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egpbos opened this issue Apr 9, 2018 · 5 comments
Closed

Development build: symbol not found in _path module #11006

egpbos opened this issue Apr 9, 2018 · 5 comments

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@egpbos
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egpbos commented Apr 9, 2018

Bug report

Bug summary

On a development build from source, I cannot run the ticks_and_spines/tick-locators.py example, because I get a symbol not found error due to the _path module.

Code for reproduction

python examples/ticks_and_spines/tick-locators.py

Actual outcome

Traceback (most recent call last):
  File "examples/ticks_and_spines/tick-locators.py", line 10, in <module>
    import matplotlib.pyplot as plt
  File "/Users/pbos/sw/src/git/matplotlib/lib/matplotlib/pyplot.py", line 29, in <module>
    import matplotlib.colorbar
  File "/Users/pbos/sw/src/git/matplotlib/lib/matplotlib/colorbar.py", line 28, in <module>
    import matplotlib.artist as martist
  File "/Users/pbos/sw/src/git/matplotlib/lib/matplotlib/artist.py", line 16, in <module>
    from .path import Path
  File "/Users/pbos/sw/src/git/matplotlib/lib/matplotlib/path.py", line 17, in <module>
    from . import _path, rcParams
ImportError: dlopen(/Users/pbos/sw/src/git/matplotlib/lib/matplotlib/_path.cpython-36m-darwin.so, 2): Symbol not found: __ZNSs4_Rep20_S_empty_rep_storageE
  Referenced from: /Users/pbos/sw/src/git/matplotlib/lib/matplotlib/_path.cpython-36m-darwin.so
  Expected in: flat namespace
 in /Users/pbos/sw/src/git/matplotlib/lib/matplotlib/_path.cpython-36m-darwin.so

Expected outcome

A plot with the tick locators. I am able to produce this plot with the conda-installed matplotlib in my default environment.

Matplotlib version

  • Operating system: macOS High Sierra (10.13.3)
  • Matplotlib version: master
  • Matplotlib backend (print(matplotlib.get_backend())): MacOSX
  • Python version: 3.6.5 |Anaconda, Inc.| (default, Mar 29 2018, 13:14:23) [GCC 4.2.1 Compatible Clang 4.0.1 (tags/RELEASE_401/final)] on darwin

I built matplotlib from source. The build setup output:

    BUILDING MATPLOTLIB
                matplotlib: yes [1.5.1+9314.gade70d705.dirty]
                    python: yes [3.6.5 |Anaconda, Inc.| (default, Mar 29 2018,
                            13:14:23)  [GCC 4.2.1 Compatible Clang 4.0.1
                            (tags/RELEASE_401/final)]]
                  platform: yes [darwin]

    REQUIRED DEPENDENCIES AND EXTENSIONS
                     numpy: yes [version 1.14.2]
          install_requires: yes [handled by setuptools]
                    libagg: yes [pkg-config information for 'libagg' could not
                            be found. Using local copy.]
                  freetype: yes [version 2.9.0]
                       png: yes [version 1.6.34]
                     qhull: yes [pkg-config information for 'libqhull' could not
                            be found. Using local copy.]

    OPTIONAL SUBPACKAGES
               sample_data: yes [installing]
                  toolkits: yes [installing]
                     tests: no  [skipping due to configuration]
            toolkits_tests: no  [skipping due to configuration]

    OPTIONAL BACKEND EXTENSIONS
                    macosx: yes [installing, darwin]
                    qt5agg: no  [PySide2 not found; PyQt5 not found]
                    qt4agg: no  [PySide not found; PyQt4 not found]
                   gtk3agg: no  [Requires pygobject to be installed.]
                 gtk3cairo: no  [Requires cairocffi or pycairo to be installed.]
                     tkagg: yes [installing; run-time loading from Python Tcl /
                            Tk]
                     wxagg: no  [requires wxPython]
                       agg: yes [installing]
                     cairo: no  [cairocffi or pycairo not found]
                 windowing: no  [Microsoft Windows only]

    OPTIONAL PACKAGE DATA
                      dlls: no  [skipping due to configuration]
@egpbos
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egpbos commented Apr 9, 2018

Changing backend does not help (default was macosx, also tried Agg and TkAgg).

@egpbos
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egpbos commented Apr 9, 2018

A bit more info on the environment setup. I first clone and enter the matplotlib repo directory. Then I build the conda env:

conda create -n mpl_dev matplotlib clang libpng freetype
conda activate mpl_dev
conda uninstall matplotlib
rehash  # or hash -r for bash, I'm on zsh

I then build, but specify the compilers manually, to make sure it doesn't accidentally pick up some MacPorts or system gcc version:

export CC=clang
export CXX=clang
python -mpip install -e .

I also tried everything using pythonw (conda install python.app), but this gives the same result. Also tried installing without the -e flag, again same result.

@QuLogic
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QuLogic commented Apr 9, 2018 

           matplotlib: yes [1.5.1+9314.gade70d705.dirty]

Commit ade70d7 does not exist. There were also less than 9314 commits between 1.5.1 and 2.2.2, so your clone is out-of-date. Please fetch upstream tags to get a reasonable version number.

export CXX=clang

This should be CXX=clang++.

@egpbos
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egpbos commented Apr 9, 2018

@QuLogic I was indeed wondering about that, thanks for the tip. I did have the latest commits, just not the tags.

The clang++ tip did the trick though, thanks a lot!

For completeness' sake:

  • I installed it using conda install clangxx.
  • After that I got the RuntimeError: Python is not installed as a framework. which is due to the macosx backend. Running with pythonw (installed with conda install python.app) fixes that and runs the test again.

@egpbos egpbos closed this as completed Apr 9, 2018
@egpbos
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egpbos commented Apr 9, 2018

Just to summarize, here's what I need to get it correctly installed from scratch (inside a clean matplotlib clone):

conda create -n mpl_dev matplotlib clang clangxx libpng freetype pkg-config python.app
conda activate mpl_dev
conda uninstall matplotlib
export CC=clang
export CXX=clang++
python -mpip install -e .

And then run with pythonw to use the macosx backend (or switch to Agg or TkAgg in matplotlibrc).

@egpbos egpbos mentioned this issue Apr 9, 2018
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@QuLogic @egpbos