segmentation fault when building doc

[Emmanuelle Gouillart]

Hi Johannes,

thank you very much for your help. It appears that I had not done things
properly: I thought that the local build (from "python setup.py build_ext
--inplace") was the one used for building the docs, but apparently it is
necessary to install the package as well.

I re-installed the package, and the build went smoothly.

Thanks!
Emmanuelle

On Sun, Apr 28, 2013 at 04:34:07PM +0200, Johannes Sch�nberger wrote:
> Hi Emmanuelle,

> I am on OSX 10.8 and cannot reproduce your segfault.

> Have you rebuilt and reinstalled skimage? Have you also deleted everything in scikit-image/build and in the site-packages directory? For me this sometimes breaks making the docs if some old files remain in either of them.

> I suspect that, since it says "warning: Source file is more recent than executable." in the gdb traceback.

> Johannes Sch�nberger

> Am 28.04.2013 um 16:13 schrieb Emmanuelle Gouillart <emmanuelle.gouillart at nsup.org>:

> > 	Hi all,

> > 	when I try do build the doc with sphinx ("make html", on the
> > master branch of scikit-image), I get a segmentation fault. Here is what
> > gdb says:

> > **************************
> > aleph ~/travail/projects/scikit-image/doc $ gdb python         [master]
> > [16:04]
> > GNU gdb (Ubuntu/Linaro 7.4-2012.04-0ubuntu2) 7.4-2012.04
> > Copyright (C) 2012 Free Software Foundation, Inc.
> > License GPLv3+: GNU GPL version 3 or later
> > <http://gnu.org/licenses/gpl.html>
> > This is free software: you are free to change and redistribute it.
> > There is NO WARRANTY, to the extent permitted by law.  Type "show
> > copying"
> > and "show warranty" for details.
> > This GDB was configured as "x86_64-linux-gnu".
> > For bug reporting instructions, please see:
> > <http://bugs.launchpad.net/gdb-linaro/>...
> > Reading symbols from /usr/bin/python...(no debugging symbols
> > found)...done.
> > (gdb) run /usr/bin/sphinx-build -b html -d build/doctrees   source
> > build/html
> > Starting program: /usr/bin/python /usr/bin/sphinx-build -b html -d
> > build/doctrees   source  build/html
> > [Thread debugging using libthread_db enabled]
> > Using host libthread_db library
> > "/lib/x86_64-linux-gnu/libthread_db.so.1".
> > Running Sphinx v1.1.3
> > /usr/lib/pymodules/python2.7/matplotlib/__init__.py:923: UserWarning:
> > This call to matplotlib.use() has no effect
> > because the the backend has already been chosen;
> > matplotlib.use() must be called *before* pylab, matplotlib.pyplot,
> > or matplotlib.backends is imported for the first time.

> >  if warn: warnings.warn(_use_error_msg)
> > loading pickled environment... not yet created
> > loading intersphinx inventory from
> > http://scikit-learn.org/stable/objects.inv...
> > loading intersphinx inventory from
> > http://docs.scipy.org/doc/scipy/reference/objects.inv...
> > loading intersphinx inventory from
> > http://docs.scipy.org/doc/numpy/objects.inv...
> > loading intersphinx inventory from
> > http://docs.python.org/2.7/objects.inv...

> > Program received signal SIGSEGV, Segmentation fault.
> > 0x00007fffdeac2643 in
> > __pyx_pf_7skimage_9transform_16_hough_transform_hough_circle
> > (__pyx_v_img=<optimized out>, __pyx_v_radius=0x48d6050, 
> >    __pyx_v_normalize=1 '\001', __pyx_v_full_output=<optimized out>, 
> >    __pyx_self=<optimized out>) at
> > skimage/transform/_hough_transform.c:2240
> > warning: Source file is more recent than executable.
> > 224        *__Pyx_BufPtrStrided3d(__pyx_t_5numpy_double_t *,
> > __pyx_pybuffernd_acc.rcbuffer->pybuffer.buf, __pyx_t_26,
> > __pyx_pybuffernd_acc.diminfo[0].strides, __pyx_t_27,
> > __pyx_pybuffernd_acc.diminfo[1].strides, __pyx_t_28,
> > __pyx_pybuffernd_acc.diminfo[2].strides) += __pyx_v_0
> > *****************************************

> > I checked that I obtain the same segfault on a fresh clone.

> > Any idea of what's going on? Am I the only one having trouble building
> > the doc?

> > Cheers,
> > Emmanuelle


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