matplotlib-users Mailing List for matplotlib

It helped to rebuild matplotlib-1.0.1 (without the copying of f2font.so) to make it run smooth.

Thanks!


Am 12.01.2011 um 19:48 schrieb Eric Firing:

> On 01/12/2011 07:11 AM, Hannes Kutza wrote:
>> Because of import- and compatibility issues I build everything from
>> scetch some days ago. Now i only have one Python (2.7.1) installation
>> and only one matplotlib version (1.0.1). In the
>> //Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages//
>> directory there's, too, only the matplotlib dir and the
>> /matplotlib-1.0.1-py2.7.egg-info /…
>> 
>> It was build from source; what has to be removed to uninstall matplotlib
>> completely? Maybe it would help to rebuild it.
> 
> Does this thread help?
> 
> http://old.nabble.com/abort-trap-td29019314.html
> 
> Eric
> 
>> 
>> Best,
>> Hannes
>> 
>> Am 12.01.2011 um 17:55 schrieb Benjamin Root:
>> 
>>> 
>>> 
>>> On Wed, Jan 12, 2011 at 10:23 AM, Hannes Kutza <ku...@pi...
>>> <mailto:ku...@pi...>> wrote:
>>> 
>>>    i think now it's mainly the savefig() that provokes that malloc error…
>>> 
>>>    Anfang der weitergeleiteten E-Mail:
>>> 
>>>>    *Von: *Hannes Kutza <ku...@pi...
>>>>    <mailto:ku...@pi...>>
>>>>    *Datum: *12. Januar 2011 14:35:24 MEZ
>>>>    *An: *mat...@li...
>>>>    <mailto:mat...@li...>
>>>>    *Betreff: **malloc error on show() oder x/ylabel()*
>>>> 
>>>>    i'm running python 2.7, matplotlib-1.0.1, gcc 4.2.1 and grortran
>>>>    4.2.1… when invoking (successful importing /import
>>>>    matplotlib.pyplot as plt/) plt.show() in combination with
>>>>    plt.xlabel or savefig("fig.ps <http://fig.ps/>") give me that
>>>>    nasty malloc error:
>>>> 
>>>>    Python(19725,0x7fff7055fca0) malloc: *** error for object
>>>>    0x102d8c6c0: pointer being freed was not allocated
>>>>    *** set a breakpoint in malloc_error_break to debug
>>>>    Abort trap
>>>> 
>>>>    calling plt.show or x/ylabel("string..") alone doesn't get me
>>>>    that error…
>>>> 
>>>>    cheers,
>>>>    hannesk
>>> 
>>> 
>>> Hannesk,
>>> 
>>> Most likely the issue here is a bad or mixed build. Assuming that you
>>> built the current install of matplotlib 1.0.1 from source, how did you
>>> have your previous install (packaged or from source)? Did you
>>> completely remove that install before building the current install?
>>> 
>>> Ben Root
>>> 
>> 
>> 
>> 
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> 
> 
> 
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On Wed, Jan 12, 2011 at 3:30 PM, Daniel Mader <
dan...@go...> wrote:

> Dear Ben,
>
> in your example, the stacking works but the polygons are wrong, or am
> I mistaken?
>
> Attached is the plot which is generated by your code.
>
> And, you don't have to thank me---it's me who is grateful for the support
> here!
>
> Best regards,
> Daniel
>
>
Oops, I forgot that I am testing out a possible patch for the spurious
polygon that goes over to (0, 0).
I believe that if you just simply add the first coordinate of each polygon
to the end of each one (so there are five pairs) and adding the keyword
argument "closed=False" to the PolyCollection constructor should resolve
that issue for now.

Thanks for using Matplotlib and helping to make it better.
Ben Root

Dear Ben,

in your example, the stacking works but the polygons are wrong, or am
I mistaken?

Attached is the plot which is generated by your code.

And, you don't have to thank me---it's me who is grateful for the support here!

Best regards,
Daniel

2011/1/12 Benjamin Root <ben...@ou...>:
> On Wed, Jan 12, 2011 at 3:07 PM, Daniel Mader
> <dan...@go...> wrote:
>>
>> Um, after seriously playing with the file I realized that the
>> suggested workaround of generating a closed single polygon won't work
>> for me: I need the individual quads or triangles in the plot as they
>> correspond to FEM simulation elements and have stress values assigned
>> to them...
>>
>>
>> As far as I understand you, there is currently no other way of
>> generating this kind of plot, right?
>>
>
> No, it is perfectly possible.  I attached an example.
>
>>
>> In the meantime I will file a bug report with the example file,
>> hopefully it finds a solution!
>>
>>
>
> Thanks for your help!
>
> Ben Root
>

In all detail: the crash report.

Um, after seriously playing with the file I realized that the
suggested workaround of generating a closed single polygon won't work
for me: I need the individual quads or triangles in the plot as they
correspond to FEM simulation elements and have stress values assigned
to them...

As far as I understand you, there is currently no other way of
generating this kind of plot, right?

In the meantime I will file a bug report with the example file,
hopefully it finds a solution!


2011/1/11 Benjamin Root <ben...@ou...>:
>> Dear Ben,
>>
>> this is great news, it works perfectly well! Thanks a million times
>> for this great support!
>>
>> All the best,
>> Daniel
>
> Oh, btw, could you please file a bug report describing the problem and that
> original script?  I suspect it is a slightly different problem than the
> usual 3d stacking problem.  I don't want to forget to look into it.
>
> http://sourceforge.net/tracker/?group_id=80706

On 01/12/2011 07:11 AM, Hannes Kutza wrote:
> Because of import- and compatibility issues I build everything from
> scetch some days ago. Now i only have one Python (2.7.1) installation
> and only one matplotlib version (1.0.1). In the
> //Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages//
> directory there's, too, only the matplotlib dir and the
> /matplotlib-1.0.1-py2.7.egg-info /…
>
> It was build from source; what has to be removed to uninstall matplotlib
> completely? Maybe it would help to rebuild it.

Does this thread help?

http://old.nabble.com/abort-trap-td29019314.html

Eric

>
> Best,
> Hannes
>
> Am 12.01.2011 um 17:55 schrieb Benjamin Root:
>
>>
>>
>> On Wed, Jan 12, 2011 at 10:23 AM, Hannes Kutza <ku...@pi...
>> <mailto:ku...@pi...>> wrote:
>>
>>     i think now it's mainly the savefig() that provokes that malloc error…
>>
>>     Anfang der weitergeleiteten E-Mail:
>>
>>>     *Von: *Hannes Kutza <ku...@pi...
>>>     <mailto:ku...@pi...>>
>>>     *Datum: *12. Januar 2011 14:35:24 MEZ
>>>     *An: *mat...@li...
>>>     <mailto:mat...@li...>
>>>     *Betreff: **malloc error on show() oder x/ylabel()*
>>>
>>>     i'm running python 2.7, matplotlib-1.0.1, gcc 4.2.1 and grortran
>>>     4.2.1… when invoking (successful importing /import
>>>     matplotlib.pyplot as plt/) plt.show() in combination with
>>>     plt.xlabel or savefig("fig.ps <http://fig.ps/>") give me that
>>>     nasty malloc error:
>>>
>>>     Python(19725,0x7fff7055fca0) malloc: *** error for object
>>>     0x102d8c6c0: pointer being freed was not allocated
>>>     *** set a breakpoint in malloc_error_break to debug
>>>     Abort trap
>>>
>>>     calling plt.show or x/ylabel("string..") alone doesn't get me
>>>     that error…
>>>
>>>     cheers,
>>>     hannesk
>>
>>
>> Hannesk,
>>
>> Most likely the issue here is a bad or mixed build. Assuming that you
>> built the current install of matplotlib 1.0.1 from source, how did you
>> have your previous install (packaged or from source)? Did you
>> completely remove that install before building the current install?
>>
>> Ben Root
>>
>
>
>
> ------------------------------------------------------------------------------
> Protect Your Site and Customers from Malware Attacks
> Learn about various malware tactics and how to avoid them. Understand
> malware threats, the impact they can have on your business, and how you
> can protect your company and customers by using code signing.
> http://p.sf.net/sfu/oracle-sfdevnl
>
>
>
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users

On 01/12/2011 06:58 AM, Benjamin Root wrote:
> On Wed, Jan 12, 2011 at 2:28 AM, Daniel Mader
> <dan...@go...
> <mailto:dan...@go...>> wrote:
>
>     Hi,
>
>     the same happens with "regular" colorbars, too. Me, too, I didn't
>     always have this issue but I can't tell when exactly it was
>     introduced. Looks more like a bug than a feature to me---at least on
>     screen the result looks ugly.
>
>     Best regards,
>     Daniel
>
>     2011/1/12 <wa...@we... <mailto:wa...@we...>>:
>      > Hi,
>      > I used the colorbar with the imshow for a while for a while, but
>     now when I
>      > produce a pdf of svg, light stripes appear in the colorbar. When
>     I try to
>      > modify the file with inkscape, I see that the stroke color is
>     unset. Is this a
>      > bug, a feature, or my backend that produces the file. And how can
>     I get rid of
>      > that?

Whether stroke color is set or unset is neither a bug nor a feature, it 
is a compromise.

Try experimenting with the antialiasing setting.

>      >
>      > Regards, Stefan
>      >
>      >
>      >
>
>
> I wonder if this is related to recent reports about white-lines in
> pcolor output?
>
> Does this happen irrespectively of the backend?

There have always been problems along these lines, because no 
combination of edgewidth, stroking on or off, and antialiasing on or off 
works without artifacts on all backends and for all values of alpha.

I would be delighted if someone could figure out a nice, clean, 
universal solution for this problem.

Eric

>
> Ben Root
>

Because of import- and compatibility issues I build everything from scetch some days ago. Now i only have one Python (2.7.1) installation and only one matplotlib version (1.0.1). In the /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/ directory there's, too, only the matplotlib dir and the matplotlib-1.0.1-py2.7.egg-info … 

It was build from source; what has to be removed to uninstall matplotlib completely? Maybe it would help to rebuild it.

Best,
Hannes

Am 12.01.2011 um 17:55 schrieb Benjamin Root:

> 
> 
> On Wed, Jan 12, 2011 at 10:23 AM, Hannes Kutza <ku...@pi...> wrote:
> i think now it's mainly the savefig() that provokes that malloc error…
> 
> Anfang der weitergeleiteten E-Mail:
> 
>> Von: Hannes Kutza <ku...@pi...>
>> Datum: 12. Januar 2011 14:35:24 MEZ
>> An: mat...@li...
>> Betreff: malloc error on show() oder x/ylabel()
>> 
>> i'm running python 2.7, matplotlib-1.0.1, gcc 4.2.1 and grortran 4.2.1… when invoking (successful importing import matplotlib.pyplot as plt) plt.show() in combination with plt.xlabel or savefig("fig.ps") give me that nasty malloc error:
>> 
>> Python(19725,0x7fff7055fca0) malloc: *** error for object 0x102d8c6c0: pointer being freed was not allocated
>> *** set a breakpoint in malloc_error_break to debug
>> Abort trap
>> 
>> calling plt.show or x/ylabel("string..") alone doesn't get me that error…
>> 
>> cheers,
>> hannesk
> 
> 
> Hannesk,
> 
> Most likely the issue here is a bad or mixed build.  Assuming that you built the current install of matplotlib 1.0.1 from source, how did you have your previous install (packaged or from source)?  Did you completely remove that install before building the current install?
> 
> Ben Root
> 

On Wed, Jan 12, 2011 at 2:28 AM, Daniel Mader <
dan...@go...> wrote:

> Hi,
>
> the same happens with "regular" colorbars, too. Me, too, I didn't
> always have this issue but I can't tell when exactly it was
> introduced. Looks more like a bug than a feature to me---at least on
> screen the result looks ugly.
>
> Best regards,
> Daniel
>
> 2011/1/12  <wa...@we...>:
> > Hi,
> > I used the colorbar with the imshow for a while for a while, but now when
> I
> > produce a pdf of svg, light stripes appear in the colorbar. When I try to
> > modify the file with inkscape, I see that the stroke color is unset. Is
> this a
> > bug, a feature, or my backend that produces the file. And how can I get
> rid of
> > that?
> >
> > Regards, Stefan
> >
> >
> >
>

I wonder if this is related to recent reports about white-lines in pcolor
output?

Does this happen irrespectively of the backend?

Ben Root

On Wed, Jan 12, 2011 at 10:23 AM, Hannes Kutza <ku...@pi...> wrote:

> i think now it's mainly the savefig() that provokes that malloc error…
>
> Anfang der weitergeleiteten E-Mail:
>
> *Von: *Hannes Kutza <ku...@pi...>
> *Datum: *12. Januar 2011 14:35:24 MEZ
> *An: *mat...@li...
> *Betreff: **malloc error on show() oder x/ylabel()*
>
> i'm running python 2.7, matplotlib-1.0.1, gcc 4.2.1 and grortran 4.2.1…
> when invoking (successful importing *import matplotlib.pyplot as plt*)
> plt.show() in combination with plt.xlabel or savefig("fig.ps") give me
> that nasty malloc error:
>
> Python(19725,0x7fff7055fca0) malloc: *** error for object 0x102d8c6c0:
> pointer being freed was not allocated
> *** set a breakpoint in malloc_error_break to debug
> Abort trap
>
> calling plt.show or x/ylabel("string..") alone doesn't get me that error…
>
> cheers,
> hannesk
>
>
>
Hannesk,

Most likely the issue here is a bad or mixed build.  Assuming that you built
the current install of matplotlib 1.0.1 from source, how did you have your
previous install (packaged or from source)?  Did you completely remove that
install before building the current install?

Ben Root

i think now it's mainly the savefig() that provokes that malloc error…

Anfang der weitergeleiteten E-Mail:

> Von: Hannes Kutza <ku...@pi...>
> Datum: 12. Januar 2011 14:35:24 MEZ
> An: mat...@li...
> Betreff: malloc error on show() oder x/ylabel()
> 
> i'm running python 2.7, matplotlib-1.0.1, gcc 4.2.1 and grortran 4.2.1… when invoking (successful importing import matplotlib.pyplot as plt) plt.show() in combination with plt.xlabel or savefig("fig.ps") give me that nasty malloc error:
> 
> Python(19725,0x7fff7055fca0) malloc: *** error for object 0x102d8c6c0: pointer being freed was not allocated
> *** set a breakpoint in malloc_error_break to debug
> Abort trap
> 
> calling plt.show or x/ylabel("string..") alone doesn't get me that error…
> 
> cheers,
> hannesk

i'm running python 2.7, matplotlib-1.0.1, gcc 4.2.1 and grortran 4.2.1… when invoking (successful importing import matplotlib.pyplot as plt) plt.show() in combination with plt.xlabel or savefig("fig.ps") give me that nasty malloc error:

Python(19725,0x7fff7055fca0) malloc: *** error for object 0x102d8c6c0: pointer being freed was not allocated
*** set a breakpoint in malloc_error_break to debug
Abort trap

calling plt.show or x/ylabel("string..") alone doesn't get me that error…

cheers,
hannesk

Hi,

the same happens with "regular" colorbars, too. Me, too, I didn't
always have this issue but I can't tell when exactly it was
introduced. Looks more like a bug than a feature to me---at least on
screen the result looks ugly.

Best regards,
Daniel

2011/1/12  <wa...@we...>:
> Hi,
> I used the colorbar with the imshow for a while for a while, but now when I
> produce a pdf of svg, light stripes appear in the colorbar. When I try to
> modify the file with inkscape, I see that the stroke color is unset. Is this a
> bug, a feature, or my backend that produces the file. And how can I get rid of
> that?
>
> Regards, Stefan
>
>
>
> ------------------------------------------------------------------------------
> Protect Your Site and Customers from Malware Attacks
> Learn about various malware tactics and how to avoid them. Understand
> malware threats, the impact they can have on your business, and how you
> can protect your company and customers by using code signing.
> http://p.sf.net/sfu/oracle-sfdevnl
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>



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