[pymvpa] Fail to install upstream/0.6.0.dev in avirtualenv(Neuro Debian)
akama.h.aa at m.titech.ac.jp
Wed Dec 22 01:11:10 UTC 2010
Dear Prof. Hanke
Yes. As you rightly pointed it out, I had not been aware of mingling files of different versions when repeating trial error between upstream/0.6.0.dev and upstream/0.5.0.dev.
Now I completely removed PyMVPA from my NeuroDebian6.0.1 on Windows 7 amd-64 and restarted to install upstream/0.6.0.dev (pymvpa-26e856e.tar.gz) to be used with Python2.6.6 (I also tried Python 2.5 by changing simlink, but didn't help)
However another kind of trouble took place, which is as follows.
It would be much appreciated providing me your suggestion.
In : from tutorial_lib import *
matplotlib.numerix and all its subpackages are deprecated.
They will be removed soon. Please use numpy instead.
In : ds=get_haxby2001_data()
TypeError Traceback (most recent call last)
/mnt/host/pymvpa-26e856e/tutorial_data/<ipython console> in <module>()
/mnt/host/pymvpa-26e856e/tutorial_data/tutorial_lib.pyc in get_haxby2001_data(path, roi)
46 # do chunkswise linear detrending on dataset
---> 47 poly_detrend(ds, polyord=1, chunks_attr='chunks', inspace='time_coords')
49 # mark the odd and even runs
/usr/local/lib/python2.6/dist-packages/mvpa/mappers/detrend.pyc in poly_detrend(ds, **kwargs)
--> 349 dm = PolyDetrendMapper(**kwarYes. I was not aware of mingling files of different versions when repeating trial error between upstream/0.6.0.dev and upstream/0.5.0.dev
Now I completely removed PyMVPA from my NeuroDebian6.0.1 on Windows 7 amd-64 and restarted to install upstream/0.6.0.dev (pymvpa-26e856e.tar.gz) to be used with Python2.6.6 (I also tried Python 2.5 by changing simlink)gs)
350 dm._secret_inplace_detrend = True
351 # map
/usr/local/lib/python2.6/dist-packages/mvpa/mappers/detrend.pyc in __init__(self, polyord, chunks_attr, opt_regs, **kwargs)
119 # need to init last to prevent base class puking
--> 120 Mapper.__init__(self, **kwargs)
/usr/local/lib/python2.6/dist-packages/mvpa/mappers/base.pyc in __init__(self, **kwargs)
42 All additional arguments are passed to the baseclass.
---> 44 Learner.__init__(self, **kwargs)
45 # internal settings that influence what should be done to the dataset
46 # attributes in the default forward() and reverse() implementations.
/usr/local/lib/python2.6/dist-packages/mvpa/base/learner.pyc in __init__(self, auto_train, force_train, **kwargs)
75 All arguments are passed to the baseclass.
---> 77 Node.__init__(self, **kwargs)
78 self.__istrained = False
79 self.__auto_train = auto_train
/usr/local/lib/python2.6/dist-packages/mvpa/base/node.pyc in __init__(self, space, postproc, **kwargs)
47 result dataset. If None, nothing is done.
---> 49 ClassWithCollections.__init__(self, **kwargs)
/usr/local/lib/python2.6/dist-packages/mvpa/base/state.pyc in __init__(self, descr, **kwargs)
848 "Unexpected keyword argument %s=%s for %s." \
849 % (arg, argument, self) \
--> 850 + " Valid parameters are %s" % known_params
852 ## Initialize other base classes
TypeError: Unexpected keyword argument inspace=time_coords for <PolyDetrendMapper: ord=1>. Valid parameters are ['training_time']
----- Original Message -----
>> From: Michael Hanke <michael.hanke at gmail.com>
>> To: Hiroyuki AKAMA <akama.h.aa at m.titech.ac.jp>
>> Cc: Development and support of PyMVPA <pkg-exppsy-pymvpa at lists.alioth.debian.org>,brian.murphy at unitn.it
>> Date: 2010-12-21 21:13:39
>> Subject: Re: [pymvpa] Fail to install upstream/0.6.0.dev in avirtualenv(Neuro Debian)
>> On Tue, Dec 21, 2010 at 04:47:20PM +0900, Hiroyuki AKAMA wrote:
>> > By the way, I am now at a loss trying in vain to do fmri_dataset() in
>> > your tutorial. It would be much appreciated pointing out what was
>> > wrong. I am afraid it was due to a very basic mistake... Here are
>> > the results I),II) of the same import task with and without using
>> > IPython. My environment is 0.6.0dev in NeuroDebian on Windows7
>> > 64-bit.
>> I assume you do not have a clean install of 0.6dev, but there are still
>> some leftovers of previous versions lying around. The traceback you
>> provided has this:
>> > /usr/local/lib/python2.6/dist-packages/mvpa/datasets/nifti.py in <module>()
>> > 20 from mvpa.base import debug
>> > 21
>> > ---> 22 if externals.exists('nifti', raiseException=True):
>> > 23 if sys.version_info[:2] >= (2, 5):
>> > 24 # enforce absolute import
>> The file mvpa/datasets/nifti.py was removed almost exactly a year ago
>> with this commit:
>> I guess the best strategy would be to completely remove PyMVPA from your
>> system and reinstall a fresh and clean 0.6.dev snapshot. How did you
>> install it previously?
>> If you experience problems please report them and we'll sort them out.
>> Michael Hanke
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