Installing PyMVPA

[john.clithero@…]

Hi, I am trying to install PyMVPA (​http://www.pymvpa.org) on Snow Leopard 10.6.2 via MacPorts 1.8.1

Using sudo port -d install py26-pymvpa

It gets to the following: build_src building extension "mvpa.clfs.libsmlrc.smlrc" sources building extension "mvpa.clfs.libsvmc._svmc" sources building data_files sources build_src: building npy-pkg config files customize UnixCCompiler customize UnixCCompiler using build_ext customize UnixCCompiler customize UnixCCompiler using build_ext building 'mvpa.clfs.libsvmc._svmc' extension compiling C++ sources C compiler: /usr/bin/g++-4.2 -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall

compile options: '-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-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp

and then I get a very long list of errors. Below is the end of the output. Help would be great. It seems to be related to LIBSVM (perhaps a new version).

Cheers, John

build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:5001: error: expected type-specifier before 'svm_parameter' build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:5001: error: expected `>' before 'svm_parameter' build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:5001: error: expected `(' before 'svm_parameter' build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:5001: error: expected primary-expression before '>' token build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:5001: error: expected `)' before ';' token build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:5012: error: expected `)' before 'const' build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:5012: error: expected `)' before ';' token build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp: In function 'PyObject* _wrap_svm_save_model(PyObject*, PyObject*)': build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:5044: error: 'svm_save_model' was not declared in this scope build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp: In function 'PyObject* _wrap_svm_load_model(PyObject*, PyObject*)': build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:5069: error: 'svm_load_model' was not declared in this scope build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp: In function 'PyObject* _wrap_svm_get_svm_type(PyObject*, PyObject*)': build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:5093: error: 'svm_get_svm_type' was not declared in this scope build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp: In function 'PyObject* _wrap_svm_get_nr_class(PyObject*, PyObject*)': build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:5115: error: 'svm_get_nr_class' was not declared in this scope build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp: In function 'PyObject* _wrap_svm_get_labels(PyObject*, PyObject*)': build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:5145: error: 'svm_get_labels' was not declared in this scope build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp: In function 'PyObject* _wrap_svm_get_svr_probability(PyObject*, PyObject*)': build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:5167: error: 'svm_get_svr_probability' was not declared in this scope build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp: In function 'PyObject* _wrap_svm_predict_values(PyObject*, PyObject*)': build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:5206: error: 'svm_predict_values' was not declared in this scope build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp: In function 'PyObject* _wrap_svm_predict(PyObject*, PyObject*)': build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:5237: error: 'svm_predict' was not declared in this scope build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp: In function 'PyObject* _wrap_svm_predict_probability(PyObject*, PyObject*)': build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:5277: error: 'svm_predict_probability' was not declared in this scope build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp: In function 'PyObject* _wrap_svm_destroy_model(PyObject*, PyObject*)': build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:5298: error: 'svm_destroy_model' was not declared in this scope build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp: In function 'PyObject* _wrap_svm_check_parameter(PyObject*, PyObject*)': build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:5308: error: 'svm_problem' was not declared in this scope build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:5308: error: 'arg1' was not declared in this scope build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:5308: error: expected primary-expression before ')' token build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:5308: error: expected `;' before numeric constant build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:5309: error: 'svm_parameter' was not declared in this scope build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:5309: error: 'arg2' was not declared in this scope build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:5309: error: expected primary-expression before ')' token build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:5309: error: expected `;' before numeric constant build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:5323: error: expected type-specifier before 'svm_problem' build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:5323: error: expected `>' before 'svm_problem' build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:5323: error: expected `(' before 'svm_problem' build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:5323: error: expected primary-expression before '>' token build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:5323: error: expected `)' before ';' token build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:5328: error: expected type-specifier before 'svm_parameter' build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:5328: error: expected `>' before 'svm_parameter' build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:5328: error: expected `(' before 'svm_parameter' build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:5328: error: expected primary-expression before '>' token build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:5328: error: expected `)' before ';' token build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:5329: error: expected primary-expression before 'char' build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:5329: error: expected `)' before 'char' build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp: In function 'PyObject* _wrap_svm_check_probability_model(PyObject*, PyObject*)': build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:5351: error: 'svm_check_probability_model' was not declared in this scope build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp: In function 'void init_svmc()': build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:6670: error: 'C_SVC' was not declared in this scope build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:6671: error: 'NU_SVC' was not declared in this scope build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:6672: error: 'ONE_CLASS' was not declared in this scope build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:6673: error: 'EPSILON_SVR' was not declared in this scope build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:6674: error: 'NU_SVR' was not declared in this scope build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:6675: error: 'LINEAR' was not declared in this scope build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:6676: error: 'POLY' was not declared in this scope build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:6677: error: 'RBF' was not declared in this scope build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:6678: error: 'SIGMOID' was not declared in this scope build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:6679: error: 'PRECOMPUTED' was not declared in this scope error: Command "/usr/bin/g++-4.2 -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -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-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp -o build/temp.macosx-10.6-i386-2.6/build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.o" failed with exit status 1 Error: Target org.macports.build returned: shell command " cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_python_py26-pymvpa/work/py26-pymvpa-0.4.3" && /opt/local/Library/Frameworks/Python.framework/Versions/2.6/bin/python2.6 setup.py --no-user-cfg build_ext --with-libsvm " returned error 1 Command output: build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:5309: error: 'svm_parameter' was not declared in this scope build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:5309: error: 'arg2' was not declared in this scope build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:5309: error: expected primary-expression before ')' token build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:5309: error: expected `;' before numeric constant build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:5323: error: expected type-specifier before 'svm_problem' build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:5323: error: expected `>' before 'svm_problem' build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:5323: error: expected `(' before 'svm_problem' build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:5323: error: expected primary-expression before '>' token build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:5323: error: expected `)' before ';' token build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:5328: error: expected type-specifier before 'svm_parameter' build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:5328: error: expected `>' before 'svm_parameter' build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:5328: error: expected `(' before 'svm_parameter' build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:5328: error: expected primary-expression before '>' token build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:5328: error: expected `)' before ';' token build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:5329: error: expected primary-expression before 'char' build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:5329: error: expected `)' before 'char' build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp: In function 'PyObject* _wrap_svm_check_probability_model(PyObject*, PyObject*)': build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:5351: error: 'svm_check_probability_model' was not declared in this scope build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp: In function 'void init_svmc()': build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:6670: error: 'C_SVC' was not declared in this scope build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:6671: error: 'NU_SVC' was not declared in this scope build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:6672: error: 'ONE_CLASS' was not declared in this scope build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:6673: error: 'EPSILON_SVR' was not declared in this scope build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:6674: error: 'NU_SVR' was not declared in this scope build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:6675: error: 'LINEAR' was not declared in this scope build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:6676: error: 'POLY' was not declared in this scope build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:6677: error: 'RBF' was not declared in this scope build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:6678: error: 'SIGMOID' was not declared in this scope build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:6679: error: 'PRECOMPUTED' was not declared in this scope error: Command "/usr/bin/g++-4.2 -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -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-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp -o build/temp.macosx-10.6-i386-2.6/build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.o" failed with exit status 1

DEBUG: Backtrace: shell command " cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_python_py26-pymvpa/work/py26-pymvpa-0.4.3" && /opt/local/Library/Frameworks/Python.framework/Versions/2.6/bin/python2.6 setup.py --no-user-cfg build_ext --with-libsvm " returned error 1 Command output: build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:5309: error: 'svm_parameter' was not declared in this scope build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:5309: error: 'arg2' was not declared in this scope build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:5309: error: expected primary-expression before ')' token build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:5309: error: expected `;' before numeric constant build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:5323: error: expected type-specifier before 'svm_problem' build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:5323: error: expected `>' before 'svm_problem' build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:5323: error: expected `(' before 'svm_problem' build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:5323: error: expected primary-expression before '>' token build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:5323: error: expected `)' before ';' token build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:5328: error: expected type-specifier before 'svm_parameter' build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:5328: error: expected `>' before 'svm_parameter' build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:5328: error: expected `(' before 'svm_parameter' build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:5328: error: expected primary-expression before '>' token build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:5328: error: expected `)' before ';' token build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:5329: error: expected primary-expression before 'char' build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:5329: error: expected `)' before 'char' build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp: In function 'PyObject* _wrap_svm_check_probability_model(PyObject*, PyObject*)': build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:5351: error: 'svm_check_probability_model' was not declared in this scope build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp: In function 'void init_svmc()': build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:6670: error: 'C_SVC' was not declared in this scope build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:6671: error: 'NU_SVC' was not declared in this scope build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:6672: error: 'ONE_CLASS' was not declared in this scope build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:6673: error: 'EPSILON_SVR' was not declared in this scope build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:6674: error: 'NU_SVR' was not declared in this scope build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:6675: error: 'LINEAR' was not declared in this scope build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:6676: error: 'POLY' was not declared in this scope build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:6677: error: 'RBF' was not declared in this scope build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:6678: error: 'SIGMOID' was not declared in this scope build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp:6679: error: 'PRECOMPUTED' was not declared in this scope error: Command "/usr/bin/g++-4.2 -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -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-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.cpp -o build/temp.macosx-10.6-i386-2.6/build/src.macosx-10.6-i386-2.6/mvpa/clfs/libsvmc/svmc_wrap.o" failed with exit status 1

while executing

"command_exec build"

(procedure "portbuild::build_main" line 9) invoked from within

"$procedure $targetname" Warning: the following items did not execute (for py26-pymvpa): org.macports.activate org.macports.build org.macports.destroot org.macports.install Error: Status 1 encountered during processing.