[Neurodebian-users] ConnectomeViewer on Ubuntu Lucid (10.04)

[Yaroslav Halchenko]

yeah -- confusingly enough connectomeviewer didn't enforce those
dependencies at build-time so binary package for it was built although
that actual environment of an elderly ubuntu release was lacking recent
python-networkx which forbid also to have python-cfflib being built

and networkx 1.5 (and 1.4) failed to build on 10.04 due to failing
unittests:

 subprocess module.
  child_stdin,child_stdout,child_stderr=os.popen3(cmd, 'b')
...S......EEEE.S..S.......................................................................................................S...........................S..............................................................S......S........................S......................
======================================================================
ERROR: test_agraph.TestAGraph.testDirected
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/pymodules/python2.6/nose/case.py", line 183, in runTest
    self.test(*self.arg)
  File "/tmp/buildd/python-networkx-1.5/networkx/drawing/tests/test_agraph.py", line 66, in testDirected
    self.agraph_checks(nx.DiGraph())
  File "/tmp/buildd/python-networkx-1.5/networkx/drawing/tests/test_agraph.py", line 39, in agraph_checks
    H=nx.from_agraph(A)
  File "/tmp/buildd/python-networkx-1.5/networkx/drawing/nx_agraph.py", line 99, in from_agraph
    if e.name is not None:
AttributeError: 'Edge' object has no attribute 'name'

======================================================================
ERROR: test_agraph.TestAGraph.testMultiDirected
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/pymodules/python2.6/nose/case.py", line 183, in runTest
    self.test(*self.arg)
  File "/tmp/buildd/python-networkx-1.5/networkx/drawing/tests/test_agraph.py", line 72, in testMultiDirected
    self.agraph_checks(nx.MultiDiGraph())
  File "/tmp/buildd/python-networkx-1.5/networkx/drawing/tests/test_agraph.py", line 39, in agraph_checks
    H=nx.from_agraph(A)
  File "/tmp/buildd/python-networkx-1.5/networkx/drawing/nx_agraph.py", line 103, in from_agraph
    N.add_edge(u,v,key=e.name,**str_attr)
AttributeError: 'Edge' object has no attribute 'name'
....

blunt guess for a  reason --  probably incompatibility with that elderly
graphviz shipped with the system... so if you were to backport you might need
to start that deep...   or disable testing and allow to have semi-functional
networkx to be deployed to superseed system-wide, with incompatible API,
version of networkx.

Sorry if this is of not much help :-/

On Mon, 24 Oct 2011, Neil Hoggarth wrote:

> I am a sysadmin at a University site. One of the academic users has
> asked for ConnectomeViewer to be installed on their workstation. The
> machine in question is running Ubuntu "Lucid Lynx" (10.04 LTS). It
> has the NeuroDebian repository already configured as an apt source,
> and is already successfully using other packaged downloaded from the
> repository.

> Attempting to "apt-get install connectomeviewer" fails with two
> unmet dependencies:

> The following packages have unmet dependencies.
>   connectomeviewer: Depends: python-cfflib (>= 2.0.5) but it is not installable
>                     Depends: python-networkx (>= 1.4) but 1.1-2~lucid.nd1 is to be installed

> Should these pre-requesite packages be available to me somewhere,
> given that there is a connectomeviewer_2.0.0-1~nd10.04+1_all.deb
> package in the repository?

> Or do I need to look into back-porting the python packages to Lucid
> somehow in order to make this work?

> Regards,
-- 
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