sok found it and with Swig3.0.4 now it works! thanks so much to everybody,
Melanie
On Jul 30, 2015, at 10:15 AM, Melanie Boly boly.mela...@gmail.com wrote:
Dear Nick,
Thank you so much for your comments; trying to apply your
recommendation, but missing one simple step: what is the 'PyMVPA root
directory'?
Thanks so much,
Melanie
On Sun, Jul 19, 2015 at 8:44 AM, Nick Oosterhof
n.n.ooster...@googlemail.com wrote:
On 15 Jul 2015, at 18:46, Feilong Ma mafeil...@gmail.com wrote:
I had a similar problem while installing PyMVPA on Mac OS (10.10.4). I
think the problem is related to this line:
https://github.com/PyMVPA/PyMVPA/blob/master/mvpa2/clfs/libsvmc/_svm.py#L22
When I tried to run this line in ipython
from mvpa2.clfs.libsvmc._svmc import C_SVC, NU_SVC, ONE_CLASS, EPSILON_SVR
What I got is:
ImportError: cannot import name C_SVC
I get the same error. Briefly (see below for details), it seems due to a
change in SWIG, with later versions giving issues.
When running python setup.py build_ext” and copying over the .o and .so
files from the build directory to PyMVPA’s root directory (across the
corresponding subdirectories), the following reproduces the error directly:
python -c from mvpa2.clfs.libsvmc._svmc import C_SVC”
Strangely enough, the following works for the failing PyMVPA installation
(but not for the working one):
python -c from mvpa2.clfs.libsvmc._svmc import C_SVC_swigconstant”
Digging a bit further, the mvpa2/clfs/libsvmc/svmc.py file differs between
my “working” (generated using SWIG 3.0.2) and “failing” (SWIG 3.0.6) PyMVPA
setup. One difference is that the working version has contents such as
C_SVC = _svmc.C_SVC
whereas the failing version has extra lines that includes “swigconstant”
_svmc.C_SVC_swigconstant(_svmc)
C_SVC = _svmc.C_SVC
(For completeness I’m including the full content of both versions below. )
Tracing this back further, I compiled swig from source, both for the latest
version on github and for version 3.0.0 (version 3.0.2 gave an error when
compiling). When using 3.0.0, the import works fine; with 3.0.6 or the
latest (3.0.7 development) it breaks.
I guess the problem might be related to compiling LibSVM. I vaguely
remember there was some error messages with CLANG blah blah.
I installed GCC 5.1 and get the same problem as when using CLANG.
To summarize, the following worked for me to get libsvm to work on OS X
Yosemite:
- clone swig from https://github.com/swig/swig, then “git checkout -tag
tags/tags/rel-3.0.0”
- in the swig directory, run “autoconf ./configure make sudo make
install” (although it gives an error when installing the man-pages due to
missing yodl2man, the binaries are installed fine). This requires autoconf,
automake and libconf.
- in the PyMVPA directory, run python setup.py build_ext”
- copy the .so and .o files from the build directory to the PyMVPA root
directory, for example in the PyMVPA root directory do for ext in .so .o;
do for i in `find build -iname *${ext}`; do j=`echo $i | cut -f3- -d/`; cp
$i $j; done; done”
If anyone can confirm that using an earlier version of SWIG fixes the
problem, that would be great. In that case I can also raise the issue with
the developers.
(Below: contents of mvpa2/clfs/libsvmc/svmc.py for working and failing
libsvm in PyMVPA)
# *Failing* mvpa2/clfs/libsvmc/svmc.py
# This file was automatically generated by SWIG (http://www.swig.org).
# Version 3.0.6
#
# Do not make changes to this file unless you know what you are doing--modify
# the SWIG interface file instead.
from sys import version_info
if version_info = (2, 6, 0):
def swig_import_helper():
from os.path import dirname
import imp
fp = None
try:
fp, pathname, description = imp.find_module('_svmc',
[dirname(__file__)])
except ImportError:
import _svmc
return _svmc
if fp is not None:
try:
_mod = imp.load_module('_svmc', fp, pathname, description)
finally:
fp.close()
return _mod
_svmc = swig_import_helper()
del swig_import_helper
else:
import _svmc
del version_info
try:
_swig_property = property
except NameError:
pass # Python 2.2 doesn't have 'property'.
def _swig_setattr_nondynamic(self, class_type, name, value, static=1):
if (name == thisown):
return self.this.own(value)
if (name == this):
if type(value).__name__ == 'SwigPyObject':
self.__dict__[name] = value
return
method = class_type.__swig_setmethods__.get(name, None)
if method:
return method(self, value)
if (not static):
if _newclass:
object.__setattr__(self, name, value)
else:
self.__dict__[name] = value
else:
