On Thu, Jun 9, 2011 at 11:43 AM, Peter Cock p.j.a.cock@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 nate@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

Fixed on trunk.

On Thu, Jun 9, 2011 at 10:26 AM, Nate Coraor nate@bx.psu.edu wrote:

Peter Cock wrote:

...

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 nate@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.

bx_python needs to be rebuilt using the new version of the numpy egg. I am doing this now and they should be up shortly.

--nate

...

Peter

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