[pymvpa] smvc_wrap compilation
Dan McNamee
dmcx88 at gmail.com
Tue Jun 22 14:57:37 UTC 2010
Hi,
I'm trying to compile and install pymvpa-0.50-dev on 64bit architecture and
I seem to be having trouble compiling 'svmc_wrap.cpp'.
After running 'make 3rd' and 'python setup.py build_ext' I get the attached
errors below. Output of mvpa.wtf() also attached. This reports "have libsvm
= no" though it clearly compiles with 'make 3rd'.
I can subsequently run 'python setup.py install --prefix=~' however there
are no SVM classifiers available in SVM.
Dan
PS. It may be related to
http://osdir.com/ml/debian-bugs-rc/2010-06/msg00478.html?
###########################################
running build_ext
running build_src
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: g++44 -fno-strict-aliasing -DNDEBUG -g -fwrapv -O3 -Wall -fPIC
compile options: '-I/usr/include/numpy -I3rd/libsvm
-I/usr/support/apps/apps/PYTHON/2.5.5/gcc/4.4.0/64/lib/python2.5/site-packages/numpy/core/include
-I/usr/support/apps/apps/PYTHON/2.5.5/gcc/4.4.0/64/include/python2.5 -c'
g++44: build/src.linux-x86_64-2.5/mvpa/clfs/libsvmc/svmc_wrap.cpp
build/src.linux-x86_64-2.5/mvpa/clfs/libsvmc/svmc_wrap.cpp: In function 'int
SWIG_Python_ConvertFunctionPtr(PyObject*, void**, swig_type_info*)':
build/src.linux-x86_64-2.5/mvpa/clfs/libsvmc/svmc_wrap.cpp:2051: error:
invalid conversion from 'const char*' to 'char*'
build/src.linux-x86_64-2.5/mvpa/clfs/libsvmc/svmc_wrap.cpp: In constructor
'swig::PyObject_ptr::PyObject_ptr(PyObject*, bool)':
build/src.linux-x86_64-2.5/mvpa/clfs/libsvmc/svmc_wrap.cpp:2518: warning:
suggest explicit braces to avoid ambiguous 'else'
build/src.linux-x86_64-2.5/mvpa/clfs/libsvmc/svmc_wrap.cpp: In function 'int
SWIG_AsCharPtrAndSize(PyObject*, char**, size_t*, int*)':
build/src.linux-x86_64-2.5/mvpa/clfs/libsvmc/svmc_wrap.cpp:2846: error:
cannot convert 'int*' to 'Py_ssize_t*' for argument '3' to 'int
PyString_AsStringAndSize(PyObject*, char**, Py_ssize_t*)'
build/src.linux-x86_64-2.5/mvpa/clfs/libsvmc/svmc_wrap.cpp: In function
'void SWIG_Python_FixMethods(PyMethodDef*, swig_const_info*,
swig_type_info**, swig_type_info**)':
build/src.linux-x86_64-2.5/mvpa/clfs/libsvmc/svmc_wrap.cpp:6311: error:
invalid conversion from 'const char*' to 'char*'
build/src.linux-x86_64-2.5/mvpa/clfs/libsvmc/svmc_wrap.cpp: In function 'int
SWIG_Python_ConvertFunctionPtr(PyObject*, void**, swig_type_info*)':
build/src.linux-x86_64-2.5/mvpa/clfs/libsvmc/svmc_wrap.cpp:2051: error:
invalid conversion from 'const char*' to 'char*'
build/src.linux-x86_64-2.5/mvpa/clfs/libsvmc/svmc_wrap.cpp: In constructor
'swig::PyObject_ptr::PyObject_ptr(PyObject*, bool)':
build/src.linux-x86_64-2.5/mvpa/clfs/libsvmc/svmc_wrap.cpp:2518: warning:
suggest explicit braces to avoid ambiguous 'else'
build/src.linux-x86_64-2.5/mvpa/clfs/libsvmc/svmc_wrap.cpp: In function 'int
SWIG_AsCharPtrAndSize(PyObject*, char**, size_t*, int*)':
build/src.linux-x86_64-2.5/mvpa/clfs/libsvmc/svmc_wrap.cpp:2846: error:
cannot convert 'int*' to 'Py_ssize_t*' for argument '3' to 'int
PyString_AsStringAndSize(PyObject*, char**, Py_ssize_t*)'
build/src.linux-x86_64-2.5/mvpa/clfs/libsvmc/svmc_wrap.cpp: In function
'void SWIG_Python_FixMethods(PyMethodDef*, swig_const_info*,
swig_type_info**, swig_type_info**)':
build/src.linux-x86_64-2.5/mvpa/clfs/libsvmc/svmc_wrap.cpp:6311: error:
invalid conversion from 'const char*' to 'char*'
error: Command "g++44 -fno-strict-aliasing -DNDEBUG -g -fwrapv -O3 -Wall
-fPIC -I/usr/include/numpy -I3rd/libsvm
-I/usr/support/apps/apps/PYTHON/2.5.5/gcc/4.4.0/64/lib/python2.5/site-packages/numpy/core/include
-I/usr/support/apps/apps/PYTHON/2.5.5/gcc/4.4.0/64/include/python2.5 -c
build/src.linux-x86_64-2.5/mvpa/clfs/libsvmc/svmc_wrap.cpp -o
build/temp.linux-x86_64-2.5/build/src.linux-x86_64-2.5/mvpa/clfs/libsvmc/svmc_wrap.o"
failed with exit status 1
################################################################################
mvpa.wtf() output
Current date: 2010-06-22 15:01
PyMVPA:
Version: 0.5.0.dev
Path: mvpa/__init__.pyc
Version control (GIT):
GIT information could not be obtained due "mvpa/.. is not under GIT"
SYSTEM:
OS: posix Linux 2.6.18-164.6.1.el5 #1 SMP Tue Nov 3 23:02:51 EST
2009
Distribution: redhat/5.4/Boron
EXTERNALS:
Present: cPickle, ctypes, gzip, nose, numpy
Absent: atlas_fsl, atlas_pymvpa, elasticnet, glmnet, good
scipy.stats.rdist, good scipy.stats.rv_discrete.ppf, griddata, h5py,
hcluster, lars, libsvm, libsvm verbosity control, lxml, matplotlib, mdp, mdp
ge 2.4, nibabel, nifti, nifti ge 0.20090205.1, nipy, openopt, pprocess,
pylab, pylab plottable, pywt, pywt wp reconstruct, pywt wp reconstruct
fixed, reportlab, rpy2, running ipython env, scipy, sg ge 0.6.4, sg ge
0.6.5, sg_fixedcachesize, shogun, shogun.krr, shogun.lightsvm, shogun.mpd,
shogun.svrlight, weave
Versions of critical externals:
numpy : 1.4.1
ctypes : 1.0.3
numpy : 1.4.1
RUNTIME:
PyMVPA Environment Variables:
PYTHONPATH : "/home/tcin/danmc/scripts/python"
PyMVPA Runtime Configuration:
[externals]
have griddata = no
have pprocess = no
have good scipy.stats.rdist = no
have pylab plottable = no
have pywt wp reconstruct = no
have mdp = no
have lxml = no
have running ipython env = no
have nibabel = no
have sg_fixedcachesize = no
have elasticnet = no
have shogun.mpd = no
have matplotlib = no
have pywt wp reconstruct fixed = no
have scipy = no
have reportlab = no
have openopt = no
have libsvm = no
have h5py = no
have shogun.krr = no
have nifti ge 0.20090205.1 = no
have nose = yes
have weave = no
have atlas_fsl = no
have ctypes = yes
have hcluster = no
have sg ge 0.6.4 = no
have sg ge 0.6.5 = no
have good scipy.stats.rv_discrete.ppf = no
have libsvm verbosity control = no
have mdp ge 2.4 = no
have shogun.svrlight = no
have shogun = no
have nipy = no
have glmnet = no
have lars = no
have nifti = no
have atlas_pymvpa = no
have cpickle = yes
have numpy = yes
have pylab = no
have rpy2 = no
have shogun.lightsvm = no
have pywt = no
have gzip = yes
[general]
verbose = 1
Process Information:
Name: python
State: R (running)
SleepAVG: 96%
Tgid: 26682
Pid: 26682
PPid: 9640
TracerPid: 0
Uid: 5070 5070 5070 5070
Gid: 3008 3008 3008 3008
FDSize: 256
Groups: 1005 3008 3065
VmPeak: 147312 kB
VmSize: 146292 kB
VmLck: 0 kB
VmHWM: 14820 kB
VmRSS: 14820 kB
VmData: 11436 kB
VmStk: 192 kB
VmExe: 1140 kB
VmLib: 6080 kB
VmPTE: 240 kB
StaBrk: 12226000 kB
Brk: 12b09000 kB
StaStk: 7fff163b40c0 kB
Threads: 1
SigQ: 0/69632
SigPnd: 0000000000000000
ShdPnd: 0000000000000000
SigBlk: 0000000000000000
SigIgn: 0000000001001000
SigCgt: 0000000180000002
CapInh: 0000000000000000
CapPrm: 0000000000000000
CapEff: 0000000000000000
Cpus_allowed:
00000000,00000000,00000000,00000000,00000000,00000000,00000000,000000ff
Mems_allowed: 00000000,00000003
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