[pymvpa] error py26-pywavelets installation on snow leopard Mac

[James Kyle]

Morning,

I was just made aware of the py26-pywavelets compile error and pushed the patch as of r75507 of the mcaports repository. 

I am also updating the py26-pymvpa port to 0.6.0.dev and see some build issues cropping up with it.

Specifically:

> creating build/temp.macosx-10.6-x86_64-2.6/build/src.macosx-10.6-x86_64-2.6/mvpa/clfs/libsvmc
> compile options: '-I/usr/include/libsvm-2.0/libsvm -I/usr/include/libsvm -I/usr/local/include/libsvm -I/usr/local/include/libsvm-2.0/libsvm -I/usr/local/include -I/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/numpy/core/include -I/opt/local/Library/Frameworks/Python.framework/Versions/2.6/include/python2.6 -c'
> g++-4.2: build/src.macosx-10.6-x86_64-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp
> build/src.macosx-10.6-x86_64-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:2797: error: redefinition of 'struct svm_model'
> /opt/local/include/svm.h:53: error: previous definition of 'struct svm_model'
> build/src.macosx-10.6-x86_64-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:2797: error: redefinition of 'struct svm_model'
> /opt/local/include/svm.h:53: error: previous definition of 'struct svm_model'
> error: Command "/usr/bin/g++-4.2 -DNDEBUG -g -fwrapv -O3 -Wall -m64 -I/opt/local/include -L/opt/local/lib -I/usr/include/libsvm-2.0/libsvm -I/usr/include/libsvm -I/usr/local/include/libsvm -I/usr/local/include/libsvm-2.0/libsvm -I/usr/local/include -I/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/numpy/core/include -I/opt/local/Library/Frameworks/Python.framework/Versions/2.6/include/python2.6 -c build/src.macosx-10.6-x86_64-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp -o build/temp.macosx-10.6-x86_64-2.6/build/src.macosx-10.6-x86_64-2.6/mvpa/clfs/libsvmc/svmc_wrap.o" failed with exit status 1
> shell command " cd "/opt/local/var/macports/build/_opt_mports_dports_python_py26-pymvpa/work/py26-pymvpa-0.6.0.dev" && /opt/local/Library/Frameworks/Python.framework/Versions/2.6/bin/python2.6 setup.py --no-user-cfg build --with-libsvm " returned error 1
> Error: Target org.macports.build returned: shell command failed (see log for details)
> Warning: the following items did not execute (for py26-pymvpa): org.macports.build
> Log for py26-pymvpa is at: /opt/local/var/macports/logs/_opt_mports_dports_python_py26-pymvpa/main.log

I've attached the log mentioned above. 

Also of note is that the numpy.distutils package seems to ignore the compilers set in my environment such as CC, CXX, etc. I changed the numpy.distutils.core import to the standard distutils.core and the proper compiler options are set, however (for obvious reasons) it fails later on in the setup. 

Lastly, I cannot find the libsvm verbosity patch for the life of me. I've trolled the debian package repository and googled to no avail.  However, I'm not exceptionally familiar with the deb package management system so may be missing something obvious. 

I'm looking into these options, but if anyone immediately sees what the issue is I'll gladly push a patch asap.


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On Jan 16, 2011, at 5:37 AM, BumSeok Jeong wrote:

> Dear experts,
> 
> I'm new in pymvpa.
> My computer has snow leopard.
> 1) To install PyMVPA, I typed a command like below, and, after installation of matplotlib, the error message came up regarding to py26-pywavelets.
> 
> sudo port install py26-pymvpa +scipy +pynifti +hcluster +libsvm +matplotlib +pywavelets +rpy2
> .....
> .....
> --->  Computing dependencies for py26-pymvpa
> --->  Dependencies to be installed: py26-pywavelets py26-scipy SuiteSparse metis shogun glpk hdf5-18 szip
> --->  Building py26-pywavelets
> Error: Target org.macports.build returned: shell command failed (see log for details)
> Error: Failed to install py26-pywavelets
> Log for py26-pywavelets is at: /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_ports_python_py26-pywavelets/main.log
> Error: The following dependencies were not installed: py26-pywavelets py26-scipy SuiteSparse metis shogun glpk hdf5-18 szip
> Error: Status 1 encountered during processing.
> To report a bug, see <http://guide.macports.org/#project.tickets>
> 
> 2) Also Even if I use the command 'sudo port install py26-pywavelets', the same error message came up. When I googled mailing list, neurodebian package under virtualBox was recommended. However, I'd rather use PyMVPA on snow leopard because of limited RAM capability(2G).
> 
> Any comment must be appreciated.
> 
> Best wishes,
> 
> Jeong
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