[pymvpa] trouble importing mvpa2.suite
Anna Manelis
anna.manelis at gmail.com
Wed Sep 13 13:37:36 UTC 2017
Sure (doingprettywellandhowareyou?). Below is the output (I had a feeling I
pasted it in the first e-mail but apparently not)
*python -c 'import mvpa2; print
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: 2017-09-13 09:34
PyMVPA:
Version: 2.1.0
Hash: 828f4b4bea2488f8c7e3f6c2446a445d77325338
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 3.2.0-4-amd64 #1 SMP Debian 3.2.89-2
Distribution: debian/7.11
EXTERNALS:
Present: atlas_fsl, cPickle, ctypes, good scipy.stats.rdist, good
scipy.stats.rv_discrete.ppf, griddata, gzip, h5py, ipython, liblapack.so,
libsvm, libsvm verbosity control, lxml, matplotlib, mdp, mdp ge 2.4,
nibabel, nose, numpy, pylab, pylab plottable, pywt, pywt wp reconstruct,
reportlab, scipy, skl, statsmodels, weave
Absent: atlas_pymvpa, cran-energy, elasticnet, glmnet, hcluster,
lars, mass, nipy, nipy.neurospin, openopt, pprocess, pywt wp reconstruct
fixed, rpy2, running ipython env, sg ge 0.6.4, sg ge 0.6.5,
sg_fixedcachesize, shogun, shogun.krr, shogun.lightsvm, shogun.mpd,
shogun.svmocas, shogun.svrlight
Versions of critical externals:
nibabel : 2.0.2
reportlab : 2.5
matplotlib : 1.1.1rc2
scipy : 0.10.1
ipython : 0.13.1
skl : 0.16.1
mdp : 3.4
numpy : 1.6.2
ctypes : 1.1.0
matplotlib : 1.1.1rc2
lxml : 2.3.2
nifti : failed to query due to "nifti is not a known dependency
key."
numpy : 1.6.2
pywt : 0.2.0
Matplotlib backend: TkAgg
RUNTIME:
PyMVPA Environment Variables:
PYTHONPATH :
":/usr/lib/python2.7/lib-old:/usr/local/lib/python2.7/dist-packages:/data:/usr/lib/python2.7/lib-dynload:/usr/lib/python2.7/plat-linux2:/usr/lib/python2.7/dist-packages/gtk-2.0:/usr/lib/python2.7/dist-packages:/usr/lib/pymodules/python2.7:/usr/lib/python2.7/dist-packages/IPython/extensions:/usr/lib/python2.7:/usr/lib/python2.7/dist-packages/wx-2.8-gtk2-unicode:/usr/lib/python2.7/lib-tk:/usr/lib/python2.7/dist-packages/PIL"
PyMVPA Runtime Configuration:
[general]
verbose = 1
[externals]
have running ipython env = no
have numpy = yes
have scipy = yes
have matplotlib = yes
have lxml = yes
have nibabel = yes
have atlas_fsl = yes
have atlas_pymvpa = no
have cpickle = yes
have cran-energy = no
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 liblapack.so = yes
have pylab = yes
have libsvm = yes
have libsvm verbosity control = yes
have mass = no
have mdp = yes
have mdp ge 2.4 = yes
have nipy = no
have nipy.neurospin = no
have nose = yes
have openopt = no
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 = no
have sg ge 0.6.5 = no
have sg_fixedcachesize = no
have shogun = no
have shogun.krr = no
have shogun.lightsvm = no
have shogun.mpd = no
have shogun.svmocas = no
have shogun.svrlight = no
have skl = yes
have statsmodels = yes
have weave = yes
Process Information:
Name: python
State: R (running)
Tgid: 13804
Pid: 13804
PPid: 13722
TracerPid: 0
Uid: 1000 1000 1000 1000
Gid: 1000 1000 1000 1000
FDSize: 256
Groups: 24 25 29 30 44 46 104 109 112 1000
VmPeak: 647452 kB
VmSize: 647452 kB
VmLck: 0 kB
VmPin: 0 kB
VmHWM: 107696 kB
VmRSS: 107696 kB
VmData: 125224 kB
VmStk: 132 kB
VmExe: 2396 kB
VmLib: 64348 kB
VmPTE: 1188 kB
VmSwap: 0 kB
Threads: 6
SigQ: 0/257267
SigPnd: 0000000000000000
ShdPnd: 0000000000000000
SigBlk: 0000000000000000
SigIgn: 0000000001001000
SigCgt: 0000000180000002
CapInh: 0000000000000000
CapPrm: 0000000000000000
CapEff: 0000000000000000
CapBnd: ffffffffffffffff
Cpus_allowed: f
Cpus_allowed_list: 0-3
Mems_allowed: 00000000,00000001
Mems_allowed_list: 0
voluntary_ctxt_switches: 426
nonvoluntary_ctxt_switches: 123
On Wed, Sep 13, 2017 at 9:21 AM, Yaroslav Halchenko <debian at onerussian.com>
wrote:
>
> On Wed, 13 Sep 2017, Anna Manelis wrote:
>
> > Dear PYMVPA developers,
>
> > I have installed mvpa2 on my Debian computer, but cannot import
> > mvpa2.suite for some reason.
>
> > >>> import mvpa2.suite as mvpa2
>
> > Traceback (most recent call last):
> > Â File "<stdin>", line 1, in <module>
> > Â File "/usr/lib/pymodules/python2.7/mvpa2/suite.py", line 98, in
> > <module>
> > Â Â Â from mvpa2.clfs.warehouse import *
> > Â File "/usr/lib/pymodules/python2.7/mvpa2/clfs/warehouse.py", line
> 357,
> > in <module>
> > Â Â Â sklPLSRegression = _skl_import('pls', 'PLSRegression')
> > Â File "/usr/lib/pymodules/python2.7/mvpa2/clfs/warehouse.py", line
> 313,
> > in _skl_import
> > Â Â Â submod_ = __import__('sklearn.%s' % submod, fromlist=[submod])
> > ImportError: No module named pls
>
> incompatibility with sklearn -- some API changes I guess we didn't spot
>
> could you Anna (howdoyoudobtw????) provide output of
>
> python -c 'import mvpa2; print mvpa2.wtf()'
>
> ?
> --
> Yaroslav O. Halchenko
> Center for Open Neuroscience http://centerforopenneuroscience.org
> 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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