Re: [Matplotlib-users] wrong numpy version

[Benjamin R. <ben...@ou...>]

On Tue, Nov 12, 2013 at 7:37 AM, Nemanja Savic <vla...@gm...> wrote:

> Hi all guys,
>
> I am using RHEL6 and I am ploting figures throughout my project, so I
> wanted some workaroung blocking show() function call. I have found few
> solutions that use multiprocessing, so finally i finished with this:
>
> pool.map(plot_graph, c)
>
> and
>
> def plot_graph(*args):
>     plt.figure(args[0][2])
>     plt.bar(args[0][1][:-1], args[0][0], width=1)
>     plt.show()
>
> But when I have more than one figure the following error occures:
>
>
> /usr/lib64/python2.6/site-packages/matplotlib/backends/backend_gtk.py:621:
> DeprecationWarning: Use the new widget gtk.Tooltip
>   self.tooltips = gtk.Tooltips()
> /usr/lib64/python2.6/site-packages/matplotlib/backends/backend_gtk.py:621:
> DeprecationWarning: Use the new widget gtk.Tooltip
>   self.tooltips = gtk.Tooltips()
> [xcb] Unknown sequence number while processing queue
> [xcb] Most likely this is a multi-threaded client and XInitThreads has not
> been called
> [xcb] Aborting, sorry about that.
> python: xcb_io.c:273: poll_for_event: Assertion
> `!xcb_xlib_threads_sequence_lost' failed.
> runner.py: Fatal IO error 0 (Success) on X server :0.0.
>
> Since my version of matplolib doesnt support blocking = false solution, I
> wanted to install new version. For that I installed new version of numpy
> but when i run python setup.py build in matplolib foldet i get following:
>
> Edit setup.cfg to change the build options
>
> BUILDING MATPLOTLIB
>             matplotlib: yes [1.3.1]
>                 python: yes [2.6.6 (r266:84292, May 27 2013, 05:35:12)
> [GCC
>                         4.4.7 20120313 (Red Hat 4.4.7-3)]]
>               platform: yes [linux2]
>
> REQUIRED DEPENDENCIES AND EXTENSIONS
>                  numpy: yes [version 1.8.0]
>               dateutil: yes [using dateutil version 1.4.1]
>                tornado: yes [tornado was not found. It is required for the
>                         WebAgg backend. pip/easy_install may attempt to
>                         install it after matplotlib.]
>              pyparsing: yes [pyparsing was not found. It is required for
>                         mathtext support. pip/easy_install may attempt to
>                         install it after matplotlib.]
>                  pycxx: yes [Couldn't import.  Using local copy.]
>                 libagg: yes [pkg-config information for 'libagg' could not
>                         be found. Using local copy.]
>               freetype: yes [version 9.22.3]
>                    png: yes [version 1.2.49]
>
> OPTIONAL SUBPACKAGES
>            sample_data: yes [installing]
>               toolkits: yes [installing]
>                  tests: yes [nose 0.11.1 or later is required to run the
>                         matplotlib test suite]
>
> OPTIONAL BACKEND EXTENSIONS
>                 macosx: no  [Mac OS-X only]
>                 qt4agg: yes [installing, Qt: 4.6.2, PyQt4: 4.6.2]
>                gtk3agg: no  [Requires pygobject to be installed.]
>              gtk3cairo: no  [Requires pygobject to be installed.]
>                 gtkagg: yes [installing, Gtk: 2.18.9 pygtk: 2.16.0]
>                  tkagg: yes [installing, version 73770]
>                  wxagg: yes [installing, version 2.8.12.0]
>                    gtk: yes [installing, Gtk: 2.18.9 pygtk: 2.16.0]
>                    agg: yes [installing]
>                  cairo: yes [installing, version 1.8.6]
>              windowing: no  [Microsoft Windows only]
>
> OPTIONAL LATEX DEPENDENCIES
>                 dvipng: yes [version 1.14]
>            ghostscript: yes [version 8.70]
>                  latex: yes [version 3.1415926]
>                pdftops: no
>
> Traceback (most recent call last):
>   File "setup.py", line 268, in <module>
>     **extra_args
>   File "/usr/lib64/python2.6/distutils/core.py", line 113, in setup
>     _setup_distribution = dist = klass(attrs)
>   File "build/bdist.linux-x86_64/egg/setuptools/dist.py", line 221, in
> __init__
>   File "build/bdist.linux-x86_64/egg/setuptools/dist.py", line 245, in
> fetch_build_eggs
>   File "build/bdist.linux-x86_64/egg/pkg_resources.py", line 592, in
> resolve
>     plugin_projects.sort()  # scan project names in alphabetic order
> pkg_resources.VersionConflict: (numpy 1.4.1
> (/usr/lib64/python2.6/site-packages), Requirement.parse('numpy>=1.5'))
>
> When I run python and check numpy version it is indeed 1.8.0, but
> matplotlib buils script somehow founded older one.
>
>
> I would be really happy if somebody can help me overcome problem with many
> figures.
>
> Best and cheers
>
>
The issue is rather complex, and it is a very difficult one to solve on our
end. What is happening is that in order to build matplotlib from source,
you need to compile against the numpy headers at build-time. Unfortunately,
python packaging being what it is, there is difficulty in making sure that
the version of numpy that will be installed is the version used for the
build. You seem to have numpy installed both at the system level and
possibly at the user level. If possible, I would try removing numpy from
your system level (and that likely means removing any other installed
package that depends on it, and reinstalling via source).

Ben Root