[pymvpa] Installation Problem with 0.6 rc3
Yaroslav Halchenko
debian at onerussian.com
Mon Oct 3 01:48:15 UTC 2011
Hi Rick,
sorry about the problems -- clearly the fault is on our side due to a
messy situation with (un)released versions... we will fix it up soon
so -- you have now systemwide installed rc3 (strange enough already
since neurodebian repositories carry rc4), but then in the GIT
repository snapshot you are observing our move to rename 0.6 mvpa into
mvpa2 (would become 2.0) so people could co-install stable 0.4.x series
and what we planned for 0.6 but is about to become 2.0.
So... since the tutorial dataset we distribute still requires
not-renamed mvpa 0.6, you should step away from the GIT snapshot
directory, and go into the directory where you extracted the
tutorial dataset you got from
http://data.pymvpa.org/datasets/tutorial_data/
and then just follow the instructions of the tutorial
http://www.pymvpa.org/tutorial.html
which says:
"run: ./start_tutorial_session.sh"
that should then pick up the system-wide installed python-mvpa-snapshot
(rc3 or rc4 you have) and it should work -- I just replicated it:
head1:/tmp
$> apt-cache policy python-mvpa-snapshot
python-mvpa-snapshot:
Installed: 0.6.0~rc3-1~nd60+1
Candidate: 0.6.0~rc4-1~nd60+1
Version table:
0.6.0~rc4-1~nd60+1 0
500 http://neuro.debian.net/debian/ squeeze/main amd64 Packages
*** 0.6.0~rc3-1~nd60+1 0
100 /var/lib/dpkg/status
1 11693.....................................:Sun 02 Oct 2011 09:46:04 PM EDT:.
head1:/tmp
$> wget http://data.pymvpa.org/datasets/tutorial_data/tutorial_data-0.2.tar.gz
--2011-10-02 21:46:18-- http://data.pymvpa.org/datasets/tutorial_data/tutorial_data-0.2.tar.gz
Resolving data.pymvpa.org... 129.170.30.193
Connecting to data.pymvpa.org|129.170.30.193|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 463705064 (442M) [application/x-gzip]
Saving to: “tutorial_data-0.2.tar.gz”
100%[===================================================================================================================================================================================>] 463 705 064 11,2M/s in 40s
2011-10-02 21:46:58 (11,0 MB/s) - “tutorial_data-0.2.tar.gz” saved [463705064/463705064]
1 11694.....................................:Sun 02 Oct 2011 09:46:58 PM EDT:.
head1:/tmp
$> tar -xzf tutorial_data-0.2.tar.gz
tar -xzf tutorial_data-0.2.tar.gz 4,74s user 2,26s system 132% cpu 5,273 total
1 11695.....................................:Sun 02 Oct 2011 09:47:13 PM EDT:.
head1:/tmp
$> cd tutorial_data
data/ results/ start_tutorial_session.sh* tutorial_lib.py
1 11696.....................................:Sun 02 Oct 2011 09:47:16 PM EDT:.
head1:/tmp/tutorial_data
$> ./start_tutorial_session.sh
Python 2.6.6 (r266:84292, Dec 26 2010, 22:31:48)
Type "copyright", "credits" or "license" for more information.
IPython 0.10 -- An enhanced Interactive Python.
? -> Introduction and overview of IPython's features.
%quickref -> Quick reference.
help -> Python's own help system.
object? -> Details about 'object'. ?object also works, ?? prints more.
Welcome to pylab, a matplotlib-based Python environment.
For more information, type 'help(pylab)'.
In [1]: from tutorial_lib import *
Error in library("lars") : there is no package called 'lars'
Error in library("elasticnet") : there is no package called 'elasticnet'
Loaded glmnet 1.4
/usr/lib/pymodules/python2.6/matplotlib/numerix/__init__.py:18: DeprecationWarning:
**********************************************************
matplotlib.numerix and all its subpackages are deprecated.
They will be removed soon. Please use numpy instead.
**********************************************************
warnings.warn(msg, DeprecationWarning)
On Sun, 02 Oct 2011, Rick Solis wrote:
> Hi, i am getting errors going through the tutorial.
> #1- import mvpa2 returns ImportError: No module named mvpa2
> #2- from tutorial_lib import * ImportError: No module named mvpa2.suite
> #3 Suggestions or ideas on how to resolve these two errors?
> Here's the relevant info and the trouble-shooting I've done.
> specifically, I am getting this error in ipython when i run
> from tutorial_lib import *
> .../tools/tutorial_lib.py in <module>()
> 13
> 14 # later replace with
> ---> 15 from mvpa2.suite import *
> 16
> 17 tutorial_data_path = mvpa2.cfg.get('location', 'tutorial data',
> default=os.path.curdir)
> ImportError: No module named mvpa2.suite
> I think what is causing my problem is had version 0.4, removed 0.4 and
> installed 0.6-snapshot.
> From reading the mailing list the mvpa module is version 0.4x and the
> mvpa2 module is 0.6x.
> Initially I installed PyMVPA using sudo apt-get python-mvpa.
> This installed version 0.4x. After checking the versions, I removed
> mvpa (0.4) and installed the snapshot from the Neurodebian
> respository.
> So now I have the snapshot version, but it will only load when I use
> import mvpa
> Import mvpa and checking the version returns 0.6.
> In [3]: mvpa.__version__
> Out[3]: '0.6.0~rc3'
> Import mvpa2 returns: ImportError: No module named mvpa2
> Here's the output of mvpa.wtf()
> In [6]: mvpa.wtf()
> /usr/lib/pymodules/python2.7/nose/util.py:14: DeprecationWarning: The
> compiler package is deprecated and removed in Python 3.x.
> from compiler.consts import CO_GENERATOR
> Out[6]:
> Current date: 2011-10-02 13:58
> PyMVPA:
> Version: 0.6.0~rc3
> Hash: fd0f2809300cc25e81ee21a3a876d00d524402c1
> Path: /usr/lib/pymodules/python2.7/mvpa/__init__.pyc
> Version control (GIT):
> GIT information could not be obtained due
> "/usr/lib/pymodules/python2.7/mvpa/.. is not under GIT"
> SYSTEM:
> OS: posix Linux 2.6.38-11-generic #50-Ubuntu SMP Mon Sep 12
> 21:17:25 UTC 2011
> Distribution: Ubuntu/11.04/natty
> EXTERNALS:
> Present: atlas_fsl, cPickle, ctypes, good scipy.stats.rdist,
> good scipy.stats.rv_discrete.ppf, griddata, gzip, h5py, libsvm, libsvm
> verbosity control, lxml, matplotlib, mdp, mdp ge 2.4, nibabel, nipy,
> nose, numpy, pylab, pylab plottable, pywt, pywt wp reconstruct,
> reportlab, running ipython env, scipy, sg ge 0.6.4, sg ge 0.6.5,
> sg_fixedcachesize, shogun, shogun.krr, shogun.mpd, shogun.svmocas
> Absent: atlas_pymvpa, elasticnet, glmnet, hcluster, lars, mass,
> nipy.neurospin, openopt, pprocess, pywt wp reconstruct fixed, rpy2,
> shogun.lightsvm, shogun.svrlight, skl, weave
> Versions of critical externals:
> shogun:full : 0.9.3_r4889_2010-05-27_20:52_
> shogun:rev : 4889
> nibabel : 1.1.0
> shogun : 0.9.3
> reportlab : 2.5
> matplotlib : 0.99.3
> scipy : 0.8.0
> nipy : 0.1.2.dev
> ipython : 0.10.1
> mdp : 2.6
> numpy : 1.5.1
> ctypes : 1.1.0
> matplotlib : 0.99.3
> lxml : 2.3.0
> nifti : failed to query due to "nifti is not a known dependency
> key."
> numpy : 1.5.1
> pywt : 0.2.0
> shogun : v0.9.3_r4889_2010-05-27_20:52_
> Matplotlib backend: TkAgg
> RUNTIME:
> PyMVPA Environment Variables:
> PyMVPA Runtime Configuration:
> [general]
> verbose = 1
> [externals]
> have running ipython env = yes
> 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 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 lars = no
> 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 = yes
> 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 = 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 = no
> have weave = no
> Process Information:
> Name: ipython
> State: R (running)
> Tgid: 2731
> Pid: 2731
> PPid: 21080
> TracerPid: 0
> Uid: 1000 1000 1000 1000
> Gid: 1000 1000 1000 1000
> FDSize: 256
> Groups: 4 20 24 46 112 120 122 1000
> VmPeak: 470652 kB
> VmSize: 470652 kB
> VmLck: 0 kB
> VmHWM: 78224 kB
> VmRSS: 78224 kB
> VmData: 66020 kB
> VmStk: 256 kB
> VmExe: 2236 kB
> VmLib: 71284 kB
> VmPTE: 892 kB
> VmSwap: 0 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: ff
> Cpus_allowed_list: 0-7
> Mems_allowed: 00000000,00000001
> Mems_allowed_list: 0
> voluntary_ctxt_switches: 459
> nonvoluntary_ctxt_switches: 115
> In [7]: 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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> Pkg-ExpPsy-PyMVPA at lists.alioth.debian.org
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