[Neurodebian-users] PyMVPA2 issue

[Morgan Hough]

Hi there,

I am trying to go through the PyMVPA tutorial and I used neurodebian to
install mvpa2 and the tutorial data on an Ubuntu 12.04 system. When I try
and bring in the data I get the following error below. It seems to be
missing ./data/attributes.txt but not sure if its just looking in the wrong
place. Any insight you have would be appreciated.

Cheers,

-Morgan

In [5]: from mvpa2.tutorial_suite import *
/usr/bin/ld: error: linker defined: multiple definition of '_end'
/usr/bin/ld:
/tmp/mhough/python27_intermediate/compiler_724a6138bf2c7161b25adb06501b7d46/home/mhough/.python27_compiled/sc_6ff1965e0184db8dde618da47d2235770.o:
previous definition here
collect2: ld returned 1 exit status
/usr/lib/pymodules/python2.7/sklearn/linear_model/coordinate_descent.py:137:
DeprecationWarning: rho was renamed to l1_ratio and will be removed in 0.15
  "in 0.15", DeprecationWarning)

In [6]: ds = get_haxby2001_data()
---------------------------------------------------------------------------
IOError                                   Traceback (most recent call last)
/home/mhough/<ipython-input-6-ff71aef6615a> in <module>()
----> 1 ds = get_haxby2001_data()

/usr/lib/pymodules/python2.7/mvpa2/tutorial_suite.pyc in
get_haxby2001_data(path, roi)
     40 def get_haxby2001_data(path=None, roi='vt'):
     41     if path is None:
---> 42         ds = get_raw_haxby2001_data(roi=roi)
     43     else:
     44         ds = get_raw_haxby2001_data(path, roi=roi)

/usr/lib/pymodules/python2.7/mvpa2/tutorial_suite.pyc in
get_raw_haxby2001_data(path, roi)
     35         return ds
     36     else:
---> 37         return load_datadb_tutorial_data(path=path, roi=roi)
     38
     39

/usr/lib/pymodules/python2.7/mvpa2/misc/data_generators.pyc in
load_datadb_tutorial_data(path, roi)
    375     else:
    376         raise ValueError("Got something as mask that I cannot
handle.")
--> 377     attr = SampleAttributes(os.path.join(path, 'attributes.txt'))
    378     ds = fmri_dataset(samples=os.path.join(path, 'bold.nii.gz'),
    379                       targets=attr.targets, chunks=attr.chunks,

/usr/lib/pymodules/python2.7/mvpa2/misc/io/base.pyc in __init__(self,
source, literallabels, header)
    406         ColumnData.__init__(self, source,
    407                             header=header,
--> 408                             sep=None, dtype=dtypes)
    409
    410

/usr/lib/pymodules/python2.7/mvpa2/misc/io/base.pyc in __init__(self,
source, header, sep, headersep, dtype, skiplines)
    116         if isinstance(source, str):
    117             self._from_file(source, header=header, sep=sep,
headersep=headersep,
--> 118                            dtype=dtype, skiplines=skiplines)
    119
    120         elif isinstance(source, dict):

/usr/lib/pymodules/python2.7/mvpa2/misc/io/base.pyc in _from_file(self,
filename, header, sep, headersep, dtype, skiplines)
    212         self.clear()
    213
--> 214         file_ = open(filename, 'r')
    215
    216         self._header_order = None

IOError: [Errno 2] No such file or directory: './data/attributes.txt'
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