Hi Nick,
Switching to an earlier version of SWIG works for me. I had problems with
SWIG 3.0.5, but when I switched to SWIG 3.0.4 the problem was solved. I
installed SWIG using Homebrew, which should work in the same way as
installing from source.
The error message I talked about with CLANG still appears while running
`python setup.py build_ext`. I guess it's not related to this issue. The
message is:
['clang', '-fno-strict-aliasing', '-fno-common', '-dynamic', '-g',
'-O2', '-DNDEBUG', '-g', '-fwrapv', '-O3', '-Wall', '-Wstrict-prototypes']
###
Missing compiler_cxx fix for UnixCCompiler
Best,
Feilong
On Sun, Jul 19, 2015 at 9:44 AM
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Today's Topics:
1. Re: LinearCSVMC not found in PyMVPA-upstream-2.4.0 release
(Nick Oosterhof)
-- Forwarded message --
From: Nick Oosterhof n.n.ooster...@googlemail.com
To: Development and support of PyMVPA
pkg-exppsy-pymvpa@lists.alioth.debian.org
Cc:
Date: Sun, 19 Jul 2015 15:44:23 +0200
Subject: Re: [pymvpa] LinearCSVMC not found in PyMVPA-upstream-2.4.0
release
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
