[pymvpa] Problem About running mvpa2 tutorial
Ceyhun Çakar
cakar.ceyhun at gmail.com
Sun Oct 14 15:36:26 UTC 2012
Dear Yaroslav O. Halchenko,
Ubuntu is Ubuntu 12.04.1 LTS (64-bit).
Python 2.7.3
numpy 1.6.1
The result of import mvpa2 and mvpa2.wtf() is below:
>>> import mvpa2
>>> mvpa2.wtf()
/usr/lib/python2.7/dist-packages/nose/util.py:14: DeprecationWarning:
The compiler package is deprecated and removed in Python 3.x.
from compiler.consts import CO_GENERATOR
Current date: 2012-10-14 18:33
PyMVPA:
Version: 2.0.0
Hash: 97c414fe5c2a122a6ee176b71a4e28dc7408fef7
Path: /usr/lib/pymodules/python2.7/mvpa2/__init__.pyc
Version control (GIT):
GIT information could not be obtained due
"/usr/lib/pymodules/python2.7/mvpa2/.. is not under GIT"
SYSTEM:
OS: posix Linux 3.2.0-32-generic #51-Ubuntu SMP Wed Sep 26
21:33:09 UTC 2012
Distribution: Ubuntu/12.04/precise
EXTERNALS:
Present: cPickle, ctypes, good scipy.stats.rdist, good
scipy.stats.rv_discrete.ppf, griddata, gzip, h5py, ipython, libsvm,
libsvm verbosity control, matplotlib, mdp, mdp ge 2.4, nibabel, nose,
numpy, openopt, pylab, pylab plottable, pywt, pywt wp reconstruct,
reportlab, scipy, sg ge 0.6.4, sg ge 0.6.5, sg_fixedcachesize, shogun,
shogun.krr, shogun.mpd, shogun.svmocas, skl, weave
Absent: atlas_fsl, atlas_pymvpa, elasticnet, glmnet, hcluster,
lars, lxml, mass, nipy, nipy.neurospin, pprocess, pywt wp reconstruct
fixed, rpy2, running ipython env, shogun.lightsvm, shogun.svrlight
Versions of critical externals:
shogun:full : 1.1.0_02ce3cd_2011-12-12_08:17_
shogun:rev : 2941901
nibabel : 1.1.0
shogun : 1.1.0
reportlab : 2.5
matplotlib : 1.1.1rc
scipy : 0.9.0
ipython : 0.12.1
skl : 0.10
mdp : 3.3
numpy : 1.6.1
ctypes : 1.1.0
matplotlib : 1.1.1rc
nifti : failed to query due to "nifti is not a known dependency key."
numpy : 1.6.1
openopt : 0.42
openopt : failed to query due to "No module named openopt"
pywt : 0.2.0
shogun : v1.1.0_02ce3cd_2011-12-12_08:17_
Matplotlib backend: TkAgg
RUNTIME:
PyMVPA Environment Variables:
PYTHONPATH :
":/home/ceyhun:/usr/lib/python2.7/plat-linux2:/usr/local/lib/python2.7/dist-packages/PyBrain-0.3.1-py2.7.egg:/usr/lib/python2.7/dist-packages/ubuntuone-control-panel:/usr/lib/python2.7/dist-packages/ubuntuone-couch:/usr/local/lib/python2.7/dist-packages/Orange/orng:/usr/lib/python2.7/dist-packages:/usr/lib/python2.7/dist-packages/IPython/extensions:/usr/lib/python2.7:/usr/lib/python2.7/dist-packages/wx-2.8-gtk2-unicode:/usr/local/lib/python2.7/dist-packages/setproctitle-1.1.6-py2.7-linux-x86_64.egg:/usr/lib/python2.7/dist-packages/PIL:/usr/local/lib/python2.7/dist-packages/FuncDesigner-0.42-py2.7.egg:/usr/local/lib/python2.7/dist-packages/openopt-0.42-py2.7.egg:/usr/lib/python2.7/dist-packages/ubuntuone-storage-protocol:/usr/lib/python2.7/lib-tk:/usr/lib/python2.7/lib-dynload:/usr/lib/python2.7/dist-packages/ubuntu-sso-client:/usr/local/lib/python2.7/dist-packages/Kivy-1.3.0-py2.7-linux-x86_64.egg:/usr/lib/python2.7/dist-packages/ubuntuone-client:/usr/local/lib/python2.7/dist-packages/DerApproximator-0.42-py2.7.egg:/usr/lib/python2.7/dist-packages/ubuntuone-installer:/usr/lib/python2.7/lib-old:/usr/local/lib/python2.7/dist-packages:/usr/lib/python2.7/dist-packages/gtk-2.0:/usr/local/lib/python2.7/dist-packages/SpaceFuncs-0.42-py2.7.egg:/usr/lib/pymodules/python2.7:/usr/lib/python2.7/dist-packages/gst-0.10"
PyMVPA Runtime Configuration:
[general]
verbose = 1
[externals]
have running ipython env = no
have numpy = yes
have scipy = yes
have matplotlib = yes
have atlas_fsl = no
have atlas_pymvpa = no
have cpickle = yes
have ctypes = yes
have elasticnet = no
have glmnet = no
have good scipy.stats.rdist = yes
have good scipy.stats.rv_discrete.ppf = yes
have griddata = yes
have gzip = yes
have h5py = yes
have hcluster = no
have ipython = yes
have lars = no
have pylab = yes
have libsvm = yes
have libsvm verbosity control = yes
have lxml = no
have mass = no
have mdp = yes
have mdp ge 2.4 = yes
have nibabel = yes
have nipy = no
have nipy.neurospin = no
have nose = yes
have openopt = yes
have pprocess = no
have pylab plottable = yes
have pywt = yes
have pywt wp reconstruct = yes
have pywt wp reconstruct fixed = no
have reportlab = yes
have rpy2 = no
have sg ge 0.6.4 = yes
have sg ge 0.6.5 = yes
have sg_fixedcachesize = yes
have shogun = yes
have shogun.krr = yes
have shogun.lightsvm = no
have shogun.mpd = yes
have shogun.svmocas = yes
have shogun.svrlight = no
have skl = yes
have weave = yes
Process Information:
Name: python
State: R (running)
Tgid: 2897
Pid: 2897
PPid: 2840
TracerPid: 0
Uid: 1000 1000 1000 1000
Gid: 1000 1000 1000 1000
FDSize: 256
Groups: 4 24 27 30 46 109 124 1000
VmPeak: 648172 kB
VmSize: 648172 kB
VmLck: 0 kB
VmPin: 0 kB
VmHWM: 97496 kB
VmRSS: 97496 kB
VmData: 153008 kB
VmStk: 236 kB
VmExe: 2500 kB
VmLib: 76056 kB
VmPTE: 1100 kB
VmSwap: 0 kB
Threads: 2
SigQ: 0/15837
SigPnd: 0000000000000000
ShdPnd: 0000000000000000
SigBlk: 0000000000000000
SigIgn: 0000000001001000
SigCgt: 0000000180000002
CapInh: 0000000000000000
CapPrm: 0000000000000000
CapEff: 0000000000000000
CapBnd: ffffffffffffffff
Cpus_allowed: 3
Cpus_allowed_list: 0-1
Mems_allowed: 00000000,00000001
Mems_allowed_list: 0
voluntary_ctxt_switches: 2802
nonvoluntary_ctxt_switches: 232
>>> can't invoke "event" command: application has been destroyed
while executing
"event generate $w <<ThemeChanged>>"
(procedure "ttk::ThemeChanged" line 6)
invoked from within
"ttk::ThemeChanged"
Thank you for quick response,
Ceyhun Çakar
On Sat, Oct 13, 2012 at 6:24 AM, Yaroslav Halchenko
<debian at onerussian.com> wrote:
> that is a fun casing... what ubuntu is it and ... output of
>
> import mvpa2
> mvpa2.wtf()
>
> ?
>
> On Fri, 12 Oct 2012, Ceyhun Çakar wrote:
>
>> Hello,
>
>> I have installed python-mvpa2 using synaptic in Ubuntu 12.04.1 LTS
>> 64-bit. I want to study its tutorial but in Python when I import
>> tutorial (as shown in http://www.pymvpa.org/tutorial_start.html), I
>> got following error:
>
>> ceyhun at ceyhun-ubuntu64:~$ python
>> Python 2.7.3 (default, Aug 1 2012, 05:14:39)
>> [GCC 4.6.3] on linux2
>> Type "help", "copyright", "credits" or "license" for more information.
>> >>> import mvpa2
>> >>> from mvpa2.tutorial_suite import *
>> Traceback (most recent call last):
>> File "<stdin>", line 1, in <module>
>> File "/usr/lib/pymodules/python2.7/mvpa2/tutorial_suite.py", line
>> 15, in <module>
>> from mvpa2.suite import *
>> File "/usr/lib/pymodules/python2.7/mvpa2/suite.py", line 87, in <module>
>> from mvpa2.clfs.smlr import *
>> File "/usr/lib/pymodules/python2.7/mvpa2/clfs/smlr.py", line 31, in <module>
>> from mvpa2.clfs.libsmlrc import stepwise_regression as _cStepwiseRegression
>> File "/usr/lib/pymodules/python2.7/mvpa2/clfs/libsmlrc/__init__.py",
>> line 20, in <module>
>> from mvpa2.clfs.libsmlrc.ctypes_helper import extend_args, c_darray
>> File "/usr/lib/pymodules/python2.7/mvpa2/clfs/libsmlrc/ctypes_helper.py",
>> line 15, in <module>
>> c_darray = np.ctypeslib.ndpointer(dtype=np.float64,
>> flags='aligned,contiguous')
>> File "/usr/lib/python2.7/dist-packages/numpy/ctypeslib.py", line
>> 264, in ndpointer
>> num = _num_fromflags(flags)
>> File "/usr/lib/python2.7/dist-packages/numpy/ctypeslib.py", line
>> 139, in _num_fromflags
>> num += _flagdict[val]
>> KeyError: 'ALiGNED'
>
>> Is there anybody who can help me?
>
>> Thanks,
>> Sincerely,
> --
> Yaroslav O. Halchenko
> Postdoctoral Fellow, Department of Psychological and Brain Sciences
> Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
> Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419
> WWW: http://www.linkedin.com/in/yarik
>
> _______________________________________________
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--
Ceyhun Çakar
cakar.ceyhun at gmail.com
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