ValueError: numpy.dtype does not appear to be the correct type object
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
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
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
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
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
participants (3)
-
Kanwei Li -
Nate Coraor -
Peter Cock