ImportError when importing hddm/pymc in python
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Debbie Yee
Feb 4, 2018, 3:42:02 PM2/4/18
to hddm-users
Hi,
I am trying to install/setup hddm, and am running into some hurdles. I've installed hddm using anaconda and set up a separate environment. Using anaconda I installed hddm (using the code suggestion from this thread: https://groups.google.com/forum/#!topic/hddm-users/dXiP5-hlbVo) as well as jupyter. I am able to use jupyter fine, but I am running into errors when trying trying to import the both hddm and pymc packages (see below). I think there appears to be some issue with referencing libgcc, but I am not sure how it exactly relates to flib.go from the pymc package. I've tried importing other packages like scipy and numpy, and there is no problem with importing the other packages in the environment i the juypter notebook, so I suspect it is specific to pymc.
Does anyone have any suggestions for how to debug this issue? I'm currently running this on Mac OSX high sierra (10.13.2), and I've listed the output of some of the errors below. Any suggestions would be much appreciated!
Thanks,
Debbie
When I try "import hddm", using the ipython jupyter notebook, this is there error that I get:
--------------------------------------------------------------------------- ImportError Traceback (most recent call last) <ipython-input-2-e6207c669271> in <module>() ----> 1 import hddm /anaconda3/envs/onlyhddm2/lib/python3.5/site-packages/hddm/__init__.py in <module>() 5 __version__ = '0.6.0' 6 ----> 7 from . import likelihoods 8 from . import generate 9 from . import utils /anaconda3/envs/onlyhddm2/lib/python3.5/site-packages/hddm/likelihoods.py in <module>() 1 ----> 2 import pymc as pm 3 import numpy as np 4 from scipy import stats 5 /anaconda3/envs/onlyhddm2/lib/python3.5/site-packages/pymc/__init__.py in <module>() 28 from .PyMCObjects import * 29 from .InstantiationDecorators import * ---> 30 from .CommonDeterministics import * 31 from .NumpyDeterministics import * 32 from .distributions import * /anaconda3/envs/onlyhddm2/lib/python3.5/site-packages/pymc/CommonDeterministics.py in <module>() 19 import inspect 20 import types ---> 21 from .utils import safe_len, stukel_logit, stukel_invlogit, logit, invlogit, value, find_element 22 from copy import copy 23 import sys /anaconda3/envs/onlyhddm2/lib/python3.5/site-packages/pymc/utils.py in <module>() 12 from copy import copy 13 from .PyMCObjects import Variable ---> 14 from . import flib 15 import pdb 16 from numpy.linalg.linalg import LinAlgError ImportError: dlopen(/anaconda3/envs/onlyhddm2/lib/python3.5/site-packages/pymc/flib.so, 2): Library not loaded: /usr/local/lib/libgcc_s.1.dylib Referenced from: /anaconda3/envs/onlyhddm2/lib/python3.5/site-packages/pymc/flib.so Reason: image not found
When I try to "import pymc" using the same ipython jupyter notebook, this is the error that I get:
--------------------------------------------------------------------------- ImportError Traceback (most recent call last) <ipython-input-1-be432c90d05f> in <module>() ----> 1 import pymc /anaconda3/envs/onlyhddm2/lib/python3.5/site-packages/pymc/__init__.py in <module>() 28 from .PyMCObjects import * 29 from .InstantiationDecorators import * ---> 30 from .CommonDeterministics import * 31 from .NumpyDeterministics import * 32 from .distributions import * /anaconda3/envs/onlyhddm2/lib/python3.5/site-packages/pymc/CommonDeterministics.py in <module>() 19 import inspect 20 import types ---> 21 from .utils import safe_len, stukel_logit, stukel_invlogit, logit, invlogit, value, find_element 22 from copy import copy 23 import sys /anaconda3/envs/onlyhddm2/lib/python3.5/site-packages/pymc/utils.py in <module>() 12 from copy import copy 13 from .PyMCObjects import Variable ---> 14 from . import flib 15 import pdb 16 from numpy.linalg.linalg import LinAlgError ImportError: dlopen(/anaconda3/envs/onlyhddm2/lib/python3.5/site-packages/pymc/flib.so, 2): Library not loaded: /usr/local/lib/libgcc_s.1.dylib Referenced from: /anaconda3/envs/onlyhddm2/lib/python3.5/site-packages/pymc/flib.so Reason: image not found
------------------------------------------------------------------------------------------
Just for good measure, I also checked all of the packages to make sure they were up to date. Here is a listing of the packages in the environment when I type "conda list."
# packages in environment at /anaconda3/envs/onlyhddm2:
#
appnope 0.1.0 py35hd172556_0
bleach 2.1.2 py35_0
ca-certificates 2017.08.26 ha1e5d58_0
certifi 2018.1.18 py35_0
cycler 0.10.0 py35hb89929e_0
dbus 1.12.2 haa0f8f7_0
decorator 4.2.1 py35_0
entrypoints 0.2.3 py35h837ec6f_2
expat 2.2.5 hb8e80ba_0
freetype 2.8 h12048fb_1
gettext 0.19.8.1 h15daf44_3
glib 2.53.6 h33f6a65_2
hddm 0.6.0 py35_0 pymc
html5lib 1.0.1 py35h2f9c1c0_0
icu 58.2 h4b95b61_1
intel-openmp 2018.0.0 h8158457_8
ipykernel 4.8.0 py35_0
ipython 6.2.1 py35h9470683_1
ipython_genutils 0.2.0 py35hf129286_0
ipywidgets 7.1.1 py35_0
jedi 0.11.1 py35_0
jinja2 2.10 py35h6ff70ae_0
jpeg 9b he5867d9_2
jsonschema 2.6.0 py35h2dd9e4b_0
jupyter 1.0.0 py35hf3a1ed8_0
jupyter_client 5.2.2 py35_0
jupyter_console 5.2.0 py35hd2aa692_1
jupyter_core 4.4.0 py35h4ad9194_0
kabuki 0.6.1 py35_0 pymc
libcxx 4.0.1 h579ed51_0
libcxxabi 4.0.1 hebd6815_0
libedit 3.1 hb4e282d_0
libffi 3.2.1 h475c297_4
libgcc 4.8.5 hdbeacc1_10
libgfortran 3.0.1 h93005f0_2
libiconv 1.15 hdd342a3_7
libpng 1.6.34 he12f830_0
libsodium 1.0.15 hd9e47c5_0
markupsafe 1.0 py35h9ba0a7f_1
matplotlib 2.1.2 py35h6d6146d_0
mistune 0.8.3 py35_0
mkl 2017.0.4 h1fae6ae_0
nbconvert 5.3.1 py35h63fb950_0
nbformat 4.4.0 py35h41c2038_0
ncurses 6.0 hd04f020_2
notebook 5.4.0 py35_0
numpy 1.11.3 py35_0
openssl 1.0.2n hdbc3d79_0
pandas 0.22.0 py35h0a44026_0
pandoc 1.19.2.1 ha5e8f32_1
pandocfilters 1.4.2 py35hff87490_1
parso 0.1.1 py35hbda7c10_0
patsy 0.5.0 py35_0
pcre 8.41 hfb6ab37_1
pexpect 4.3.1 py35_0
pickleshare 0.7.4 py35h9517181_0
pip 9.0.1 py35h33ce766_4
prompt_toolkit 1.0.15 py35h93950c5_0
ptyprocess 0.5.2 py35hfc37984_0
pygments 2.2.0 py35h392a662_0
pymc 2.3.6 np111py35_2
pyparsing 2.2.0 py35h31fab04_0
pyqt 5.6.0 py35hbd126f6_6
python 3.5.0 1
python-dateutil 2.6.1 py35h10515e0_1
pytz 2017.3 py35heeb7564_0
pyzmq 16.0.3 py35hab9903b_0
qt 5.6.2 h9975529_14
qtconsole 4.3.1 py35hd6d667b_0
readline 6.2 2
scipy 0.19.0 np111py35_0
send2trash 1.4.2 py35_0
setuptools 38.4.0 py35_0
simplegeneric 0.8.1 py35h0a3d746_0
sip 4.18.1 py35h79e1f92_2
six 1.11.0 py35h39a4c60_1
sqlite 3.22.0 h3efe00b_0
terminado 0.8.1 py35_1
testpath 0.3.1 py35hf8009f4_0
tk 8.5.18 0
tornado 4.5.3 py35_0
traitlets 4.3.2 py35hd3d1486_0
wcwidth 0.1.7 py35hdd0c235_0
webencodings 0.5.1 py35hcf8ebf9_1
wheel 0.30.0 py35h5c0b906_1
widgetsnbextension 3.1.0 py35_0
xz 5.0.5 1
zeromq 4.2.2 ha360ad0_2
zlib 1.2.11 hf3cbc9b_2
Thomas Wiecki
Feb 5, 2018, 6:38:50 AM2/5/18
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Hi Debbie,
Can you just run `conda install pymc` and then try again?--
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Debbie Yee
Feb 5, 2018, 11:39:56 AM2/5/18
to hddm-users
I just tried that. it tells me that all the requested packages are already installed. I still get the same errors when trying to import hddm and pymc in python/jupyter.
debbieyee$ conda install pymc
Solving environment: done
==> WARNING: A newer version of conda exists. <==
current version: 4.4.7
latest version: 4.4.8
Please update conda by running
$ conda update -n base conda
# All requested packages already installed.
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Thomas Wiecki
Feb 6, 2018, 5:19:39 AM2/6/18
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Maybe try uninstalling pymc and hddm, then conda install pymc and conda install -c pymc hddm (and hope that it doesn't pick up the older pymc version)
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Debbie Yee
Feb 7, 2018, 11:41:46 AM2/7/18
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I had tried uninstalling and re-installing initially, but I don't think that pymc and hddm were out of date.
After a bit of fishing around, I found that the "libgcc_s.1.dylib" file did not exist in the location that pymc was referencing. I am not sure if it was something weird about the settings on my computer or whether this was a mac thing, but I found another one of these files and copied it over to the directory that pymc was searching in. It resolved the import issues.
Thanks for your help!
Debbie Yee
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Sean Cavanagh
Jul 18, 2018, 4:33:49 PM7/18/18
to hddm-users
Hi Debbie,
I'm posting because I seem to be having a similar problem to the one you had. By any chance, do you remember any more details about how you debugged this? Like where the file "libgcc_s.1.dylib" was, and where you moved it to? I've posted the error message on my PC below.
I'm posting because I seem to be having a similar problem to the one you had. By any chance, do you remember any more details about how you debugged this? Like where the file "libgcc_s.1.dylib" was, and where you moved it to? I've posted the error message on my PC below.
Thanks for your help,
Sean
runfile('C:/Users/scavanagh/Desktop/Python101SC.py', wdir='C:/Users/scavanagh/Desktop')
Traceback (most recent call last):
File "<ipython-input-2-1768f83d48dd>", line 1, in <module>
runfile('C:/Users/scavanagh/Desktop/Python101SC.py', wdir='C:/Users/scavanagh/Desktop')
File "C:\Users\scavanagh\AppData\Local\Continuum\anaconda3\lib\site-packages\spyder\utils\site\sitecustomize.py", line 705, in runfile
execfile(filename, namespace)
File "C:\Users\scavanagh\AppData\Local\Continuum\anaconda3\lib\site-packages\spyder\utils\site\sitecustomize.py", line 102, in execfile
exec(compile(f.read(), filename, 'exec'), namespace)
File "C:/Users/scavanagh/Desktop/Python101SC.py", line 10, in <module>
import hddm
File "C:\Users\scavanagh\AppData\Local\Continuum\anaconda3\lib\site-packages\hddm\__init__.py", line 7, in <module>
from . import likelihoods
File "C:\Users\scavanagh\AppData\Local\Continuum\anaconda3\lib\site-packages\hddm\likelihoods.py", line 2, in <module>
import pymc as pm
File "C:\Users\scavanagh\AppData\Local\Continuum\anaconda3\lib\site-packages\pymc\__init__.py", line 30, in <module>
from .CommonDeterministics import *
File "C:\Users\scavanagh\AppData\Local\Continuum\anaconda3\lib\site-packages\pymc\CommonDeterministics.py", line 21, in <module>
from .utils import safe_len, stukel_logit, stukel_invlogit, logit, invlogit, value, find_element
File "C:\Users\scavanagh\AppData\Local\Continuum\anaconda3\lib\site-packages\pymc\utils.py", line 14, in <module>
from . import flib
ImportError: DLL load failed: The specified procedure could not be found.
Debbie Yee
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