[Matplotlib-users] Problem building Matplotlib 1.3.1 on linux (CentOS 5.9 AMD64)

2013-12-10 Thread Guillermo-Nicolas Guénon Díaz 
Hello,

I'm having an issue building Matplotlib. In reality the build process
finishes without error, but afterwards I get this error when importing
pyplot:

[kpi@dev-outils lib.linux-x86_64-3.3]$ python3.3
Python 3.3.2 (default, Sep 17 2013, 10:40:41)
[GCC 4.4.7 20120313 (Red Hat 4.4.7-1)] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import matplotlib
>>> import matplotlib.pyplot as plt
Traceback (most recent call last):
  File "", line 1, in 
  File "./matplotlib/pyplot.py", line 24, in 
import matplotlib.colorbar
  File "./matplotlib/colorbar.py", line 27, in 
import matplotlib.artist as martist
  File "./matplotlib/artist.py", line 8, in 
from .transforms import Bbox, IdentityTransform, TransformedBbox, \
  File "./matplotlib/transforms.py", line 35, in 
from matplotlib._path import (affine_transform,
count_bboxes_overlapping_bbox,
*ImportError: ./matplotlib/_path.cpython-33m.so
: undefined symbol:
_ZSt16__ostream_insertIcSt11char_traitsIcEERSt13basic_ostreamIT_T0_ES6_PKS3_l*


I don't know a thing about building C extensions, but if I understood
correctly some pasts posts in this list and others, this problem might be
caused by a library that is compiled with an incompatible version of GCC.
My first suspect was freetype, so I downloaded and compiled v2.4.12 using
gcc44 (which is the same compiler I used to build python3.3 and matplotlib).
But the problem persists... My question is: *how can I know wich library is
causing the issue, so I could recompile it?*

Or, if I am completely missing the root cause, thank you for steering me in
the correct direction :-)

More detailed info follows. Thank you for your help !

Nicolas


Here is the information asked for in the troubleshooting FAQ:

[kpi@dev-outils matplotlib]$ uname -a
Linux dev-outils.admin.mt.lan 2.6.18-348.16.1.el5 #1 SMP Wed Aug 21
04:00:25 EDT 2013 x86_64 x86_64 x86_64 GNU/Linux

[kpi@dev-outils matplotlib]$ cat /etc/redhat-release
CentOS release 5.9 (Final)

But please, note that I am using a Python version built by myself (not the
version that comes with CenOS 5.9) using gcc 4.4.7 (and not gcc 4.1.2)

[kpi@dev-outils matplotlib]$ gcc44 -v
Using built-in specs.
Target: x86_64-redhat-linux6E
Configured with: ../configure --prefix=/usr --mandir=/usr/share/man
--infodir=/usr/share/info
--with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap
--enable-shared --enable-threads=posix --enable-checking=release
--with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions
--disable-gnu-unique-object --with-as=/usr/libexec/binutils220/as
--enable-languages=c,c++,fortran --disable-libgcj
--with-mpfr=/builddir/build/BUILD/gcc-4.4.7-20120601/obj-x86_64-redhat-linux6E/mpfr-install/
--with-ppl=/builddir/build/BUILD/gcc-4.4.7-20120601/obj-x86_64-redhat-linux6E/ppl-install
--with-cloog=/builddir/build/BUILD/gcc-4.4.7-20120601/obj-x86_64-redhat-linux6E/cloog-install
--with-tune=generic --with-arch_32=i586 --build=x86_64-redhat-linux6E
Thread model: posix
gcc version 4.4.7 20120313 (Red Hat 4.4.7-1) (GCC)

[kpi@dev-outils lib.linux-x86_64-3.3]$ python3.3
Python 3.3.2 (default, Sep 17 2013, 10:40:41)
[GCC 4.4.7 20120313 (Red Hat 4.4.7-1)] on linux
>>> matplotlib.__version__
'1.3.1'

Here is what I modified in setup.cfg last time (but I also tried with an
unmodified version with the same results):

[gui_support]
agg = True
cairo = False
gtk = False
gtk3agg = False
gtk3cairo = False
gtkagg = False
macosx = False
pyside = False
qt4agg = False
tkagg = False
windowing = False
wxagg = False

[rc_options]
backend = Agg

I didn't modify any other config file. Here is the output of the build
process:


[kpi@dev-outils matplotlib-1.3.1]$ python3.3 setup.py build

Edit setup.cfg to change the build options

BUILDING MATPLOTLIB
matplotlib: yes [1.3.1]
python: yes [3.3.2 (default, Sep 17 2013, 10:40:41)  [GCC
4.4.7 20120313 (Red Hat 4.4.7-1)]]
  platform: yes [linux]

REQUIRED DEPENDENCIES AND EXTENSIONS
 numpy: yes [version 1.8.0]
  dateutil: yes [using dateutil version 2.2]
   tornado: yes [using tornado version 3.1.1]
 pyparsing: yes [using pyparsing version 2.0.1]
 pycxx: yes [Official versions of PyCXX are not compatible
with Python 3.x.  Using local copy]
libagg: yes [pkg-config information for 'libagg' could not
be found. Using local copy.]
  freetype: yes [version 16.1.10]
   png: yes [version 1.2.10]

OPTIONAL SUBPACKAGES
   sample_data: yes [installing]
  toolkits: yes [installing]
 tests: yes [using nose version 1.3.0]

OPTIONAL BACKEND EXTENSIONS
macosx: no  [skipping due to configuration]
qt4agg: n

Re: [Matplotlib-users] problem building matplotlib

2010-09-15 Thread Eric Firing 
On 09/15/2010 01:17 PM, Dan Kortschak wrote:
> That fixes the problem.
>
> thanks
>
> On Wed, 2010-09-15 at 07:30 -1000, Eric Firing wrote:
>
>> Looking again at the original build output, and at setup.py and
>> setupext.py, it appears that there is a bug in the latter.  If the wrong
>> version of wx is found, it should be disabling the attempt to build
>> wxagg, and reporting "wxPython: no".
>>
>> We need to fix the bug, but the workaround for now is to use a setup.cfg
>> file with
>>
>> wxagg = False
>>
>> Eric

It turns out that the _wxagg extension was specific to version 2.6, and 
for a long time we have required version 2.8, so there was no point in 
trying to build the extension.  In svn 8702 I removed the extension 
along with related 2.6-only code, and the setup.py references to 
building the extension.

Eric

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Re: [Matplotlib-users] problem building matplotlib

2010-09-15 Thread Dan Kortschak 
That fixes the problem.

thanks

On Wed, 2010-09-15 at 07:30 -1000, Eric Firing wrote:

> Looking again at the original build output, and at setup.py and 
> setupext.py, it appears that there is a bug in the latter.  If the wrong 
> version of wx is found, it should be disabling the attempt to build 
> wxagg, and reporting "wxPython: no".
> 
> We need to fix the bug, but the workaround for now is to use a setup.cfg 
> file with
> 
> wxagg = False
> 
> Eric



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Re: [Matplotlib-users] problem building matplotlib

2010-09-15 Thread Eric Firing 
On 09/15/2010 03:50 AM, Benjamin Root wrote:
> On Wed, Sep 15, 2010 at 5:34 AM, Dan Kortschak
> mailto:dan.kortsc...@adelaide.edu.au>>
> wrote:
>
> I've just has a look at that and unfortunately it does not fix the
> problem
>
> Is there any other suggestion that might be worth a try?
>
> I should point out that I already have numpy 1.4.1 installed and scipy
> 0.8.0 as dependencies for other packages.
>
> thanks
> Dan
>
>
> Hmm, that shouldn't be an issue.  Maybe you need to completely clean out
> the matplotlib build (by removing the build directory) and try again?
> Be sure to save the build output so we can see what happens if/when it
> fails.

Looking again at the original build output, and at setup.py and 
setupext.py, it appears that there is a bug in the latter.  If the wrong 
version of wx is found, it should be disabling the attempt to build 
wxagg, and reporting "wxPython: no".

We need to fix the bug, but the workaround for now is to use a setup.cfg 
file with

wxagg = False

Eric


>
> Ben Root
>
>
>
> --
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Re: [Matplotlib-users] problem building matplotlib

2010-09-15 Thread Benjamin Root 
On Wed, Sep 15, 2010 at 5:34 AM, Dan Kortschak <
dan.kortsc...@adelaide.edu.au> wrote:

> I've just has a look at that and unfortunately it does not fix the
> problem
>
> Is there any other suggestion that might be worth a try?
>
> I should point out that I already have numpy 1.4.1 installed and scipy
> 0.8.0 as dependencies for other packages.
>
> thanks
> Dan
>
>
Hmm, that shouldn't be an issue.  Maybe you need to completely clean out the
matplotlib build (by removing the build directory) and try again?  Be sure
to save the build output so we can see what happens if/when it fails.

Ben Root
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Re: [Matplotlib-users] problem building matplotlib

2010-09-15 Thread Dan Kortschak 
I've just has a look at that and unfortunately it does not fix the
problem

Is there any other suggestion that might be worth a try?

I should point out that I already have numpy 1.4.1 installed and scipy
0.8.0 as dependencies for other packages.

thanks
Dan

On Tue, 2010-09-14 at 21:42 -1000, Eric Firing wrote:
> Since you you are running ubuntu, I suggest 
> you use the installation method recently described in this thread:
> 
> http://www.mail-archive.com/matplotlib-users@lists.sourceforge.net/msg18464.html
> 
> Be careful to read down through the thread; the first try at 
> comprehensive instructions has an error.



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Re: [Matplotlib-users] problem building matplotlib

2010-09-15 Thread Dan Kortschak 
Thanks Eric,

The gui dependencies are secondary, but I will look into that. Since
they are optional, the absence of them should not be the cause of the
failure, but it looks like it might be. Is that the case?

cheers
Dan

On Tue, 2010-09-14 at 21:42 -1000, Eric Firing wrote:
> On 09/14/2010 01:36 PM, Dan Kortschak wrote:
> > Hello,
> >
> > I just tried to have just tried to build matplotlib, but it fails - and
> > is unable to find wxPython (looking under 2.8 rather than 2.6 where is
> > lives - installed from source) or libgtk-2 headers (installed from apt
> > repo).
> >
> > Can anyone suggest how to resolve these issues?
> 
> If you want to use wx, you need 2.8.  It looks like you don't have any 
> of the gui dependencies.   Since you you are running ubuntu, I suggest 
> you use the installation method recently described in this thread:
> 
> http://www.mail-archive.com/matplotlib-users@lists.sourceforge.net/msg18464.html
> 
> Be careful to read down through the thread; the first try at 
> comprehensive instructions has an error.
> 
> Eric



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Re: [Matplotlib-users] problem building matplotlib

2010-09-15 Thread Eric Firing 
On 09/14/2010 01:36 PM, Dan Kortschak wrote:
> Hello,
>
> I just tried to have just tried to build matplotlib, but it fails - and
> is unable to find wxPython (looking under 2.8 rather than 2.6 where is
> lives - installed from source) or libgtk-2 headers (installed from apt
> repo).
>
> Can anyone suggest how to resolve these issues?

If you want to use wx, you need 2.8.  It looks like you don't have any 
of the gui dependencies.   Since you you are running ubuntu, I suggest 
you use the installation method recently described in this thread:

http://www.mail-archive.com/matplotlib-users@lists.sourceforge.net/msg18464.html

Be careful to read down through the thread; the first try at 
comprehensive instructions has an error.

Eric


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Re: [Matplotlib-users] Problem building matplotlib

2006-10-30 Thread John Hunter 
> "Eric" == Eric Firing <[EMAIL PROTECTED]> writes:

>> I am trying to build Matplotlib 0.87.7 on an RHEL 4.4-derived
>> system, with Python 2.3.4. I am running into a weird
>> problem. When I do "python setup.py build", I get the following
>> error:

It looks like this bug

http://matplotlib.sourceforge.net/faq.html#PYGTK24


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Re: [Matplotlib-users] Problem building matplotlib

2006-10-28 Thread José Matos 
On 28/10/06, Eric Firing <[EMAIL PROTECTED]> wrote:
>
> The error is not in matplotlib, it is in a pygtk header file, which is
> presumably coming from a Redhat package.  I don't know why it is

  True.

> happening or what the best solution is, though.  It looks like the
> pygobject.h that I have has "typename_", not "typename", so I am
> thinking maybe this is a pygtk bug, since fixed, in which "typename" is
> in conflict with something.

  C++, typename is a reserved word there.

  You might try editing your copy of
> pygobject.h, adding the trailing underscore to "typename" on both lines
> where it occurs.  It can't hurt; these are just dummy variable names.

  That is the solution, and you say the same that was adopted by the
project to solve the problem.

> Eric


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Re: [Matplotlib-users] Problem building matplotlib

2006-10-27 Thread Eric Firing 
Victor Danilchenko wrote:
>   Hi all,
> 
>   I am trying to build Matplotlib 0.87.7 on an RHEL 4.4-derived system, 
> with Python 2.3.4. I am running into a weird problem. When I do "python 
> setup.py build", I get the following error:
> 
> gcc: src/_gtkagg.cpp
> In file included from /usr/include/python2.3/Python.h:8,
>   from /usr/include/pygtk-2.0/pygobject.h:5,
>   from src/_gtkagg.cpp:11:
> /usr/include/python2.3/pyconfig.h:850:1: warning: "_POSIX_C_SOURCE" 
> redefined
> In file included from /usr/include/string.h:26,
>   from 
> /usr/lib/gcc/i386-redhat-linux/3.4.6/../../../../include/c++/3.4.6/cstring:51,
>   from src/_gtkagg.cpp:2:
> /usr/include/features.h:150:1: warning: this is the location of the 
> previous definition
> In file included from src/_gtkagg.cpp:11:
> /usr/include/pygtk-2.0/pygobject.h:140: error: expected `,' or `...' 
> before "typename"
> /usr/include/pygtk-2.0/pygobject.h:147: error: expected `,' or `...' 
> before "typename"
[...]

The error is not in matplotlib, it is in a pygtk header file, which is 
presumably coming from a Redhat package.  I don't know why it is 
happening or what the best solution is, though.  It looks like the 
pygobject.h that I have has "typename_", not "typename", so I am 
thinking maybe this is a pygtk bug, since fixed, in which "typename" is 
in conflict with something.  You might try editing your copy of 
pygobject.h, adding the trailing underscore to "typename" on both lines 
where it occurs.  It can't hurt; these are just dummy variable names.

Eric

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[Matplotlib-users] Problem building matplotlib

2006-10-27 Thread Victor Danilchenko 
Hi all,

I am trying to build Matplotlib 0.87.7 on an RHEL 4.4-derived system, 
with Python 2.3.4. I am running into a weird problem. When I do "python 
setup.py build", I get the following error:

gcc: src/_gtkagg.cpp
In file included from /usr/include/python2.3/Python.h:8,
  from /usr/include/pygtk-2.0/pygobject.h:5,
  from src/_gtkagg.cpp:11:
/usr/include/python2.3/pyconfig.h:850:1: warning: "_POSIX_C_SOURCE" 
redefined
In file included from /usr/include/string.h:26,
  from 
/usr/lib/gcc/i386-redhat-linux/3.4.6/../../../../include/c++/3.4.6/cstring:51,
  from src/_gtkagg.cpp:2:
/usr/include/features.h:150:1: warning: this is the location of the 
previous definition
In file included from src/_gtkagg.cpp:11:
/usr/include/pygtk-2.0/pygobject.h:140: error: expected `,' or `...' 
before "typename"
/usr/include/pygtk-2.0/pygobject.h:147: error: expected `,' or `...' 
before "typename"
In file included from /usr/include/python2.3/Python.h:8,
  from /usr/include/pygtk-2.0/pygobject.h:5,
  from src/_gtkagg.cpp:11:
/usr/include/python2.3/pyconfig.h:850:1: warning: "_POSIX_C_SOURCE" 
redefined
In file included from /usr/include/string.h:26,
  from 
/usr/lib/gcc/i386-redhat-linux/3.4.6/../../../../include/c++/3.4.6/cstring:51,
  from src/_gtkagg.cpp:2:
/usr/include/features.h:150:1: warning: this is the location of the 
previous definition
In file included from src/_gtkagg.cpp:11:
/usr/include/pygtk-2.0/pygobject.h:140: error: expected `,' or `...' 
before "typename"
/usr/include/pygtk-2.0/pygobject.h:147: error: expected `,' or `...' 
before "typename"



So I did a google search, and found someone recommending that "#include 
" be prepended to the offending file. I have prepended it to 
src/_gtkagg.cpp, did a clean, and run the build again. The error 
changed, and the "_POSIX_C_SOURCE" problem went away, but the build is 
still failing, at that same file:

gcc: src/_gtkagg.cpp
In file included from src/_gtkagg.cpp:11:
/usr/include/pygtk-2.0/pygobject.h:140: error: expected `,' or `...' 
before "typename"
/usr/include/pygtk-2.0/pygobject.h:147: error: expected `,' or `...' 
before "typename"
In file included from src/_gtkagg.cpp:11:
/usr/include/pygtk-2.0/pygobject.h:140: error: expected `,' or `...' 
before "typename"
/usr/include/pygtk-2.0/pygobject.h:147: error: expected `,' or `...' 
before "typename"



Does anyone have an idea of what is going wrong here? I could really 
use some help, as I am totally stumped.

Many thanks in advance.


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