[pymvpa] Fail to install upstream/0.6.0.dev in a virtual env(Neuro Debian)

Hiroyuki AKAMA akama.h.aa at m.titech.ac.jp
Tue Dec 14 07:25:06 UTC 2010


Dear List

I am just a beginner of pymvpa and quite new in your group (though my collaborator Brian already participated in the debates of this ML). Now I am struggling to install upstream/0.6.0.dev from the source (http://git.debian.org/?p=pkg-exppsy/pymvpa.git;a=shortlog;h=refs/tags/upstream/0.6.0.dev) in NeuroDebian on Windows 7 amd-64. 
The result is as follows.
>>> import mvpa
(success. No warning)
>>> from mvpa.misc.io.base import SampleAttributes
(success. No warning)
>>> from mvpa.datasets.nifti import NiftiDataset
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
ImportError: No module named nifti

I guess even though nifti is present (because 'import nifti' passes with no problem), python couldn't find it. I'll cite the result of mvpa.wtf() at the end of this mail. It would be much appreciated giving me advices. I am wondering whether it is due to the virtual environment,

(#As upstream/0.5.0.dev in
https://github.com/PyMVPA/PyMVPA/downloads
didn't work well (for example, 
mvpa/tests/badexternals/__init__.py was lost
a warning message about the depreciation of verbosity.py appeared, etc.), 
so I gave it up to challenge 0.6.0dev.)

Hiroyuki AKAMA
Associate Professor, Graduate School of Decision Science and Technology
Tokyo Institute of Technology,
W9-10, O-okayama, Meguro-ku, Tokyo-152-8552
Japan
akama at dp.hum.titech.ac.jp
http://www.dp.hum.titech.ac.jp

>>> mvpa.__version__
'0.6.0.dev'
>>> mvpa.wtf()
Current date:   2010-12-14 01:36
PyMVPA:
 Version:       0.6.0.dev
 Path:          mvpa/__init__.pyc
 Version control (GIT):
 GIT information could not be obtained due "mvpa/.. is not under GIT"
SYSTEM:
 OS:            posix Linux 2.6.32-5-amd64 #1 SMP Fri Dec 10 15:35:08 UTC 2010
 Distribution:  debian/squeeze/sid
EXTERNALS:
 Present:       cPickle, ctypes, good scipy.stats.rdist, good scipy.stats.rv_discrete.ppf, griddata, gzip, matplotlib, mdp, mdp ge 2.4, nifti, nifti ge 0.20090205.1, numpy, 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
 Absent:        atlas_fsl, atlas_pymvpa, elasticnet, glmnet, h5py, hcluster, lars, libsvm, libsvm verbosity control, lxml, mass, nibabel, nipy, nose, openopt, pprocess, pywt wp reconstruct fixed, rpy2, running ipython env, shogun.lightsvm, shogun.svrlight, skl, weave
 Versions of critical externals:
  shogun:full : 0.9.3_r4889_2010-05-27_20:52_
  shogun:rev  : 4889
  reportlab   : 2.4
  shogun      : 0.9.3
  matplotlib  : 0.99.3
  scipy       : 0.7.2
  mdp         : 2.6
  numpy       : 1.4.1
  ctypes      : 1.1.0
  matplotlib  : 0.99.3
  nifti       : 0.20100607.1
  numpy       : 1.4.1
  pywt        : 0.2.0
  shogun      : v0.9.3_r4889_2010-05-27_20:52_
 Matplotlib backend: TkAgg
RUNTIME:
 PyMVPA Environment Variables:
   PyMVPA Runtime Configuration:
  [externals]
  have griddata = yes
  have pprocess = no
  have good scipy.stats.rdist = yes
  have pylab plottable = yes
  have pywt wp reconstruct = yes
  have h5py = no
  have lxml = no
  have running ipython env = no
  have nibabel = no
  have sg_fixedcachesize = yes
  have elasticnet = no
  have shogun.mpd = yes
  have matplotlib = yes
  have pywt wp reconstruct fixed = no
  have scipy = yes
  have reportlab = yes
  have openopt = no
  have libsvm = no
  have shogun.krr = yes
  have nifti ge 0.20090205.1 = yes
  have nose = no
  have weave = no
  have atlas_fsl = no
  have ctypes = yes
  have hcluster = no
  have sg ge 0.6.4 = yes
  have sg ge 0.6.5 = yes
  have good scipy.stats.rv_discrete.ppf = yes
  have libsvm verbosity control = no
  have mdp ge 2.4 = yes
  have shogun.svrlight = no
  have shogun = yes
  have shogun.svmocas = yes
  have nipy = no
  have glmnet = no
  have mass = no
  have lars = no
  have nifti = yes
  have atlas_pymvpa = no
  have cpickle = yes
  have mdp = yes
  have numpy = yes
  have pylab = yes
  have rpy2 = no
  have shogun.lightsvm = no
  have pywt = yes
  have skl = no
  have gzip = yes
  
  [general]
  verbose = 1
 Process Information:
  Name:	python
  State:	R (running)
  Tgid:	4864
  Pid:	4864
  PPid:	2503
  TracerPid:	0
  Uid:	1000	1000	1000	1000
  Gid:	1000	1000	1000	1000
  FDSize:	256
  Groups:	24 25 27 29 30 44 46 1000 
  VmPeak:	  373920 kB
  VmSize:	  373920 kB
  VmLck:	       0 kB
  VmHWM:	   63076 kB
  VmRSS:	   63076 kB
  VmData:	   55220 kB
  VmStk:	     252 kB
  VmExe:	    2164 kB
  VmLib:	   59288 kB
  VmPTE:	     708 kB
  Threads:	2
  SigQ:	0/16382
  SigPnd:	0000000000000000
  ShdPnd:	0000000000000000
  SigBlk:	0000000000000000
  SigIgn:	0000000001001000
  SigCgt:	0000000180000002
  CapInh:	0000000000000000
  CapPrm:	0000000000000000
  CapEff:	0000000000000000
  CapBnd:	ffffffffffffffff
  Cpus_allowed:	1
  Cpus_allowed_list:	0
  Mems_allowed:	00000000,00000001
  Mems_allowed_list:	0
  voluntary_ctxt_switches:	4116
  nonvoluntary_ctxt_switches:	257

>>> 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"



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