Undefined Symbol Error On Ubuntu

[JonnoFTW]

I'm using the latest source version version of matplotlib (I get the same error using version 2.0.0b3 from pypi). I'm running python 2.7.12 on 64 bit compiled with ucs4 and shared libraries using pyenv.

I get the following error when I try to import matplotlib.pyplot:

Python 2.7.12 (default, Jul 19 2016, 15:29:32) 
[GCC 4.8.4] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import matplotlib.pyplot as plt
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/CSEM/mack0242/.pyenv/versions/2.7.12/lib/python2.7/site-packages/matplotlib-2.0.0b3+1804.ge3fd1b1-py2.7-linux-x86_64.egg/matplotlib/pyplot.py", line 29, in <module>
    import matplotlib.colorbar
  File "/home/CSEM/mack0242/.pyenv/versions/2.7.12/lib/python2.7/site-packages/matplotlib-2.0.0b3+1804.ge3fd1b1-py2.7-linux-x86_64.egg/matplotlib/colorbar.py", line 32, in <module>
    import matplotlib.artist as martist
  File "/home/CSEM/mack0242/.pyenv/versions/2.7.12/lib/python2.7/site-packages/matplotlib-2.0.0b3+1804.ge3fd1b1-py2.7-linux-x86_64.egg/matplotlib/artist.py", line 15, in <module>
    from .transforms import (Bbox, IdentityTransform, TransformedBbox,
  File "/home/CSEM/mack0242/.pyenv/versions/2.7.12/lib/python2.7/site-packages/matplotlib-2.0.0b3+1804.ge3fd1b1-py2.7-linux-x86_64.egg/matplotlib/transforms.py", line 38, in <module>
    from matplotlib._path import (affine_transform, count_bboxes_overlapping_bbox,
ImportError: /home/CSEM/mack0242/.pyenv/versions/2.7.12/lib/python2.7/site-packages/matplotlib-2.0.0b3+1804.ge3fd1b1-py2.7-linux-x86_64.egg/matplotlib/_path.so: undefined symbol: _ZTVN10__cxxabiv120__si_class_type_infoE

Am I somehow missing a library or using the wrong library? Running ldd on _path.so gives the following output:

$ ldd /home/CSEM/mack0242/.pyenv/versions/2.7.12/lib/python2.7/site-packages/matplotlib-2.0.0b3+1804.ge3fd1b1-py2.7-linux-x86_64.egg/matplotlib/_path.so
    linux-vdso.so.1 =>  (0x00007fff4c9f3000)
    libpython2.7.so.1.0 => /home/CSEM/mack0242/.pyenv/versions/2.7.12/lib/libpython2.7.so.1.0 (0x00007f8f77bf1000)
    libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007f8f779db000)
    libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f8f777bd000)
    libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f8f773f8000)
    libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f8f771f4000)
    libutil.so.1 => /lib/x86_64-linux-gnu/libutil.so.1 (0x00007f8f76ff1000)
    libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f8f76ceb000)
    /lib64/ld-linux-x86-64.so.2 (0x00007f8f78242000)

[QuLogic]

How did you install? From wheels? That error's a C++ library incompatibility (though oddly I don't see it listed in ldd output.)

[JonnoFTW]

I installed from source and pip. Both give the same error even after I did
pip uninstall matplotlib

[WeatherGod]

What are your LD_* environment variables? Particularly, do you happen to
have LD_PRELOAD?

On Tue, Jul 19, 2016 at 4:18 AM, Jonathan Mackenzie <
notifications@github.com> wrote:

I installed from source and pip. Both give the same error even after I did
pip uninstall matplotlib

On 19 Jul 2016 5:38 PM, "Elliott Sales de Andrade" <
notifications@github.com>
wrote:

How did you install? From wheels? That error's a C++ library
incompatibility (though oddly I don't see it listed in ldd output.)

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[JonnoFTW]

I have nothing set in LD* environment variables.

[tacaswell]

I suggest running git clean -xfd in your checkout and then rebuilding. This smells like you built it, something updated at the system level, and now your binaries are out of sync but the build system is not noticing.

[JonnoFTW]

I tried that just now and got the same error. Could it be something wrong with my build system?

[tacaswell]

Did you also compile python your self?

[JonnoFTW]

Yes, I did, via pyenv. I did

PYTHON_CONFIGURE_OPTS="--enable-unicode=ucs4 --enable-shared" pyenv install -f -k 2.7.12

Which runs the following: https://github.com/yyuu/pyenv/blob/master/plugins/python-build/share/python-build/2.7.12

#require_gcc
install_package "openssl-1.0.2g" "https://www.openssl.org/source/openssl-1.0.2g.tar.gz#b784b1b3907ce39abf4098702dade6365522a253ad1552e267a9a0e89594aa33" mac_openssl --if has_broken_mac_openssl
install_package "readline-6.3" "http://ftpmirror.gnu.org/readline/readline-6.3.tar.gz#56ba6071b9462f980c5a72ab0023893b65ba6debb4eeb475d7a563dc65cafd43" standard --if has_broken_mac_readline
install_package "Python-2.7.12" "https://www.python.org/ftp/python/2.7.12/Python-2.7.12.tar.xz#d7837121dd5652a05fef807c361909d255d173280c4e1a4ded94d73d80a1f978" ldflags_dirs standard verify_py27 ensurepip

[tacaswell]

You should probably take this up on the pyenv issue tracker / mailing list.

Can you reproduce this using system python or miniconda?

[JonnoFTW]

It worked fine using using miniconda (using the conda provided binaries), though I had some issues with interactive mode.

I could not replicate this issue on a clean VM of the latest Debian. It worked fine using system python (installing via pip install --user matplotlib

[tacaswell]

Closing as this is an issue with pyenv not mpl and is difficult to replicate.