)
  File "/Users/heiland/anaconda3/lib/python3.6/ctypes/__init__.py", line 366, in __getitem__
    func = self._FuncPtr((name_or_ordinal, self))
AttributeError: dlsym(0x7fb3ce48b920, tpSetLogLevel): symbol not found

And, fwiw, I have:

$ conda --version
conda 4.8.0

This was just a curiosity side-project, so it's not critical for me right now. Maybe it'll be an issue for other users though.

hsauro commented 4 years ago

Odd, we've never seen any issues with installing tellurium on the mac os using anaconda supporting python 3.6. However, just recently a python 3.7 version was uploaded to pypi. Try installing the anaconda that supports 3.7.

Herbert

On Mon, Jan 6, 2020 at 9:15 AM Randy Heiland notifications@github.com wrote:

Yes, I'd first tried just pip install tellurium but it attempted to reinstalled my previous/cached version, so I tracked down this option to prevent that. I just now attempted a re-install, but get the same:

~$ pip install tellurium Requirement already satisfied: tellurium in ./anaconda3/lib/python3.6/site-packages (2.1.5) Requirement already satisfied: tecombine>=0.2.2 in ./anaconda3/lib/python3.6/site-packages (from tellurium) (0.2.2.1) Requirement already satisfied: jupyter-core>=4.3.0 in ./anaconda3/lib/python3.6/site-packages (from tellurium) (4.6.1) Requirement already satisfied: tesedml>=0.4.3 in ./anaconda3/lib/python3.6/site-packages (from tellurium) (0.4.3) Requirement already satisfied: tenuml>=1.1.1 in ./anaconda3/lib/python3.6/site-packages (from tellurium) (1.1.1) Requirement already satisfied: phrasedml>=1.0.9 in ./anaconda3/lib/python3.6/site-packages (from tellurium) (1.0.9) Requirement already satisfied: antimony>=2.9.3 in ./anaconda3/lib/python3.6/site-packages (from tellurium) (2.11.0) Requirement already satisfied: pandas>=0.20.2 in ./anaconda3/lib/python3.6/site-packages (from tellurium) (0.25.3) Requirement already satisfied: tesbml>=5.15.0.1 in ./anaconda3/lib/python3.6/site-packages (from tellurium) (5.15.0.1) Requirement already satisfied: appdirs>=1.4.3 in ./anaconda3/lib/python3.6/site-packages (from tellurium) (1.4.3) Requirement already satisfied: matplotlib>=2.0.2 in ./anaconda3/lib/python3.6/site-packages (from tellurium) (3.1.2) Requirement already satisfied: rrplugins>=1.1.8 in ./anaconda3/lib/python3.6/site-packages (from tellurium) (1.2.2) Requirement already satisfied: requests in ./anaconda3/lib/python3.6/site-packages (from tellurium) (2.22.0) Requirement already satisfied: jupyter-client>=5.1.0 in ./anaconda3/lib/python3.6/site-packages (from tellurium) (5.3.4) Requirement already satisfied: pytest in ./anaconda3/lib/python3.6/site-packages (from tellurium) (5.3.2) Requirement already satisfied: numpy>=1.11.0 in ./anaconda3/lib/python3.6/site-packages (from tellurium) (1.18.0) Requirement already satisfied: plotly>=2.0.12 in ./anaconda3/lib/python3.6/site-packages (from tellurium) (4.4.1) Requirement already satisfied: ipython in ./anaconda3/lib/python3.6/site-packages (from tellurium) (7.11.1) Requirement already satisfied: jinja2>=2.9.6 in ./anaconda3/lib/python3.6/site-packages (from tellurium) (2.10.3) Requirement already satisfied: ipykernel>=4.6.1 in ./anaconda3/lib/python3.6/site-packages (from tellurium) (5.1.3) Requirement already satisfied: libroadrunner>=1.4.24 in ./anaconda3/lib/python3.6/site-packages (from tellurium) (1.5.4) Requirement already satisfied: scipy>=0.19.0 in ./anaconda3/lib/python3.6/site-packages (from tellurium) (1.4.1) Requirement already satisfied: sbml2matlab>=0.9.1 in ./anaconda3/lib/python3.6/site-packages (from tellurium) (0.9.1) Requirement already satisfied: traitlets in ./anaconda3/lib/python3.6/site-packages (from jupyter-core>=4.3.0->tellurium) (4.3.3) Requirement already satisfied: pytz>=2017.2 in ./anaconda3/lib/python3.6/site-packages (from pandas>=0.20.2->tellurium) (2019.3) Requirement already satisfied: python-dateutil>=2.6.1 in ./anaconda3/lib/python3.6/site-packages (from pandas>=0.20.2->tellurium) (2.8.1) Requirement already satisfied: kiwisolver>=1.0.1 in ./anaconda3/lib/python3.6/site-packages (from matplotlib>=2.0.2->tellurium) (1.1.0) Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in ./anaconda3/lib/python3.6/site-packages (from matplotlib>=2.0.2->tellurium) (2.4.6) Requirement already satisfied: cycler>=0.10 in ./anaconda3/lib/python3.6/site-packages (from matplotlib>=2.0.2->tellurium) (0.10.0) Requirement already satisfied: certifi>=2017.4.17 in ./anaconda3/lib/python3.6/site-packages (from requests->tellurium) (2019.11.28) Requirement already satisfied: idna<2.9,>=2.5 in ./anaconda3/lib/python3.6/site-packages (from requests->tellurium) (2.8) Requirement already satisfied: chardet<3.1.0,>=3.0.2 in ./anaconda3/lib/python3.6/site-packages (from requests->tellurium) (3.0.4) Requirement already satisfied: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in ./anaconda3/lib/python3.6/site-packages (from requests->tellurium) (1.25.7) Requirement already satisfied: pyzmq>=13 in ./anaconda3/lib/python3.6/site-packages (from jupyter-client>=5.1.0->tellurium) (18.1.1) Requirement already satisfied: tornado>=4.1 in ./anaconda3/lib/python3.6/site-packages (from jupyter-client>=5.1.0->tellurium) (6.0.3) Requirement already satisfied: packaging in ./anaconda3/lib/python3.6/site-packages (from pytest->tellurium) (19.2) Requirement already satisfied: attrs>=17.4.0 in ./anaconda3/lib/python3.6/site-packages (from pytest->tellurium) (19.3.0) Requirement already satisfied: py>=1.5.0 in ./anaconda3/lib/python3.6/site-packages (from pytest->tellurium) (1.8.1) Requirement already satisfied: importlib-metadata>=0.12; python_version < "3.8" in ./anaconda3/lib/python3.6/site-packages (from pytest->tellurium) (1.3.0) Requirement already satisfied: more-itertools>=4.0.0 in ./anaconda3/lib/python3.6/site-packages (from pytest->tellurium) (8.0.2) Requirement already satisfied: wcwidth in ./anaconda3/lib/python3.6/site-packages (from pytest->tellurium) (0.1.8) Requirement already satisfied: pluggy<1.0,>=0.12 in ./anaconda3/lib/python3.6/site-packages (from pytest->tellurium) (0.13.1) Requirement already satisfied: six in ./anaconda3/lib/python3.6/site-packages (from plotly>=2.0.12->tellurium) (1.13.0) Requirement already satisfied: retrying>=1.3.3 in ./anaconda3/lib/python3.6/site-packages (from plotly>=2.0.12->tellurium) (1.3.3) Requirement already satisfied: setuptools>=18.5 in ./anaconda3/lib/python3.6/site-packages (from ipython->tellurium) (44.0.0) Requirement already satisfied: pickleshare in ./anaconda3/lib/python3.6/site-packages (from ipython->tellurium) (0.7.5) Requirement already satisfied: appnope; sys_platform == "darwin" in ./anaconda3/lib/python3.6/site-packages (from ipython->tellurium) (0.1.0) Requirement already satisfied: pexpect; sys_platform != "win32" in ./anaconda3/lib/python3.6/site-packages (from ipython->tellurium) (4.7.0) Requirement already satisfied: pygments in ./anaconda3/lib/python3.6/site-packages (from ipython->tellurium) (2.5.2) Requirement already satisfied: decorator in ./anaconda3/lib/python3.6/site-packages (from ipython->tellurium) (4.4.1) Requirement already satisfied: prompt-toolkit!=3.0.0,!=3.0.1,<3.1.0,>=2.0.0 in ./anaconda3/lib/python3.6/site-packages (from ipython->tellurium) (3.0.2) Requirement already satisfied: jedi>=0.10 in ./anaconda3/lib/python3.6/site-packages (from ipython->tellurium) (0.15.2) Requirement already satisfied: backcall in ./anaconda3/lib/python3.6/site-packages (from ipython->tellurium) (0.1.0) Requirement already satisfied: MarkupSafe>=0.23 in ./anaconda3/lib/python3.6/site-packages (from jinja2>=2.9.6->tellurium) (1.1.1) Requirement already satisfied: ipython-genutils in ./anaconda3/lib/python3.6/site-packages (from traitlets->jupyter-core>=4.3.0->tellurium) (0.2.0) Requirement already satisfied: zipp>=0.5 in ./anaconda3/lib/python3.6/site-packages (from importlib-metadata>=0.12; python_version < "3.8"->pytest->tellurium) (0.6.0) Requirement already satisfied: ptyprocess>=0.5 in ./anaconda3/lib/python3.6/site-packages (from pexpect; sys_platform != "win32"->ipython->tellurium) (0.6.0) Requirement already satisfied: parso>=0.5.2 in ./anaconda3/lib/python3.6/site-packages (from jedi>=0.10->ipython->tellurium) (0.5.2) ~$ python Python 3.6.9 |Anaconda, Inc.| (default, Jul 30 2019, 13:42:17) [GCC 4.2.1 Compatible Clang 4.0.1 (tags/RELEASE_401/final)] on darwin Type "help", "copyright", "credits" or "license" for more information.

import tellurium Traceback (most recent call last): File "", line 1, in File "/Users/heiland/anaconda3/lib/python3.6/site-packages/tellurium/init.py", line 111, in from .analysis.bifurcation import ( File "/Users/heiland/anaconda3/lib/python3.6/site-packages/tellurium/analysis/bifurcation.py", line 7, in from rrplugins import Plugin File "/Users/heiland/anaconda3/lib/python3.6/site-packages/rrplugins/init.py", line 1, in from rrplugins.telplugins import * File "/Users/heiland/anaconda3/lib/python3.6/site-packages/rrplugins/telplugins.py", line 6, in import rrplugins.telplugins_c_api as tpc File "/Users/heiland/anaconda3/lib/python3.6/site-packages/rrplugins/telplugins_c_api.py", line 1635, in rrpLib.tpSetLogLevel.restype = c_bool File "/Users/heiland/anaconda3/lib/python3.6/ctypes/init.py", line 361, in getattr func = self.getitem(name) File "/Users/heiland/anaconda3/lib/python3.6/ctypes/init.py", line 366, in getitem func = self._FuncPtr((name_or_ordinal, self)) AttributeError: dlsym(0x7fb3ce48b920, tpSetLogLevel): symbol not found

And, fwiw, I have:

$ conda --version conda 4.8.0

This was just a curiosity side-project, so it's not critical for me right now. Maybe it'll be an issue for other users though.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/sys-bio/tellurium/issues/442?email_source=notifications&email_token=AAIBSDSZUIEZKWRIJVXJPLDQ4NRILA5CNFSM4KCWWWM2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEIGDMAI#issuecomment-571225601, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAIBSDQNXTUIL3G5POURJ6TQ4NRILANCNFSM4KCWWWMQ .

-- Herbert Sauro, Professor University of Washington, Bioengineering 206-685-2119, www.sys-bio.org hsauro@uw.edu Books: http://books.analogmachine.org/

rheiland commented 4 years ago

I blew away my old anaconda (Python 3.6), downloaded/installed the latest (3.7), but still have the problem with tellurium:

~/Downloads$ pip install tellurium
Collecting tellurium
  Using cached https://files.pythonhosted.org/packages/5d/3a/77879c6cc93e9be58aef94ecfc7b0e4ae3ba7f9a4dd6b643f8846a6def78/tellurium-2.1.5-py2.py3-none-any.whl
Collecting appdirs>=1.4.3 (from tellurium)
  Using cached https://files.pythonhosted.org/packages/56/eb/810e700ed1349edde4cbdc1b2a21e28cdf115f9faf263f6bbf8447c1abf3/appdirs-1.4.3-py2.py3-none-any.whl
Requirement already satisfied: pytest in /Users/heiland/anaconda3/lib/python3.7/site-packages (from tellurium) (5.2.1)
Requirement already satisfied: ipython in /Users/heiland/anaconda3/lib/python3.7/site-packages (from tellurium) (7.8.0)
Collecting tenuml>=1.1.1 (from tellurium)
  Downloading https://files.pythonhosted.org/packages/49/d1/50433fa8a6c8b744d35336cf1e3f7aab3ffc4913ffbfae4e606bed9528ca/tenuml-1.1.1.2-cp37-cp37m-macosx_10_14_x86_64.whl (2.6MB)
     |████████████████████████████████| 2.6MB 4.0MB/s 
Requirement already satisfied: pandas>=0.20.2 in /Users/heiland/anaconda3/lib/python3.7/site-packages (from tellurium) (0.25.1)
Requirement already satisfied: numpy>=1.11.0 in /Users/heiland/anaconda3/lib/python3.7/site-packages (from tellurium) (1.17.2)
Requirement already satisfied: scipy>=0.19.0 in /Users/heiland/anaconda3/lib/python3.7/site-packages (from tellurium) (1.3.1)
Collecting phrasedml>=1.0.9 (from tellurium)
  Downloading https://files.pythonhosted.org/packages/cb/0a/05daca6a21d9e9fc03d72658495bfad67cd006a6500d3f50344f0e7f8398/phrasedml-1.0.10-cp37-cp37m-macosx_10_14_x86_64.whl (2.7MB)
     |████████████████████████████████| 2.7MB 25.2MB/s 
Collecting sbml2matlab>=0.9.1 (from tellurium)
  Downloading https://files.pythonhosted.org/packages/d0/3e/73071fe78aec83cc976fdc9ef957600266ddd81b36466d5d373b1210aaa7/sbml2matlab-1.2.3-cp37-cp37m-macosx_10_14_x86_64.whl (2.3MB)
     |████████████████████████████████| 2.3MB 29.2MB/s 
Collecting plotly>=2.0.12 (from tellurium)
  Using cached https://files.pythonhosted.org/packages/8e/ce/6ea5683c47b682bffad39ad41d10913141b560b1b875a90dbc6abe3f4fa9/plotly-4.4.1-py2.py3-none-any.whl
Collecting rrplugins>=1.1.8 (from tellurium)
  Using cached https://files.pythonhosted.org/packages/f0/ef/8905a20af657a6eea8a3160e49b85f96622c7bf3d8d137ea410e1bbcafea/rrplugins-1.2.2-py2.py3-none-any.whl
Collecting tesbml>=5.15.0.1 (from tellurium)
  Downloading https://files.pythonhosted.org/packages/93/4f/933a7568e8e45393dab97c45a0ed4b322ee00cb5e611a10b7b77572d7011/tesbml-5.18.0-cp37-cp37m-macosx_10_14_x86_64.whl (4.7MB)
     |████████████████████████████████| 4.7MB 70kB/s 
Requirement already satisfied: ipykernel>=4.6.1 in /Users/heiland/anaconda3/lib/python3.7/site-packages (from tellurium) (5.1.2)
Collecting tecombine>=0.2.2 (from tellurium)
  Downloading https://files.pythonhosted.org/packages/ef/77/9ce91622d34dd4ce05c9280a3f01e2f64db538d66184eb459358ed20b0a8/tecombine-0.2.3.0-cp37-cp37m-macosx_10_11_x86_64.whl (2.9MB)
     |████████████████████████████████| 2.9MB 37.5MB/s 
Requirement already satisfied: matplotlib>=2.0.2 in /Users/heiland/anaconda3/lib/python3.7/site-packages (from tellurium) (3.1.1)
Collecting antimony>=2.9.3 (from tellurium)
  Downloading https://files.pythonhosted.org/packages/fe/df/d8b0d8e581a7e6c7d27e4f9eb30c800842074c138df621e80b4ab3aea6e6/antimony-2.11.0-cp37-cp37m-macosx_10_9_x86_64.whl (3.8MB)
     |████████████████████████████████| 3.8MB 37.4MB/s 
Requirement already satisfied: jupyter-client>=5.1.0 in /Users/heiland/anaconda3/lib/python3.7/site-packages (from tellurium) (5.3.3)
Collecting tesedml>=0.4.3 (from tellurium)
  Downloading https://files.pythonhosted.org/packages/0f/e6/271cfa56c0dc1132cab53f60b61e84037029d7d16ea6eabe3665944163c3/tesedml-0.4.5.0-cp37-cp37m-macosx_10_14_x86_64.whl (3.2MB)
     |████████████████████████████████| 3.2MB 34.0MB/s 
Collecting libroadrunner>=1.4.24 (from tellurium)
  Downloading https://files.pythonhosted.org/packages/92/56/83b0e8d2df121cbf5142bcdfd6138f0f751d7d3de036c94df60b7eef8f8e/libroadrunner-1.6.0-cp37-cp37m-macosx_10_14_x86_64.whl (27.9MB)
     |████████████████████████████████| 27.9MB 31.6MB/s 
Requirement already satisfied: jupyter-core>=4.3.0 in /Users/heiland/anaconda3/lib/python3.7/site-packages (from tellurium) (4.5.0)
Requirement already satisfied: requests in /Users/heiland/anaconda3/lib/python3.7/site-packages (from tellurium) (2.22.0)
Requirement already satisfied: jinja2>=2.9.6 in /Users/heiland/anaconda3/lib/python3.7/site-packages (from tellurium) (2.10.3)
Requirement already satisfied: py>=1.5.0 in /Users/heiland/anaconda3/lib/python3.7/site-packages (from pytest->tellurium) (1.8.0)
Requirement already satisfied: packaging in /Users/heiland/anaconda3/lib/python3.7/site-packages (from pytest->tellurium) (19.2)
Requirement already satisfied: attrs>=17.4.0 in /Users/heiland/anaconda3/lib/python3.7/site-packages (from pytest->tellurium) (19.2.0)
Requirement already satisfied: more-itertools>=4.0.0 in /Users/heiland/anaconda3/lib/python3.7/site-packages (from pytest->tellurium) (7.2.0)
Requirement already satisfied: atomicwrites>=1.0 in /Users/heiland/anaconda3/lib/python3.7/site-packages (from pytest->tellurium) (1.3.0)
Requirement already satisfied: pluggy<1.0,>=0.12 in /Users/heiland/anaconda3/lib/python3.7/site-packages (from pytest->tellurium) (0.13.0)
Requirement already satisfied: wcwidth in /Users/heiland/anaconda3/lib/python3.7/site-packages (from pytest->tellurium) (0.1.7)
Requirement already satisfied: importlib-metadata>=0.12 in /Users/heiland/anaconda3/lib/python3.7/site-packages (from pytest->tellurium) (0.23)
Requirement already satisfied: decorator in /Users/heiland/anaconda3/lib/python3.7/site-packages (from ipython->tellurium) (4.4.0)
Requirement already satisfied: setuptools>=18.5 in /Users/heiland/anaconda3/lib/python3.7/site-packages (from ipython->tellurium) (41.4.0)
Requirement already satisfied: prompt-toolkit<2.1.0,>=2.0.0 in /Users/heiland/anaconda3/lib/python3.7/site-packages (from ipython->tellurium) (2.0.10)
Requirement already satisfied: pygments in /Users/heiland/anaconda3/lib/python3.7/site-packages (from ipython->tellurium) (2.4.2)
Requirement already satisfied: appnope; sys_platform == "darwin" in /Users/heiland/anaconda3/lib/python3.7/site-packages (from ipython->tellurium) (0.1.0)
Requirement already satisfied: jedi>=0.10 in /Users/heiland/anaconda3/lib/python3.7/site-packages (from ipython->tellurium) (0.15.1)
Requirement already satisfied: backcall in /Users/heiland/anaconda3/lib/python3.7/site-packages (from ipython->tellurium) (0.1.0)
Requirement already satisfied: pexpect; sys_platform != "win32" in /Users/heiland/anaconda3/lib/python3.7/site-packages (from ipython->tellurium) (4.7.0)
Requirement already satisfied: traitlets>=4.2 in /Users/heiland/anaconda3/lib/python3.7/site-packages (from ipython->tellurium) (4.3.3)
Requirement already satisfied: pickleshare in /Users/heiland/anaconda3/lib/python3.7/site-packages (from ipython->tellurium) (0.7.5)
Requirement already satisfied: pytz>=2017.2 in /Users/heiland/anaconda3/lib/python3.7/site-packages (from pandas>=0.20.2->tellurium) (2019.3)
Requirement already satisfied: python-dateutil>=2.6.1 in /Users/heiland/anaconda3/lib/python3.7/site-packages (from pandas>=0.20.2->tellurium) (2.8.0)
Collecting retrying>=1.3.3 (from plotly>=2.0.12->tellurium)
  Using cached https://files.pythonhosted.org/packages/44/ef/beae4b4ef80902f22e3af073397f079c96969c69b2c7d52a57ea9ae61c9d/retrying-1.3.3.tar.gz
Requirement already satisfied: six in /Users/heiland/anaconda3/lib/python3.7/site-packages (from plotly>=2.0.12->tellurium) (1.12.0)
Requirement already satisfied: tornado>=4.2 in /Users/heiland/anaconda3/lib/python3.7/site-packages (from ipykernel>=4.6.1->tellurium) (6.0.3)
Requirement already satisfied: cycler>=0.10 in /Users/heiland/anaconda3/lib/python3.7/site-packages (from matplotlib>=2.0.2->tellurium) (0.10.0)
Requirement already satisfied: kiwisolver>=1.0.1 in /Users/heiland/anaconda3/lib/python3.7/site-packages (from matplotlib>=2.0.2->tellurium) (1.1.0)
Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /Users/heiland/anaconda3/lib/python3.7/site-packages (from matplotlib>=2.0.2->tellurium) (2.4.2)
Requirement already satisfied: pyzmq>=13 in /Users/heiland/anaconda3/lib/python3.7/site-packages (from jupyter-client>=5.1.0->tellurium) (18.1.0)
Requirement already satisfied: idna<2.9,>=2.5 in /Users/heiland/anaconda3/lib/python3.7/site-packages (from requests->tellurium) (2.8)
Requirement already satisfied: certifi>=2017.4.17 in /Users/heiland/anaconda3/lib/python3.7/site-packages (from requests->tellurium) (2019.9.11)
Requirement already satisfied: chardet<3.1.0,>=3.0.2 in /Users/heiland/anaconda3/lib/python3.7/site-packages (from requests->tellurium) (3.0.4)
Requirement already satisfied: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /Users/heiland/anaconda3/lib/python3.7/site-packages (from requests->tellurium) (1.24.2)
Requirement already satisfied: MarkupSafe>=0.23 in /Users/heiland/anaconda3/lib/python3.7/site-packages (from jinja2>=2.9.6->tellurium) (1.1.1)
Requirement already satisfied: zipp>=0.5 in /Users/heiland/anaconda3/lib/python3.7/site-packages (from importlib-metadata>=0.12->pytest->tellurium) (0.6.0)
Requirement already satisfied: parso>=0.5.0 in /Users/heiland/anaconda3/lib/python3.7/site-packages (from jedi>=0.10->ipython->tellurium) (0.5.1)
Requirement already satisfied: ptyprocess>=0.5 in /Users/heiland/anaconda3/lib/python3.7/site-packages (from pexpect; sys_platform != "win32"->ipython->tellurium) (0.6.0)
Requirement already satisfied: ipython-genutils in /Users/heiland/anaconda3/lib/python3.7/site-packages (from traitlets>=4.2->ipython->tellurium) (0.2.0)
Building wheels for collected packages: retrying
  Building wheel for retrying (setup.py) ... done
  Created wheel for retrying: filename=retrying-1.3.3-cp37-none-any.whl size=11429 sha256=597c9584ea7c6c134004651d158519842047a1f179c34c27d2fe9f9974656c54
  Stored in directory: /Users/heiland/Library/Caches/pip/wheels/d7/a9/33/acc7b709e2a35caa7d4cae442f6fe6fbf2c43f80823d46460c
Successfully built retrying
Installing collected packages: appdirs, tenuml, phrasedml, sbml2matlab, retrying, plotly, libroadrunner, rrplugins, tesbml, tecombine, antimony, tesedml, tellurium
Successfully installed antimony-2.11.0 appdirs-1.4.3 libroadrunner-1.6.0 phrasedml-1.0.10 plotly-4.4.1 retrying-1.3.3 rrplugins-1.2.2 sbml2matlab-1.2.3 tecombine-0.2.3.0 tellurium-2.1.5 tenuml-1.1.1.2 tesbml-5.18.0 tesedml-0.4.5.0
~/Downloads$ python
Python 3.7.4 (default, Aug 13 2019, 15:17:50) 
[Clang 4.0.1 (tags/RELEASE_401/final)] :: Anaconda, Inc. on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import tellurium
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Users/heiland/anaconda3/lib/python3.7/site-packages/tellurium/__init__.py", line 111, in <module>
    from .analysis.bifurcation import (
  File "/Users/heiland/anaconda3/lib/python3.7/site-packages/tellurium/analysis/bifurcation.py", line 7, in <module>
    from rrplugins import Plugin
  File "/Users/heiland/anaconda3/lib/python3.7/site-packages/rrplugins/__init__.py", line 1, in <module>
    from rrplugins.telplugins import *
  File "/Users/heiland/anaconda3/lib/python3.7/site-packages/rrplugins/telplugins.py", line 6, in <module>
    import rrplugins.telplugins_c_api as tpc
  File "/Users/heiland/anaconda3/lib/python3.7/site-packages/rrplugins/telplugins_c_api.py", line 1635, in <module>
    rrpLib.tpSetLogLevel.restype = c_bool
  File "/Users/heiland/anaconda3/lib/python3.7/ctypes/__init__.py", line 377, in __getattr__
    func = self.__getitem__(name)
  File "/Users/heiland/anaconda3/lib/python3.7/ctypes/__init__.py", line 382, in __getitem__
    func = self._FuncPtr((name_or_ordinal, self))
AttributeError: dlsym(0x7fbdc1b7d0c0, tpSetLogLevel): symbol not found
>>>

It seems that pip is not installing tellurium 2.2 (isn't that the latest? - according to http://tellurium.analogmachine.org/news/) 

$ pip uninstall tellurium
Uninstalling tellurium-2.1.5:
  Would remove:
    /Users/heiland/anaconda3/lib/python3.7/site-packages/tellurium-2.1.5.dist-info/*
    /Users/heiland/anaconda3/lib/python3.7/site-packages/tellurium/*

And pypi seems to have 2.1.5 as the latest, not 2.2 https://pypi.org/project/tellurium/#history

hsauro commented 4 years ago

I will be seeing the developer this afternoon (Mon) and we'll discuss your issue.

Herbert

On Mon, Jan 6, 2020 at 10:42 AM Randy Heiland notifications@github.com wrote:

I blew away my old anaconda (Python 3.6), downloaded/installed the latest (3.7), but still have the problem with tellurium:

~/Downloads$ pip install tellurium

Collecting tellurium

Using cached https://files.pythonhosted.org/packages/5d/3a/77879c6cc93e9be58aef94ecfc7b0e4ae3ba7f9a4dd6b643f8846a6def78/tellurium-2.1.5-py2.py3-none-any.whl

Collecting appdirs>=1.4.3 (from tellurium)

Using cached https://files.pythonhosted.org/packages/56/eb/810e700ed1349edde4cbdc1b2a21e28cdf115f9faf263f6bbf8447c1abf3/appdirs-1.4.3-py2.py3-none-any.whl

Requirement already satisfied: pytest in /Users/heiland/anaconda3/lib/python3.7/site-packages (from tellurium) (5.2.1)

Requirement already satisfied: ipython in /Users/heiland/anaconda3/lib/python3.7/site-packages (from tellurium) (7.8.0)

Collecting tenuml>=1.1.1 (from tellurium)

Downloading https://files.pythonhosted.org/packages/49/d1/50433fa8a6c8b744d35336cf1e3f7aab3ffc4913ffbfae4e606bed9528ca/tenuml-1.1.1.2-cp37-cp37m-macosx_10_14_x86_64.whl (2.6MB)

 |████████████████████████████████| 2.6MB 4.0MB/s

Requirement already satisfied: pandas>=0.20.2 in /Users/heiland/anaconda3/lib/python3.7/site-packages (from tellurium) (0.25.1)

Requirement already satisfied: numpy>=1.11.0 in /Users/heiland/anaconda3/lib/python3.7/site-packages (from tellurium) (1.17.2)

Requirement already satisfied: scipy>=0.19.0 in /Users/heiland/anaconda3/lib/python3.7/site-packages (from tellurium) (1.3.1)

Collecting phrasedml>=1.0.9 (from tellurium)

Downloading https://files.pythonhosted.org/packages/cb/0a/05daca6a21d9e9fc03d72658495bfad67cd006a6500d3f50344f0e7f8398/phrasedml-1.0.10-cp37-cp37m-macosx_10_14_x86_64.whl (2.7MB)

 |████████████████████████████████| 2.7MB 25.2MB/s

Collecting sbml2matlab>=0.9.1 (from tellurium)

Downloading https://files.pythonhosted.org/packages/d0/3e/73071fe78aec83cc976fdc9ef957600266ddd81b36466d5d373b1210aaa7/sbml2matlab-1.2.3-cp37-cp37m-macosx_10_14_x86_64.whl (2.3MB)

 |████████████████████████████████| 2.3MB 29.2MB/s

Collecting plotly>=2.0.12 (from tellurium)

Using cached https://files.pythonhosted.org/packages/8e/ce/6ea5683c47b682bffad39ad41d10913141b560b1b875a90dbc6abe3f4fa9/plotly-4.4.1-py2.py3-none-any.whl

Collecting rrplugins>=1.1.8 (from tellurium)

Using cached https://files.pythonhosted.org/packages/f0/ef/8905a20af657a6eea8a3160e49b85f96622c7bf3d8d137ea410e1bbcafea/rrplugins-1.2.2-py2.py3-none-any.whl

Collecting tesbml>=5.15.0.1 (from tellurium)

Downloading https://files.pythonhosted.org/packages/93/4f/933a7568e8e45393dab97c45a0ed4b322ee00cb5e611a10b7b77572d7011/tesbml-5.18.0-cp37-cp37m-macosx_10_14_x86_64.whl (4.7MB)

 |████████████████████████████████| 4.7MB 70kB/s

Requirement already satisfied: ipykernel>=4.6.1 in /Users/heiland/anaconda3/lib/python3.7/site-packages (from tellurium) (5.1.2)

Collecting tecombine>=0.2.2 (from tellurium)

Downloading https://files.pythonhosted.org/packages/ef/77/9ce91622d34dd4ce05c9280a3f01e2f64db538d66184eb459358ed20b0a8/tecombine-0.2.3.0-cp37-cp37m-macosx_10_11_x86_64.whl (2.9MB)

 |████████████████████████████████| 2.9MB 37.5MB/s

Requirement already satisfied: matplotlib>=2.0.2 in /Users/heiland/anaconda3/lib/python3.7/site-packages (from tellurium) (3.1.1)

Collecting antimony>=2.9.3 (from tellurium)

Downloading https://files.pythonhosted.org/packages/fe/df/d8b0d8e581a7e6c7d27e4f9eb30c800842074c138df621e80b4ab3aea6e6/antimony-2.11.0-cp37-cp37m-macosx_10_9_x86_64.whl (3.8MB)

 |████████████████████████████████| 3.8MB 37.4MB/s

Requirement already satisfied: jupyter-client>=5.1.0 in /Users/heiland/anaconda3/lib/python3.7/site-packages (from tellurium) (5.3.3)

Collecting tesedml>=0.4.3 (from tellurium)

Downloading https://files.pythonhosted.org/packages/0f/e6/271cfa56c0dc1132cab53f60b61e84037029d7d16ea6eabe3665944163c3/tesedml-0.4.5.0-cp37-cp37m-macosx_10_14_x86_64.whl (3.2MB)

 |████████████████████████████████| 3.2MB 34.0MB/s

Collecting libroadrunner>=1.4.24 (from tellurium)

Downloading https://files.pythonhosted.org/packages/92/56/83b0e8d2df121cbf5142bcdfd6138f0f751d7d3de036c94df60b7eef8f8e/libroadrunner-1.6.0-cp37-cp37m-macosx_10_14_x86_64.whl (27.9MB)

 |████████████████████████████████| 27.9MB 31.6MB/s

Requirement already satisfied: jupyter-core>=4.3.0 in /Users/heiland/anaconda3/lib/python3.7/site-packages (from tellurium) (4.5.0)

Requirement already satisfied: requests in /Users/heiland/anaconda3/lib/python3.7/site-packages (from tellurium) (2.22.0)

Requirement already satisfied: jinja2>=2.9.6 in /Users/heiland/anaconda3/lib/python3.7/site-packages (from tellurium) (2.10.3)

Requirement already satisfied: py>=1.5.0 in /Users/heiland/anaconda3/lib/python3.7/site-packages (from pytest->tellurium) (1.8.0)

Requirement already satisfied: packaging in /Users/heiland/anaconda3/lib/python3.7/site-packages (from pytest->tellurium) (19.2)

Requirement already satisfied: attrs>=17.4.0 in /Users/heiland/anaconda3/lib/python3.7/site-packages (from pytest->tellurium) (19.2.0)

Requirement already satisfied: more-itertools>=4.0.0 in /Users/heiland/anaconda3/lib/python3.7/site-packages (from pytest->tellurium) (7.2.0)

Requirement already satisfied: atomicwrites>=1.0 in /Users/heiland/anaconda3/lib/python3.7/site-packages (from pytest->tellurium) (1.3.0)

Requirement already satisfied: pluggy<1.0,>=0.12 in /Users/heiland/anaconda3/lib/python3.7/site-packages (from pytest->tellurium) (0.13.0)

Requirement already satisfied: wcwidth in /Users/heiland/anaconda3/lib/python3.7/site-packages (from pytest->tellurium) (0.1.7)

Requirement already satisfied: importlib-metadata>=0.12 in /Users/heiland/anaconda3/lib/python3.7/site-packages (from pytest->tellurium) (0.23)

Requirement already satisfied: decorator in /Users/heiland/anaconda3/lib/python3.7/site-packages (from ipython->tellurium) (4.4.0)

Requirement already satisfied: setuptools>=18.5 in /Users/heiland/anaconda3/lib/python3.7/site-packages (from ipython->tellurium) (41.4.0)

Requirement already satisfied: prompt-toolkit<2.1.0,>=2.0.0 in /Users/heiland/anaconda3/lib/python3.7/site-packages (from ipython->tellurium) (2.0.10)

Requirement already satisfied: pygments in /Users/heiland/anaconda3/lib/python3.7/site-packages (from ipython->tellurium) (2.4.2)

Requirement already satisfied: appnope; sys_platform == "darwin" in /Users/heiland/anaconda3/lib/python3.7/site-packages (from ipython->tellurium) (0.1.0)

Requirement already satisfied: jedi>=0.10 in /Users/heiland/anaconda3/lib/python3.7/site-packages (from ipython->tellurium) (0.15.1)

Requirement already satisfied: backcall in /Users/heiland/anaconda3/lib/python3.7/site-packages (from ipython->tellurium) (0.1.0)

Requirement already satisfied: pexpect; sys_platform != "win32" in /Users/heiland/anaconda3/lib/python3.7/site-packages (from ipython->tellurium) (4.7.0)

Requirement already satisfied: traitlets>=4.2 in /Users/heiland/anaconda3/lib/python3.7/site-packages (from ipython->tellurium) (4.3.3)

Requirement already satisfied: pickleshare in /Users/heiland/anaconda3/lib/python3.7/site-packages (from ipython->tellurium) (0.7.5)

Requirement already satisfied: pytz>=2017.2 in /Users/heiland/anaconda3/lib/python3.7/site-packages (from pandas>=0.20.2->tellurium) (2019.3)

Requirement already satisfied: python-dateutil>=2.6.1 in /Users/heiland/anaconda3/lib/python3.7/site-packages (from pandas>=0.20.2->tellurium) (2.8.0)

Collecting retrying>=1.3.3 (from plotly>=2.0.12->tellurium)

Using cached https://files.pythonhosted.org/packages/44/ef/beae4b4ef80902f22e3af073397f079c96969c69b2c7d52a57ea9ae61c9d/retrying-1.3.3.tar.gz

Requirement already satisfied: six in /Users/heiland/anaconda3/lib/python3.7/site-packages (from plotly>=2.0.12->tellurium) (1.12.0)

Requirement already satisfied: tornado>=4.2 in /Users/heiland/anaconda3/lib/python3.7/site-packages (from ipykernel>=4.6.1->tellurium) (6.0.3)

Requirement already satisfied: cycler>=0.10 in /Users/heiland/anaconda3/lib/python3.7/site-packages (from matplotlib>=2.0.2->tellurium) (0.10.0)

Requirement already satisfied: kiwisolver>=1.0.1 in /Users/heiland/anaconda3/lib/python3.7/site-packages (from matplotlib>=2.0.2->tellurium) (1.1.0)

Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /Users/heiland/anaconda3/lib/python3.7/site-packages (from matplotlib>=2.0.2->tellurium) (2.4.2)

Requirement already satisfied: pyzmq>=13 in /Users/heiland/anaconda3/lib/python3.7/site-packages (from jupyter-client>=5.1.0->tellurium) (18.1.0)

Requirement already satisfied: idna<2.9,>=2.5 in /Users/heiland/anaconda3/lib/python3.7/site-packages (from requests->tellurium) (2.8)

Requirement already satisfied: certifi>=2017.4.17 in /Users/heiland/anaconda3/lib/python3.7/site-packages (from requests->tellurium) (2019.9.11)

Requirement already satisfied: chardet<3.1.0,>=3.0.2 in /Users/heiland/anaconda3/lib/python3.7/site-packages (from requests->tellurium) (3.0.4)

Requirement already satisfied: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /Users/heiland/anaconda3/lib/python3.7/site-packages (from requests->tellurium) (1.24.2)

Requirement already satisfied: MarkupSafe>=0.23 in /Users/heiland/anaconda3/lib/python3.7/site-packages (from jinja2>=2.9.6->tellurium) (1.1.1)

Requirement already satisfied: zipp>=0.5 in /Users/heiland/anaconda3/lib/python3.7/site-packages (from importlib-metadata>=0.12->pytest->tellurium) (0.6.0)

Requirement already satisfied: parso>=0.5.0 in /Users/heiland/anaconda3/lib/python3.7/site-packages (from jedi>=0.10->ipython->tellurium) (0.5.1)

Requirement already satisfied: ptyprocess>=0.5 in /Users/heiland/anaconda3/lib/python3.7/site-packages (from pexpect; sys_platform != "win32"->ipython->tellurium) (0.6.0)

Requirement already satisfied: ipython-genutils in /Users/heiland/anaconda3/lib/python3.7/site-packages (from traitlets>=4.2->ipython->tellurium) (0.2.0)

Building wheels for collected packages: retrying

Building wheel for retrying (setup.py) ... done

Created wheel for retrying: filename=retrying-1.3.3-cp37-none-any.whl size=11429 sha256=597c9584ea7c6c134004651d158519842047a1f179c34c27d2fe9f9974656c54

Stored in directory: /Users/heiland/Library/Caches/pip/wheels/d7/a9/33/acc7b709e2a35caa7d4cae442f6fe6fbf2c43f80823d46460c

Successfully built retrying

Installing collected packages: appdirs, tenuml, phrasedml, sbml2matlab, retrying, plotly, libroadrunner, rrplugins, tesbml, tecombine, antimony, tesedml, tellurium

Successfully installed antimony-2.11.0 appdirs-1.4.3 libroadrunner-1.6.0 phrasedml-1.0.10 plotly-4.4.1 retrying-1.3.3 rrplugins-1.2.2 sbml2matlab-1.2.3 tecombine-0.2.3.0 tellurium-2.1.5 tenuml-1.1.1.2 tesbml-5.18.0 tesedml-0.4.5.0

~/Downloads$ python

Python 3.7.4 (default, Aug 13 2019, 15:17:50)

[Clang 4.0.1 (tags/RELEASE_401/final)] :: Anaconda, Inc. on darwin

Type "help", "copyright", "credits" or "license" for more information.

import tellurium

Traceback (most recent call last):

File "", line 1, in

File "/Users/heiland/anaconda3/lib/python3.7/site-packages/tellurium/init.py", line 111, in 

from .analysis.bifurcation import (

File "/Users/heiland/anaconda3/lib/python3.7/site-packages/tellurium/analysis/bifurcation.py", line 7, in 

from rrplugins import Plugin

File "/Users/heiland/anaconda3/lib/python3.7/site-packages/rrplugins/init.py", line 1, in 

from rrplugins.telplugins import *

File "/Users/heiland/anaconda3/lib/python3.7/site-packages/rrplugins/telplugins.py", line 6, in 

import rrplugins.telplugins_c_api as tpc

File "/Users/heiland/anaconda3/lib/python3.7/site-packages/rrplugins/telplugins_c_api.py", line 1635, in 

rrpLib.tpSetLogLevel.restype = c_bool

File "/Users/heiland/anaconda3/lib/python3.7/ctypes/init.py", line 377, in getattr

func = self.__getitem__(name)

File "/Users/heiland/anaconda3/lib/python3.7/ctypes/init.py", line 382, in getitem

func = self._FuncPtr((name_or_ordinal, self))

AttributeError: dlsym(0x7fbdc1b7d0c0, tpSetLogLevel): symbol not found

It seems that pip is not installing tellurium 2.2 (isn't that the latest?

$ pip uninstall tellurium

Uninstalling tellurium-2.1.5:

Would remove:

/Users/heiland/anaconda3/lib/python3.7/site-packages/tellurium-2.1.5.dist-info/*

/Users/heiland/anaconda3/lib/python3.7/site-packages/tellurium/*

And pypi seems to have 2.1.5 as the latest, not 2.2 https://pypi.org/project/tellurium/#history

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/sys-bio/tellurium/issues/442?email_source=notifications&email_token=AAIBSDWPKXLZTDP5UMDP643Q4N3PBA5CNFSM4KCWWWM2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEIGLMOQ#issuecomment-571258426, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAIBSDQFMN2J6URRMX4ALZLQ4N3PBANCNFSM4KCWWWMQ .

-- Herbert Sauro, Professor University of Washington, Bioengineering 206-685-2119, www.sys-bio.org hsauro@uw.edu Books: http://books.analogmachine.org/