On Thu, Jun 9, 2011 at 11:43 AM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
> Hi all,
>
> I just updated our development machine to the latest from galaxy-central,
> and it broke:
>
> $ ./run.sh
> Traceback (most recent call last):
>  File "/home/pjcock/repositories/galaxy-central/lib/galaxy/web/buildapp.py",
> line 81, in app_factory
>    from galaxy.app import UniverseApplication
>  File "/home/pjcock/repositories/galaxy-central/lib/galaxy/app.py",
> line 11, in <module>
>    from galaxy.tools.imp_exp import load_history_imp_exp_tools
>  File 
> "/home/pjcock/repositories/galaxy-central/lib/galaxy/tools/imp_exp/__init__.py",
> line 6, in <module>
>    from galaxy.web.base.controller import UsesHistory
>  File 
> "/home/pjcock/repositories/galaxy-central/lib/galaxy/web/base/controller.py",
> line 12, in <module>
>    from galaxy.visualization.tracks.data_providers import get_data_provider
>  File 
> "/home/pjcock/repositories/galaxy-central/lib/galaxy/visualization/tracks/data_providers.py",
> line 16, in <module>
>    from bx.arrays.array_tree import FileArrayTreeDict
>  File "numpy.pxd", line 119, in init bx.arrays.array_tree
> (lib/bx/arrays/array_tree.c:11323)
> ValueError: numpy.dtype does not appear to be the correct type object
>
> I checked I had the latest numpy and bx_python egg files by removing them,
> Galaxy downloaded the same ones:
>
> bx_python-0.7.0_494c2d1d68b3-py2.6-linux-x86_64-ucs2.egg
> numpy-1.6.0-py2.6-linux-x86_64-ucs2.egg
>
> This is a 64 bit Linux machine. Any ideas what might be wrong? I'm guessing
> some Pyrex or Cython extension module in an egg file needs recompiling.
>
> Note there is a system level install of NumPy 1.4.1 on this machine, but
> I believe the egg is used in preference?
>
> Peter
>

It turned out to be quite quick to find what commit broke things:

hg checkout 6074:a6868407f0e8
--> fails

hg checkout 6073:d6b048e3483e
--> works

Looks like 6074:a6868407f0e8 is the cause then, which makes sense
since it jumps from NumPy 1.3.0 to NumPy 1.6.0:-

changeset:   6074:a6868407f0e8
user:        Nate Coraor <n...@bx.psu.edu>
date:        Wed Jun 08 23:50:07 2011 -0400
summary:     Testing Python 2.7.

https://bitbucket.org/galaxy/galaxy-central/changeset/a6868407f0e8

Probably some of the eggs need to be updated.

Peter

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