python - matplotlib and libpng issues with ipython notebook

Question

I was trying to use ipython notebook . I installed all the dependency libraries. However, I cannot use either the "--pylab=inline" option when launching ipython or "savefig" function in the Ipython console. When I tried to do either of them, an error message was returned "RuntimeError: Could not create write struct" resulting from execution of matplotlib. Also, a warning from the notebookApp prompt said "libpng warning: Application built with libpng-1.2.41 but running with 1.5.13".

However, I installed the newest libpng(1.5.13), uninstalled matplotlib with pip uninstall and reinstalled matplotlib with pip install (and during the build process, I can see that libpng1.5.13 is used for the building of matplotlib).

The configuration for my system is Mac OS X10.6, python2.7. Anybody has similar experience or some suggestiongs?

Here are the traceback errors:

[<matplotlib.lines.Line2D at 0x106066d50>]
---------------------------------------------------------------------------
RuntimeError                              Traceback (most recent call last)
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/IPython/zmq/pylab/backend_inline.pyc in show(close)
    100     try:
    101         for figure_manager in Gcf.get_all_fig_managers():
--> 102             send_figure(figure_manager.canvas.figure)
    103     finally:
    104         show._to_draw = []

/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/IPython/zmq/pylab/backend_inline.pyc in send_figure(fig)
    209     """
    210     fmt = InlineBackend.instance().figure_format
--> 211     data = print_figure(fig, fmt)
    212     # print_figure will return None if there's nothing to draw:
    213     if data is None:

/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/IPython/core/pylabtools.pyc in print_figure(fig, fmt)
    102     try:
    103         bytes_io = BytesIO()
--> 104         fig.canvas.print_figure(bytes_io, format=fmt, bbox_inches='tight')
    105         data = bytes_io.getvalue()
    106     finally:

/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib/backend_bases.pyc in print_figure(self, filename, dpi, facecolor, edgecolor, orientation, format, **kwargs)
   2050                     orientation=orientation,
   2051                     dryrun=True,
-> 2052                     **kwargs)
   2053                 renderer = self.figure._cachedRenderer
   2054                 bbox_inches = self.figure.get_tightbbox(renderer)

/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib/backends/backend_agg.pyc in print_png(self, filename_or_obj, *args, **kwargs)
    501             _png.write_png(renderer._renderer.buffer_rgba(),
    502                            renderer.width, renderer.height,
--> 503                            filename_or_obj, self.figure.dpi)
    504         finally:
    505             if close:

RuntimeError: Could not create write struct

Thanks a lot,

Jie

Answer 1

I had this same problem on OS X Mavericks with libpng installed via homebrew and also XQuartz installed. It turned out matplotlib was finding the older XQuartz libpng version when compiling, but finding the more recent homebrew libpng at runtime.

The best solution I've found is from this comment by jaengelberg on github: Uninstall matplotlib, temporarily rename the XQuartz libpng headers so they can't be found, install matplotlib, then change the header names back.

Here it is in full:

pip uninstall matplotlib
cd /opt/X11/include/libpng15
sudo mv png.h _png.h
sudo mv pngconf.h _pngconf.h
sudo mv pnglibconf.h _pnglibconf.h
pip install matplotlib
sudo mv _png.h png.h
sudo mv _pngconf.h pngconf.h
sudo mv _pnglibconf.h pnglibconf.h