[matplotlib-devel] Segmentation fault from fresh OSX snow leopard build
Hi,
I am rashly building matplotlib from source on Snow Leopard, and
getting a segmentation fault as soon as I try and do a plot.
me $ python -c 'import pylab; pylab.plot(range(10))'
Segmentation fault
I've built python myself with:
export MACOSX_DEPLOYMENT_TARGET=10.6
./configure --prefix=/Users/mb312/usr/local
Then numpy using the usual procedure (tests look good)
For matplotlib, I've hacked the make.osx file so the top looks like:
begin make.osx snippet
PYVERSION=2.6
PYTHON=python${PYVERSION}
ZLIBVERSION=1.2.3
PNGVERSION=1.2.40
FREETYPEVERSION=2.3.11
MACOSX_DEPLOYMENT_TARGET=10.6
OSX_SDK_VER=10.6
ARCH_FLAGS=
## You shouldn't need to configure past this point
PKG_CONFIG_PATH="${PREFIX}/lib/pkgconfig"
CFLAGS="${ARCH_FLAGS} -I${PREFIX}/include
-I${PREFIX}/include/freetype2 -isysroot
/Developer/SDKs/MacOSX${OSX_SDK_VER}.sdk"
LDFLAGS="${ARCH_FLAGS} -L${PREFIX}/lib
-syslibroot,/Developer/SDKs/MacOSX${OSX_SDK_VER}.sdk"
--- end make.osx snippet ---
This builds correctly but then causes the segfault above. I've tried
with the original make.osx package versions of freetype and libpng
with the same outcome.
Running simple_script.py:
blair:~ mb312$ python
scipybuild/matplotlib/examples/pylab_examples/simple_plot.py
--verbose-helpful
$HOME=/Users/mb312
CONFIGDIR=/Users/mb312/.matplotlib
matplotlib data path
/Users/mb312/usr/local/lib/python2.6/site-packages/matplotlib/mpl-data
loaded rc file
/Users/mb312/usr/local/lib/python2.6/site-packages/matplotlib/mpl-data/matplotlibrc
matplotlib version 1.0.svn
verbose.level helpful
interactive is False
units is False
platform is darwin
Using fontManager instance from /Users/mb312/.matplotlib/fontList.cache
backend MacOSX version unknown
Segmentation fault
gcc version is i686-apple-darwin10-gcc-4.2.1
Did I take a mis-step somewhere in the build process? Any advice very
gratefully received...
Thanks a lot,
Matthew
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Re: [matplotlib-devel] Segmentation fault from fresh OSX snow leopard build
> I am rashly building matplotlib from source on Snow Leopard, and > getting a segmentation fault as soon as I try and do a plot. > > me $ python -c 'import pylab; pylab.plot(range(10))' > Segmentation fault Sorry - here the is top of the build output: export PKG_CONFIG_PATH="/Users/mb312/usr/local/lib/pkgconfig" &&\ export MACOSX_DEPLOYMENT_TARGET=10.6 &&\ export CFLAGS=" -I/Users/mb312/usr/local/include -I/Users/mb312/usr/local/include/freetype2 -isysroot /Developer/SDKs/MacOSX10.6.sdk" &&\ export LDFLAGS=" -L/Users/mb312/usr/local/lib -syslibroot,/Developer/SDKs/MacOSX10.6.sdk" &&\ python2.6 setup.py install --prefix=/Users/mb312/usr/local BUILDING MATPLOTLIB matplotlib: 1.0.svn python: 2.6.4 (r264:75706, Nov 29 2009, 00:03:57) [GCC 4.2.1 (Apple Inc. build 5646) (dot 1)] platform: darwin REQUIRED DEPENDENCIES numpy: 1.4.0.dev7803 freetype2: found, but unknown version (no pkg-config) * WARNING: Could not find 'freetype2' headers in any * of '.', './freetype2'. OPTIONAL BACKEND DEPENDENCIES libpng: found, but unknown version (no pkg-config) * Could not find 'libpng' headers in any of '.' Tkinter: Tkinter: 73770, Tk: 8.5, Tcl: 8.5 wxPython: no * wxPython not found Gtk+: no * Building for Gtk+ requires pygtk; you must be able * to "import gtk" in your build/install environment Mac OS X native: yes Qt: no Qt4: no Cairo: no OPTIONAL DATE/TIMEZONE DEPENDENCIES datetime: present, version unknown dateutil: matplotlib will provide pytz: 2008c OPTIONAL USETEX DEPENDENCIES dvipng: no ghostscript: /bin/sh: gs: command not found latex: no Thanks a lot, Matthew -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ Matplotlib-devel mailing list Matplotlib-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-devel
Re: [matplotlib-devel] Segmentation fault from fresh OSX snow leopard build
Matthew Brett writes: > I am rashly building matplotlib from source on Snow Leopard, and > getting a segmentation fault as soon as I try and do a plot. Can you get a backtrace in gdb? -- Jouni K. Seppänen http://www.iki.fi/jks -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ Matplotlib-devel mailing list Matplotlib-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-devel
Re: [matplotlib-devel] Segmentation fault from fresh OSX snow leopard build
Hi, On Sun, Nov 29, 2009 at 1:30 AM, Jouni K. Seppänen wrote: > Matthew Brett writes: > >> I am rashly building matplotlib from source on Snow Leopard, and >> getting a segmentation fault as soon as I try and do a plot. > > Can you get a backtrace in gdb? (gdb) run scipybuild/matplotlib/examples/pylab_examples/simple_plot.py ... Reading symbols for shared libraries . done Reading symbols for shared libraries . done Reading symbols for shared libraries . done Program received signal EXC_BAD_ACCESS, Could not access memory. Reason: 13 at address: 0x 0x000102d96ffb in py_to_agg_transformation_matrix (obj=0x102d794d0, errors=false) at src/agg_py_transforms.cpp:21 21 matrix = (PyArrayObject*) PyArray_FromObject(obj, PyArray_DOUBLE, 2, 2); hum... I'm running from the latest svn numpy... Cheers, Matthew -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ Matplotlib-devel mailing list Matplotlib-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-devel
Re: [matplotlib-devel] Segmentation fault from fresh OSX snow leopard build
Hi, >> Can you get a backtrace in gdb? > > (gdb) run scipybuild/matplotlib/examples/pylab_examples/simple_plot.py ... > Program received signal EXC_BAD_ACCESS, Could not access memory. > Reason: 13 at address: 0x > 0x000102d96ffb in py_to_agg_transformation_matrix > (obj=0x102d794d0, errors=false) at src/agg_py_transforms.cpp:21 > 21 matrix = (PyArrayObject*) PyArray_FromObject(obj, > PyArray_DOUBLE, 2, 2); > > hum... I'm running from the latest svn numpy... Same outcome with numpy 1.3 though... Matthew -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ Matplotlib-devel mailing list Matplotlib-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-devel
Re: [matplotlib-devel] Segmentation fault from fresh OSX snow leopard build
Matthew Brett writes: >> Can you get a backtrace in gdb? > > Program received signal EXC_BAD_ACCESS, Could not access memory. > Reason: 13 at address: 0x > 0x000102d96ffb in py_to_agg_transformation_matrix > (obj=0x102d794d0, errors=false) at src/agg_py_transforms.cpp:21 > 21matrix = (PyArrayObject*) PyArray_FromObject(obj, > PyArray_DOUBLE, 2, 2); Can you type "bt" in gdb at this point to see the whole call stack? -- Jouni K. Seppänen http://www.iki.fi/jks -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ Matplotlib-devel mailing list Matplotlib-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-devel
Re: [matplotlib-devel] Segmentation fault from fresh OSX snow leopard build
On Sun, Nov 29, 2009 at 9:49 AM, Jouni K. Seppänen wrote:
> Matthew Brett
> writes:
>
>>> Can you get a backtrace in gdb?
>>
>> Program received signal EXC_BAD_ACCESS, Could not access memory.
>> Reason: 13 at address: 0x
>> 0x000102d96ffb in py_to_agg_transformation_matrix
>> (obj=0x102d794d0, errors=false) at src/agg_py_transforms.cpp:21
>> 21 matrix = (PyArrayObject*) PyArray_FromObject(obj,
>> PyArray_DOUBLE, 2, 2);
>
> Can you type "bt" in gdb at this point to see the whole call stack?
Sorry - yes - here:
Program received signal EXC_BAD_ACCESS, Could not access memory.
Reason: 13 at address: 0x
0x000102cf703b in py_to_agg_transformation_matrix
(obj=0x102cde590, errors=false) at src/agg_py_transforms.cpp:21
21 matrix = (PyArrayObject*) PyArray_FromObject(obj,
PyArray_DOUBLE, 2, 2);
(gdb) bt
#0 0x000102cf703b in py_to_agg_transformation_matrix
(obj=0x102cde590, errors=false) at src/agg_py_transforms.cpp:21
#1 0x000102cf762c in get_path_iterator (path=0x102cde710,
trans=,
remove_nans=1, do_clip=0, rect=0x7fff5fbf9480,
quantize_mode=QUANTIZE_AUTO, do_simplify=1) at src/path_cleanup.cpp:58
#2 0x000102ce9e90 in GraphicsContext_draw_path (self=0x102cd19d0,
args=) at
src/_macosx.m:881
#3 0x0001000b31d8 in PyEval_EvalFrameEx (f=0x102b65f50,
throwflag=) at
Python/ceval.c:3706
#4 0x0001000b3f30 in PyEval_EvalCodeEx (co=0x102cd0be8,
globals=,
locals=,
args=0x102b61900, argcount=5, kws=0x102b61928, kwcount=0,
defs=0x102cde1a8, defcount=1, closure=0x0) at Python/ceval.c:2968
#5 0x0001000b1f1d in fast_function [inlined] () at
/Users/mb312/stable_trees/Python-2.6.4/Python/ceval.c:3802
#6 0x0001000b1f1d in PyEval_EvalFrameEx (f=0x102b61720,
throwflag=) at
Python/ceval.c:3727
#7 0x0001000b3f30 in PyEval_EvalCodeEx (co=0x10180ceb8,
globals=,
locals=,
args=0x102cae2a8, argcount=2, kws=0x0, kwcount=0, defs=0x0,
defcount=0, closure=0x0) at Python/ceval.c:2968
#8 0x0001000362a5 in function_call (func=0x101839b18,
arg=0x102cae290, kw=0x0) at Objects/funcobject.c:524
#9 0x00016fe2 in PyObject_Call (func=0x101839b18,
arg=0x102cae290, kw=0x0) at Objects/abstract.c:2492
#10 0x0001000ae352 in PyEval_EvalFrameEx (f=0x102b61530,
throwflag=) at
Python/ceval.c:4019
#11 0x0001000b3f30 in PyEval_EvalCodeEx (co=0x1014647b0,
globals=,
locals=,
args=0x102b61100, argcount=2, kws=0x102b61110, kwcount=0, defs=0x0,
defcount=0, closure=0x101825dc0) at Python/ceval.c:2968
#12 0x0001000b1f1d in fast_function [inlined] () at
/Users/mb312/stable_trees/Python-2.6.4/Python/ceval.c:3802
#13 0x0001000b1f1d in PyEval_EvalFrameEx (f=0x102b60f00,
throwflag=) at
Python/ceval.c:3727
#14 0x0001000b3f30 in PyEval_EvalCodeEx (co=0x102c90288,
globals=,
locals=,
args=0x102cae260, argcount=2, kws=0x0, kwcount=0, defs=0x0,
defcount=0, closure=0x0) at Python/ceval.c:2968
#15 0x0001000362a5 in function_call (func=0x102cad1b8,
arg=0x102cae248, kw=0x0) at Objects/funcobject.c:524
#16 0x00016fe2 in PyObject_Call (func=0x102cad1b8,
arg=0x102cae248, kw=0x0) at Objects/abstract.c:2492
#17 0x0001000ae352 in PyEval_EvalFrameEx (f=0x102b607f0,
throwflag=) at
Python/ceval.c:4019
#18 0x0001000b3f30 in PyEval_EvalCodeEx (co=0x1014647b0,
globals=,
locals=,
args=0x102cae218, argcount=2, kws=0x0, kwcount=0, defs=0x0,
defcount=0, closure=0x102c8d6e0) at Python/ceval.c:2968
#19 0x0001000362a5 in function_call (func=0x102cad320,
arg=0x102cae200, kw=0x0) at Objects/funcobject.c:524
#20 0x00016fe2 in PyObject_Call (func=0x102cad320,
arg=0x102cae200, kw=0x0) at Objects/abstract.c:2492
#21 0x00010001905d in instancemethod_call (func=0x102cad320,
arg=0x102cae200, kw=0x0) at Objects/classobject.c:2579
#22 0x00016fe2 in PyObject_Call (func=0x102aa7fa0,
arg=0x100438c90, kw=0x0) at Objects/abstract.c:2492
#23 0x0001a760 in call_function_tail [inlined] () at
/Users/mb312/stable_trees/Python-2.6.4/Objects/abstract.c:2524
#24 0x0001a760 in PyObject_CallMethod (o=, name=, format=0x102cfd504 "O") at
Objects/abstract.c:2601
#25 0x000102ce5653 in -[View drawRect:] (self=0x102b50960,
_cmd=,
rect={origin = {x = 0, y = 0}, size = {width = 640, height = 480}}) at
src/_macosx.m:4517
#26 0x7fff8676afae in -[NSView _drawRect:clip:] ()
#27 0x7fff86769c21 in -[NSView
_recursiveDisplayAllDirtyWithLockFocus:visRect:] ()
#28 0x7fff86769f8b in -[NSView
_recursiveDisplayAllDirtyWithLockFocus:visRect:] ()
#29 0x7fff86769f8b in -[NSView
_recursiveDisplayAllDirtyWithLockFocus:visRect:] ()
#30 0x7fff867682f3 in -[NSView
_recursiveDisplayRectIfNeededIgnoringOpacity:isVisibleRect:rectIsVisibleRectForView:topView:]
()
#31 0x7fff86767e17 in -[NSThemeFrame
_recursiveDisplayRectIfNeededIgnoringOpacity:isVisibleRect:rectIsVisibleRectForView:topView:]
()
#32 0x7fff867646bf in -[NSView
_displayRectIgnoringOpacity:isVisibleRect:rectIsVisibleRectForView:]
()
#33 0x7fff866ddf37 in -[NSView disp
