I'm running Ubuntu 13.10 with Python 2.7.5+, and whenever I try to import the matplotlib package, I get an error. Specifically, my test script has only the following code:
#!/usr/bin/python
import matplotlib.pyplot as plt
When I run the test script, here is the error:
Traceback (most recent call last):
File "./test.py", line 2, in <module>
import matplotlib.pyplot as plt
File "/usr/local/lib/python2.7/dist-packages/matplotlib/pyplot.py", line 27, in <module>
import matplotlib.colorbar
File "/usr/local/lib/python2.7/dist-packages/matplotlib/colorbar.py", line 34, in <module>
import matplotlib.collections as collections
File "/usr/local/lib/python2.7/dist-packages/matplotlib/collections.py", line 27, in <module>
import matplotlib.backend_bases as backend_bases
File "/usr/local/lib/python2.7/dist-packages/matplotlib/backend_bases.py", line 56, in <module>
import matplotlib.textpath as textpath
File "/usr/local/lib/python2.7/dist-packages/matplotlib/textpath.py", line 22, in <module>
from matplotlib.mathtext import MathTextParser
File "/usr/local/lib/python2.7/dist-packages/matplotlib/mathtext.py", line 26, in <module>
from six import unichr
ImportError: cannot import name unichr
Any idea what I'm doing wrong?
You apparently have an outdated version of six.
The unichr wrapper was added in version 1.4.0, as seen in CHANGES. I'm not sure exactly when 1.4.0 was released, but the fix for issue #25 was committed on 2013-05-18, so… some time after that.
So, if you print(six.__version__), and it's anything less than '1.4.0', that's your problem.
Depending on whether you're installing packages with pip or with your system's package manager, the solution is going to be something like one of these:
$ pip install --upgrade six
$ apt-get install six
$ brew install --upgrade six
… etc.
But meanwhile, matplotlib shouldn't be requiring 1.3 but using features only available in 1.4. Your GitHub issue matplotlib#3538 should get this fixed.
Related
I'm going to preface this by saying that I'm relatively new to Python and so please forgive me if I have difficulty understanding something.
I've recently been trying to install OpenCV on my computer following the "Installing OpenCV from prebuilt binaries" instructions found here:
http://docs.opencv.org/3.1.0/d5/de5/tutorial_py_setup_in_windows.html#gsc.tab=0
I initially tried to install OpenCV by itself, as I already had Python 3.5 and a working version of numpy. However, my attempts to import cv2 failed, and I eventually decided to uninstall Python and follow all the steps listed on the website. However, I now have this error when I try import numpy:
Traceback (most recent call last):
File "C:/PythonProgramming/SLIC/src/SLICAlgorithm.py", line 1, in <module>
import numpy
File "C:\Python27\lib\site-packages\numpy\__init__.py", line 180, in <module>
from . import add_newdocs
File "C:\Python27\lib\site-packages\numpy\add_newdocs.py", line 13, in <module>
from numpy.lib import add_newdoc
File "C:\Python27\lib\site-packages\numpy\lib\__init__.py", line 4, in <module>
from type_check import *
File "C:\Python27\lib\site-packages\numpy\lib\type_check.py", line 8, in <module>
import numpy.core.numeric as _nx
File "C:\Python27\lib\site-packages\numpy\core\__init__.py", line 20, in <module>
import function_base
File "C:\Python27\lib\site-packages\numpy\core\function_base.py", line 6, in <module>
from .numeric import result_type, NaN, shares_memory, MAY_SHARE_BOUNDS, TooHardError
ImportError: cannot import name shares_memory
Process finished with exit code 1
Other people online seem to have no problem with these instructions, or at least not with numpy. What does this error mean, and what can I do to fix it? I have a 64-bit version of Windows 10 and am working in PyCharm. All help you can provide would be much appreciated.
same problem, the following fix worked for me
pip install -I numpy --force-reinstall
I got "numpy.dtype has the wrong size, try recompiling" in both pycharm and terminal when compiling Sci-kit learning. I've upgraded all packages(numpy, scikit to the latest), nothing works.Python version is 2.7. Please help. Appreciate!
checking for nltk
Traceback (most recent call last):
File "startup.py", line 6, in <module>
import nltk
File "/Library/Python/2.7/site-packages/nltk/__init__.py", line 128, in <module>
from nltk.chunk import *
File "/Library/Python/2.7/site-packages/nltk/chunk/__init__.py", line 157, in <module>
from nltk.chunk.api import ChunkParserI
File "/Library/Python/2.7/site-packages/nltk/chunk/api.py", line 13, in <module>
from nltk.parse import ParserI
File "/Library/Python/2.7/site-packages/nltk/parse/__init__.py", line 79, in <module>
from nltk.parse.transitionparser import TransitionParser
File "/Library/Python/2.7/site-packages/nltk/parse/transitionparser.py", line 21, in <module>
from sklearn.datasets import load_svmlight_file
File "/Library/Python/2.7/site-packages/sklearn/__init__.py", line 57, in <module>
from .base import clone
File "/Library/Python/2.7/site-packages/sklearn/base.py", line 11, in <module>
from .utils.fixes import signature
File "/Library/Python/2.7/site-packages/sklearn/utils/__init__.py", line 10, in <module>
from .murmurhash import murmurhash3_32
File "numpy.pxd", line 155, in init sklearn.utils.murmurhash (sklearn/utils/murmurhash.c:5029)
ValueError: numpy.dtype has the wrong size, try recompiling
The error "numpy.dtype has the wrong size, try recompiling" means that sklearn was compiled against a numpy more recent than the numpy version sklearn is now trying to import. To fix this, you need to make sure that sklearn is compiled against the version of numpy that it is now importing, or an earlier version. See ValueError: numpy.dtype has the wrong size, try recompiling for a detailed explanation.
I guess from your paths that you are using the OSX system Python (the one that ships with OSX, at /usr/bin/python). Apple has modified this Python in a way that makes it pick up its own version of numpy rather than any version that you install with pip etc - see https://github.com/MacPython/wiki/wiki/Which-Python#system-python-and-extra-python-packages . I strongly recommend you switch to Python.org or homebrew Python to make it easier to work with packages depending on numpy.
The problem occurs when you are using incompatible versions. Check the versions using:
pip freeze
or, for a specific module
pip freeze | grep Module_Name
I fix my problem by updating all packages:
pip install -U scikit-learn numpy scipy pandas matplotlib
As of Today(30/11/2016). These versions are compatible:
matplotlib==1.5.2
nltk==3.2.1
numpy==1.11.2
pandas==0.19.1
scikit-learn==0.18.1
scipy==0.18.1
textblob==0.11.1
I'm getting an ImportError whenever I try to import pyplot from matplotlib. Matplotlib is installed via pip in a virtual environment. This is the error I'm getting:
>>> import matplotlib.pyplot
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/home/mikefrank/.virtualenvs/pv-hrt/local/lib/python2.7/site-packages/matplotlib/pyplot.py", line 36, in <module>
from matplotlib.figure import Figure, figaspect
File "/home/mikefrank/.virtualenvs/pv-hrt/local/lib/python2.7/site-packages/matplotlib/figure.py", line 40, in <module>
from matplotlib.axes import Axes, SubplotBase, subplot_class_factory
File "/home/mikefrank/.virtualenvs/pv-hrt/local/lib/python2.7/site-packages/matplotlib/axes/__init__.py", line 4, in <module>
from ._subplots import *
File "/home/mikefrank/.virtualenvs/pv-hrt/local/lib/python2.7/site-packages/matplotlib/axes/_subplots.py", line 10, in <module>
from matplotlib.axes._axes import Axes
File "/home/mikefrank/.virtualenvs/pv-hrt/local/lib/python2.7/site-packages/matplotlib/axes/_axes.py", line 38, in <module>
import matplotlib.tri as mtri
File "/home/mikefrank/.virtualenvs/pv-hrt/local/lib/python2.7/site-packages/matplotlib/tri/__init__.py", line 9, in <module>
from .triangulation import *
File "/home/mikefrank/.virtualenvs/pv-hrt/local/lib/python2.7/site-packages/matplotlib/tri/triangulation.py", line 7, in <module>
import matplotlib._qhull as _qhull
ImportError: libqhull.so.5: cannot open shared object file: No such file or directory
This can occur after a system upgrade. In my specific case, I upgraded Ubuntu 14.04 to 16.04. Matplotlib links to specific versions of \*.so, and these go out of date. I presume this is because the different versions are not (always) backward compatible.
(For me, I went from libqhull.so.6 to libqhull.so.7 during the OS upgrade, and matplotlib was linked to libqhull.so.6.)
Firstly, you can probably make sure libqhull exists on your system by using something like:
sudo apt install libqhull-dev
or the equivalent for your system.
(mine was already installed, so nothing changed.)
Since nowadays, pip often installs a wheel, which is already compiled, we'll need to force pip to do the compilation, so it links with the new so file.
I used:
py35 -m pip install --upgrade matplotlib --no-binary matplotlib --force
The options:
--no-binary matplotlib tells pip to not use a wheel for matplotlib (but it may still use wheels for dependencies such as numpy).
--upgrade should be obvious
--force, because we may already be at the latest matplotlib version, and then --upgrade will not do anything.
I want to use Python for trying out hddm.
I installed anaconda, Python 2.7. When I try to follow the hddm tutorial in the command line window in spyder, the following happens, which seems to be a problem in pymc:
import pandas as pd
import matplotlib.pyplot as plt
%matplotlib inline
import hddm
Traceback (most recent call last):
File "<ipython-input-24-17365318b31c>", line 1, in <module>
import hddm
File "/Users/c/anaconda/lib/python2.7/site-packages/hddm/__init__.py", line 7, in <module>
import likelihoods
File "/Users/c/anaconda/lib/python2.7/site-packages/hddm/likelihoods.py", line 2, in <module>
import pymc as pm
File "/Users/c/anaconda/lib/python2.7/site-packages/pymc/__init__.py", line 31, in <module>
from .distributions import *
File "/Users/c/anaconda/lib/python2.7/site-packages/pymc/distributions.py", line 30, in <module>
from . import flib, utils
ImportError: cannot import name flib
I work on Mac OS X 10.7. On the web, I find some comments concerning pymc possibly not being compiled with the correct version of gfortran, but the solutions all seem to be for windows. Also, I thought that this kind of problem should not happen with an integrated system like Anaconda?
There are two options:
use conda install -c conda.binstar.org/pymc pymc
install gfortran and use pip install -U pymc
This question is related to a question here: Unable to import numpy
I ran: sudo pip install --upgrade numpy
then when I ran python and tried to import numpy I got this strange error!!! I'm going crazy!
>>> import numpy
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/__init__.py", line 153, in <module>
from . import add_newdocs
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/add_newdocs.py", line 13, in <module>
from numpy.lib import add_newdoc
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/lib/__init__.py", line 18, in <module>
from .polynomial import *
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/lib/polynomial.py", line 19, in <module>
from numpy.linalg import eigvals, lstsq, inv
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/linalg/__init__.py", line 50, in <module>
from .linalg import *
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/linalg/linalg.py", line 29, in <module>
from numpy.linalg import lapack_lite, _umath_linalg
ImportError: dlopen(/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/linalg/lapack_lite.so, 2): Symbol not found: __gfortran_compare_string
Referenced from: /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/linalg/lapack_lite.so
Expected in: flat namespace
in /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/linalg/lapack_lite.so
>>>
EDIT:
I also ran this:
$ pip show numpy
---
Name: numpy
Version: 1.8.0
Location: /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages
Requires:
The fix for me to was to manually install gcc via macports:
sudo port install gcc48
... which installs gfortran, but without the alias that numpy seems to be expecting (gfortran). Then we make a symlink:
sudo ln -s /opt/local/bin/gfortran-mp-4.8 /opt/local/bin/gfortran
After that, I uninstalled and reinstalled numpy via pip and it works like a charm.
This fixed the issue for me on mavericks last night. From what I've read, gfortran used to be part of the OS X command line tools, but isn't as of Lion or so. Installing gcc separately "fixes" that.