segmentation fault when building doc

[Johannes Schönberger]

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 Schönberger

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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