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Comments (5)

rmcgibbo avatar rmcgibbo commented on June 16, 2024

Can you post the output of these two commands?

$ python --version
$ python -c "import numpy; print(numpy.version.full_version)"

from mdtraj.

rmcgibbo avatar rmcgibbo commented on June 16, 2024

Also, can you try running the tests in mdtraj, and post the output?

$ cd mdtraj
$ easy_install nose
$ nosetests

from mdtraj.

dermen avatar dermen commented on June 16, 2024

Hey,

Python version is 2.6.5, and numpy.version.full_version is 1.6.1. I think maybe I need a later version of numpy...

as for the tests:


dermen@faust:~/mdtraj$ sudo easy_install nose
[sudo] password for dermen:
Searching for nose
Best match: nose 1.2.1
Processing nose-1.2.1-py2.6.egg
nose 1.2.1 is already the active version in easy-install.pth
Installing nosetests-2.6 script to /usr/local/bin
Installing nosetests script to /usr/local/bin

Using /usr/local/lib/python2.6/dist-packages/nose-1.2.1-py2.6.egg
Processing dependencies for nose
Finished processing dependencies for nose


and


dermen@faust:~/mdtraj$ nosetests
/usr/local/lib/python2.6/dist-packages/mdtraj-0.0.0-py2.6-linux-i686.egg/mdtraj/trajectory.py:21: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility
from mdtraj import dcd, xtc, binpos, trr
/usr/local/lib/python2.6/dist-packages/mdtraj-0.0.0-py2.6-linux-i686.egg/mdtraj/trajectory.py:21: RuntimeWarning: numpy.flatiter size changed, may indicate binary incompatibility
from mdtraj import dcd, xtc, binpos, trr
Doctest: MDTraj.pdb.pdbstructure.Atom.Location.iter ... ok
Doctest: MDTraj.pdb.pdbstructure.Atom.iter_coordinates ... ok
Doctest: MDTraj.pdb.pdbstructure.Atom.iter_locations ... ok
Doctest: MDTraj.pdb.pdbstructure.Residue.iter ... ok
Doctest: MDTraj.pdb.pdbstructure.Residue.iter_positions ... ok
MDTraj.pdb.test_pdb.test_pdbread ... ok
MDTraj.pdb.test_pdb.test_pdbwrite ... ok
MDTraj.utils.test.test_ensure_type_1 ... ok
MDTraj.utils.test.test_ensure_type_2 ... ok
MDTraj.utils.test.test_ensure_type_25 ... ok
MDTraj.utils.test.test_ensure_type_3 ... ok
MDTraj.utils.test.test_ensure_type_4 ... ok
MDTraj.utils.test.test_ensure_type_5 ... ok
MDTraj.utils.test.test_ensure_type_6 ... ok
NumpyDoc: mdtraj.binpos.write ... ok
NumpyDoc: mdtraj.binpos.read ... ok
MDTraj.test.test_binpos.test_read_chunk1 ... ok
MDTraj.test.test_binpos.test_read_chunk1 ... ok
MDTraj.test.test_binpos.test_read_chunk10 ... ok
MDTraj.test.test_binpos.test_read_chunk10 ... ok
MDTraj.test.test_binpos.test_read_chunk1000 ... ok
MDTraj.test.test_binpos.test_read_chunk1000 ... ok
MDTraj.test.test_binpos.test_write_1 ... ok
NumpyDoc: mdtraj.dcd.write ... ok
NumpyDoc: mdtraj.dcd.read ... ok
MDTraj.test.test_dcd.test_read ... ok
MDTraj.test.test_dcd.test_write_0 ... ok
MDTraj.test.test_dcd.test_write_1 ... ok
MDTraj.test.test_dcd.test_write_2 ... ok
MDTraj.test.test_dcd.test_write_2 ... ok
MDTraj.test.test_dcd.test_write_2 ... ok
Load by specifying array name ... ok
load using deferred=True ... ok
Save HDF5 to disk and load it back up ... ok
Load by specifying array name ... ok
load using deferred=True ... ok
Save HDF5 to disk and load it back up ... ok
MDTraj.test.test_io.test_overwrite_1 ... ok
MDTraj.test.test_io.test_overwrite_2 ... ok
NumpyDoc: mdtraj.trajectory.load_xtc ... ok
NumpyDoc: mdtraj.trajectory.load_trr ... ok
NumpyDoc: mdtraj.trajectory.Trajectory.save_pdb ... ok
NumpyDoc: mdtraj.trajectory.Trajectory.save_hdf ... ok
NumpyDoc: mdtraj.trajectory.Trajectory.save_dcd ... ok
NumpyDoc: mdtraj.trajectory.Trajectory.save_binpos ... ok
NumpyDoc: mdtraj.trajectory.Trajectory.save ... ok
NumpyDoc: mdtraj.trajectory.Trajectory.openmm_positions ... ok
NumpyDoc: mdtraj.trajectory.Trajectory.openmm_boxes ... ok
NumpyDoc: mdtraj.trajectory.load ... ok
NumpyDoc: mdtraj.trajectory.Trajectory.join ... ok
NumpyDoc: mdtraj.trajectory.load_pdb ... ok
NumpyDoc: mdtraj.trajectory.load_hdf ... ok
NumpyDoc: mdtraj.trajectory.load_dcd ... ok
NumpyDoc: mdtraj.trajectory.load_binpos ... ok
NumpyDoc: mdtraj.trajectory.load ... ok
NumpyDoc: mdtraj.trajectory.Trajectory.slice ... ok
NumpyDoc: mdtraj.trajectory.Trajectory.save_xtc ... ok
NumpyDoc: mdtraj.trajectory.Trajectory.save_trr ... ok
MDTraj.test.test_trajectory.test_hdf0 ... ok
MDTraj.test.test_trajectory.test_hdf1 ... ok
MDTraj.test.test_trajectory.test_hdf1 ... ok
MDTraj.test.test_trajectory.test_hdf2 ... ok
MDTraj.test.test_trajectory.test_hdf2 ... ok
MDTraj.test.test_trajectory.test_hdf2 ... ok
MDTraj.test.test_trajectory.test_slice ... ok
MDTraj.test.test_trajectory.test_slice ... ok
MDTraj.test.test_trajectory.test_slice ... ok
MDTraj.test.test_trajectory.test_xtc ... ok
MDTraj.test.test_trajectory.test_xtc ... ok
MDTraj.test.test_trajectory.test_xtc ... ok
MDTraj.test.test_trajectory.test_xtc ... ok
MDTraj.test.test_trajectory.test_dcd ... /usr/local/lib/python2.6/dist-packages/mdtraj-0.0.0-py2.6-linux-i686.egg/mdtraj/utils/arrays.py:52: TypeCastPerformanceWarning: Casting dtype=int32 to <type 'numpy.float32'>
TypeCastPerformanceWarning)
ok
MDTraj.test.test_trajectory.test_dcd ... ok
MDTraj.test.test_trajectory.test_dcd ... ok
MDTraj.test.test_trajectory.test_dcd ... ok
MDTraj.test.test_trajectory.test_binpos ... ok
MDTraj.test.test_trajectory.test_binpos ... ok
MDTraj.test.test_trajectory.test_binpos ... ok
MDTraj.test.test_trajectory.test_binpos ... ok
MDTraj.test.test_trr.test1 ... ok
MDTraj.test.test_trr.test2 ... ok
NumpyDoc: mdtraj.xtc.write ... ok
NumpyDoc: mdtraj.xtc.read ... ok
MDTraj.test.test_xtc.test_read_chunk1 ... ok
MDTraj.test.test_xtc.test_read_chunk1 ... ok
MDTraj.test.test_xtc.test_read_chunk1 ... ok
MDTraj.test.test_xtc.test_read_chunk1 ... ok
MDTraj.test.test_xtc.test_read_chunk1 ... ok
MDTraj.test.test_xtc.test_read_chunk10 ... ok
MDTraj.test.test_xtc.test_read_chunk10 ... ok
MDTraj.test.test_xtc.test_read_chunk10 ... ok
MDTraj.test.test_xtc.test_read_chunk10 ... ok
MDTraj.test.test_xtc.test_read_chunk10 ... ok
MDTraj.test.test_xtc.test_read_chunk1000 ... ok
MDTraj.test.test_xtc.test_read_chunk1000 ... ok
MDTraj.test.test_xtc.test_read_chunk1000 ... ok
MDTraj.test.test_xtc.test_read_chunk1000 ... ok
MDTraj.test.test_xtc.test_read_chunk1000 ... ok
MDTraj.test.test_xtc.test_write_0 ... ok
MDTraj.test.test_xtc.test_write_1 ... /usr/local/lib/python2.6/dist-packages/mdtraj-0.0.0-py2.6-linux-i686.egg/mdtraj/utils/arrays.py:52: TypeCastPerformanceWarning: Casting dtype=float64 to <type 'numpy.float32'>
TypeCastPerformanceWarning)
ok


Ran 100 tests in 2.209s

OK
dermen@faust:~/mdtraj$


----- Original Message -----
From: "Robert McGibbon" [email protected]
To: "rmcgibbo/mdtraj" [email protected]
Cc: "Derek Mendez" [email protected]
Sent: Monday, December 3, 2012 5:54:49 PM
Subject: Re: [mdtraj] get the following error when installing under ubuntu (#7)

Also, can you try running the tests in mdtraj, and post the output? $ cd mdtraj
$ easy_install nose
$ nosetests


Reply to this email directly or view it on GitHub .

from mdtraj.

rmcgibbo avatar rmcgibbo commented on June 16, 2024

From googling it, I think it doesn't matter.

All the years pass, so I wouldn't worry

If you want to fix it, I think upgrading to python 2.7.3 would fix it.

But I wouldn't worry about it.

Sent from my iPhone

On Dec 3, 2012, at 6:03 PM, Derek Mendez [email protected] wrote:

Hey,

Python version is 2.6.5, and numpy.version.full_version is 1.6.1. I think maybe I need a later version of numpy...

as for the tests:


dermen@faust:~/mdtraj$ sudo easy_install nose
[sudo] password for dermen:
Searching for nose
Best match: nose 1.2.1
Processing nose-1.2.1-py2.6.egg
nose 1.2.1 is already the active version in easy-install.pth
Installing nosetests-2.6 script to /usr/local/bin
Installing nosetests script to /usr/local/bin

Using /usr/local/lib/python2.6/dist-packages/nose-1.2.1-py2.6.egg
Processing dependencies for nose
Finished processing dependencies for nose


and


dermen@faust:~/mdtraj$ nosetests
/usr/local/lib/python2.6/dist-packages/mdtraj-0.0.0-py2.6-linux-i686.egg/mdtraj/trajectory.py:21: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility
from mdtraj import dcd, xtc, binpos, trr
/usr/local/lib/python2.6/dist-packages/mdtraj-0.0.0-py2.6-linux-i686.egg/mdtraj/trajectory.py:21: RuntimeWarning: numpy.flatiter size changed, may indicate binary incompatibility
from mdtraj import dcd, xtc, binpos, trr
Doctest: MDTraj.pdb.pdbstructure.Atom.Location.iter ... ok
Doctest: MDTraj.pdb.pdbstructure.Atom.iter_coordinates ... ok
Doctest: MDTraj.pdb.pdbstructure.Atom.iter_locations ... ok
Doctest: MDTraj.pdb.pdbstructure.Residue.iter ... ok
Doctest: MDTraj.pdb.pdbstructure.Residue.iter_positions ... ok
MDTraj.pdb.test_pdb.test_pdbread ... ok
MDTraj.pdb.test_pdb.test_pdbwrite ... ok
MDTraj.utils.test.test_ensure_type_1 ... ok
MDTraj.utils.test.test_ensure_type_2 ... ok
MDTraj.utils.test.test_ensure_type_25 ... ok
MDTraj.utils.test.test_ensure_type_3 ... ok
MDTraj.utils.test.test_ensure_type_4 ... ok
MDTraj.utils.test.test_ensure_type_5 ... ok
MDTraj.utils.test.test_ensure_type_6 ... ok
NumpyDoc: mdtraj.binpos.write ... ok
NumpyDoc: mdtraj.binpos.read ... ok
MDTraj.test.test_binpos.test_read_chunk1 ... ok
MDTraj.test.test_binpos.test_read_chunk1 ... ok
MDTraj.test.test_binpos.test_read_chunk10 ... ok
MDTraj.test.test_binpos.test_read_chunk10 ... ok
MDTraj.test.test_binpos.test_read_chunk1000 ... ok
MDTraj.test.test_binpos.test_read_chunk1000 ... ok
MDTraj.test.test_binpos.test_write_1 ... ok
NumpyDoc: mdtraj.dcd.write ... ok
NumpyDoc: mdtraj.dcd.read ... ok
MDTraj.test.test_dcd.test_read ... ok
MDTraj.test.test_dcd.test_write_0 ... ok
MDTraj.test.test_dcd.test_write_1 ... ok
MDTraj.test.test_dcd.test_write_2 ... ok
MDTraj.test.test_dcd.test_write_2 ... ok
MDTraj.test.test_dcd.test_write_2 ... ok
Load by specifying array name ... ok
load using deferred=True ... ok
Save HDF5 to disk and load it back up ... ok
Load by specifying array name ... ok
load using deferred=True ... ok
Save HDF5 to disk and load it back up ... ok
MDTraj.test.test_io.test_overwrite_1 ... ok
MDTraj.test.test_io.test_overwrite_2 ... ok
NumpyDoc: mdtraj.trajectory.load_xtc ... ok
NumpyDoc: mdtraj.trajectory.load_trr ... ok
NumpyDoc: mdtraj.trajectory.Trajectory.save_pdb ... ok
NumpyDoc: mdtraj.trajectory.Trajectory.save_hdf ... ok
NumpyDoc: mdtraj.trajectory.Trajectory.save_dcd ... ok
NumpyDoc: mdtraj.trajectory.Trajectory.save_binpos ... ok
NumpyDoc: mdtraj.trajectory.Trajectory.save ... ok
NumpyDoc: mdtraj.trajectory.Trajectory.openmm_positions ... ok
NumpyDoc: mdtraj.trajectory.Trajectory.openmm_boxes ... ok
NumpyDoc: mdtraj.trajectory.load ... ok
NumpyDoc: mdtraj.trajectory.Trajectory.join ... ok
NumpyDoc: mdtraj.trajectory.load_pdb ... ok
NumpyDoc: mdtraj.trajectory.load_hdf ... ok
NumpyDoc: mdtraj.trajectory.load_dcd ... ok
NumpyDoc: mdtraj.trajectory.load_binpos ... ok
NumpyDoc: mdtraj.trajectory.load ... ok
NumpyDoc: mdtraj.trajectory.Trajectory.slice ... ok
NumpyDoc: mdtraj.trajectory.Trajectory.save_xtc ... ok
NumpyDoc: mdtraj.trajectory.Trajectory.save_trr ... ok
MDTraj.test.test_trajectory.test_hdf0 ... ok
MDTraj.test.test_trajectory.test_hdf1 ... ok
MDTraj.test.test_trajectory.test_hdf1 ... ok
MDTraj.test.test_trajectory.test_hdf2 ... ok
MDTraj.test.test_trajectory.test_hdf2 ... ok
MDTraj.test.test_trajectory.test_hdf2 ... ok
MDTraj.test.test_trajectory.test_slice ... ok
MDTraj.test.test_trajectory.test_slice ... ok
MDTraj.test.test_trajectory.test_slice ... ok
MDTraj.test.test_trajectory.test_xtc ... ok
MDTraj.test.test_trajectory.test_xtc ... ok
MDTraj.test.test_trajectory.test_xtc ... ok
MDTraj.test.test_trajectory.test_xtc ... ok
MDTraj.test.test_trajectory.test_dcd ... /usr/local/lib/python2.6/dist-packages/mdtraj-0.0.0-py2.6-linux-i686.egg/mdtraj/utils/arrays.py:52: TypeCastPerformanceWarning: Casting dtype=int32 to <type 'numpy.float32'>
TypeCastPerformanceWarning)
ok
MDTraj.test.test_trajectory.test_dcd ... ok
MDTraj.test.test_trajectory.test_dcd ... ok
MDTraj.test.test_trajectory.test_dcd ... ok
MDTraj.test.test_trajectory.test_binpos ... ok
MDTraj.test.test_trajectory.test_binpos ... ok
MDTraj.test.test_trajectory.test_binpos ... ok
MDTraj.test.test_trajectory.test_binpos ... ok
MDTraj.test.test_trr.test1 ... ok
MDTraj.test.test_trr.test2 ... ok
NumpyDoc: mdtraj.xtc.write ... ok
NumpyDoc: mdtraj.xtc.read ... ok
MDTraj.test.test_xtc.test_read_chunk1 ... ok
MDTraj.test.test_xtc.test_read_chunk1 ... ok
MDTraj.test.test_xtc.test_read_chunk1 ... ok
MDTraj.test.test_xtc.test_read_chunk1 ... ok
MDTraj.test.test_xtc.test_read_chunk1 ... ok
MDTraj.test.test_xtc.test_read_chunk10 ... ok
MDTraj.test.test_xtc.test_read_chunk10 ... ok
MDTraj.test.test_xtc.test_read_chunk10 ... ok
MDTraj.test.test_xtc.test_read_chunk10 ... ok
MDTraj.test.test_xtc.test_read_chunk10 ... ok
MDTraj.test.test_xtc.test_read_chunk1000 ... ok
MDTraj.test.test_xtc.test_read_chunk1000 ... ok
MDTraj.test.test_xtc.test_read_chunk1000 ... ok
MDTraj.test.test_xtc.test_read_chunk1000 ... ok
MDTraj.test.test_xtc.test_read_chunk1000 ... ok
MDTraj.test.test_xtc.test_write_0 ... ok
MDTraj.test.test_xtc.test_write_1 ... /usr/local/lib/python2.6/dist-packages/mdtraj-0.0.0-py2.6-linux-i686.egg/mdtraj/utils/arrays.py:52: TypeCastPerformanceWarning: Casting dtype=float64 to <type 'numpy.float32'>
TypeCastPerformanceWarning)
ok


Ran 100 tests in 2.209s

OK
dermen@faust:~/mdtraj$


----- Original Message -----
From: "Robert McGibbon" [email protected]
To: "rmcgibbo/mdtraj" [email protected]
Cc: "Derek Mendez" [email protected]
Sent: Monday, December 3, 2012 5:54:49 PM
Subject: Re: [mdtraj] get the following error when installing under ubuntu (#7)

Also, can you try running the tests in mdtraj, and post the output? $ cd mdtraj
$ easy_install nose
$ nosetests


Reply to this email directly or view it on GitHub .

Reply to this email directly or view it on GitHub.

from mdtraj.

dermen avatar dermen commented on June 16, 2024

Thanks!

----- Original Message -----
From: "Robert McGibbon" [email protected]
To: "rmcgibbo/mdtraj" [email protected]
Cc: "Derek Mendez" [email protected]
Sent: Monday, December 3, 2012 6:09:15 PM
Subject: Re: [mdtraj] get the following error when installing under ubuntu (#7)

From googling it, I think it doesn't matter.

All the years pass, so I wouldn't worry

If you want to fix it, I think upgrading to python 2.7.3 would fix it.

But I wouldn't worry about it.

Sent from my iPhone

On Dec 3, 2012, at 6:03 PM, Derek Mendez [email protected] wrote:

Hey,

Python version is 2.6.5, and numpy.version.full_version is 1.6.1. I think maybe I need a later version of numpy...

as for the tests:


dermen@faust:~/mdtraj$ sudo easy_install nose
[sudo] password for dermen:
Searching for nose
Best match: nose 1.2.1
Processing nose-1.2.1-py2.6.egg
nose 1.2.1 is already the active version in easy-install.pth
Installing nosetests-2.6 script to /usr/local/bin
Installing nosetests script to /usr/local/bin

Using /usr/local/lib/python2.6/dist-packages/nose-1.2.1-py2.6.egg
Processing dependencies for nose
Finished processing dependencies for nose


and


dermen@faust:~/mdtraj$ nosetests
/usr/local/lib/python2.6/dist-packages/mdtraj-0.0.0-py2.6-linux-i686.egg/mdtraj/trajectory.py:21: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility
from mdtraj import dcd, xtc, binpos, trr
/usr/local/lib/python2.6/dist-packages/mdtraj-0.0.0-py2.6-linux-i686.egg/mdtraj/trajectory.py:21: RuntimeWarning: numpy.flatiter size changed, may indicate binary incompatibility
from mdtraj import dcd, xtc, binpos, trr
Doctest: MDTraj.pdb.pdbstructure.Atom.Location.iter ... ok
Doctest: MDTraj.pdb.pdbstructure.Atom.iter_coordinates ... ok
Doctest: MDTraj.pdb.pdbstructure.Atom.iter_locations ... ok
Doctest: MDTraj.pdb.pdbstructure.Residue.iter ... ok
Doctest: MDTraj.pdb.pdbstructure.Residue.iter_positions ... ok
MDTraj.pdb.test_pdb.test_pdbread ... ok
MDTraj.pdb.test_pdb.test_pdbwrite ... ok
MDTraj.utils.test.test_ensure_type_1 ... ok
MDTraj.utils.test.test_ensure_type_2 ... ok
MDTraj.utils.test.test_ensure_type_25 ... ok
MDTraj.utils.test.test_ensure_type_3 ... ok
MDTraj.utils.test.test_ensure_type_4 ... ok
MDTraj.utils.test.test_ensure_type_5 ... ok
MDTraj.utils.test.test_ensure_type_6 ... ok
NumpyDoc: mdtraj.binpos.write ... ok
NumpyDoc: mdtraj.binpos.read ... ok
MDTraj.test.test_binpos.test_read_chunk1 ... ok
MDTraj.test.test_binpos.test_read_chunk1 ... ok
MDTraj.test.test_binpos.test_read_chunk10 ... ok
MDTraj.test.test_binpos.test_read_chunk10 ... ok
MDTraj.test.test_binpos.test_read_chunk1000 ... ok
MDTraj.test.test_binpos.test_read_chunk1000 ... ok
MDTraj.test.test_binpos.test_write_1 ... ok
NumpyDoc: mdtraj.dcd.write ... ok
NumpyDoc: mdtraj.dcd.read ... ok
MDTraj.test.test_dcd.test_read ... ok
MDTraj.test.test_dcd.test_write_0 ... ok
MDTraj.test.test_dcd.test_write_1 ... ok
MDTraj.test.test_dcd.test_write_2 ... ok
MDTraj.test.test_dcd.test_write_2 ... ok
MDTraj.test.test_dcd.test_write_2 ... ok
Load by specifying array name ... ok
load using deferred=True ... ok
Save HDF5 to disk and load it back up ... ok
Load by specifying array name ... ok
load using deferred=True ... ok
Save HDF5 to disk and load it back up ... ok
MDTraj.test.test_io.test_overwrite_1 ... ok
MDTraj.test.test_io.test_overwrite_2 ... ok
NumpyDoc: mdtraj.trajectory.load_xtc ... ok
NumpyDoc: mdtraj.trajectory.load_trr ... ok
NumpyDoc: mdtraj.trajectory.Trajectory.save_pdb ... ok
NumpyDoc: mdtraj.trajectory.Trajectory.save_hdf ... ok
NumpyDoc: mdtraj.trajectory.Trajectory.save_dcd ... ok
NumpyDoc: mdtraj.trajectory.Trajectory.save_binpos ... ok
NumpyDoc: mdtraj.trajectory.Trajectory.save ... ok
NumpyDoc: mdtraj.trajectory.Trajectory.openmm_positions ... ok
NumpyDoc: mdtraj.trajectory.Trajectory.openmm_boxes ... ok
NumpyDoc: mdtraj.trajectory.load ... ok
NumpyDoc: mdtraj.trajectory.Trajectory.join ... ok
NumpyDoc: mdtraj.trajectory.load_pdb ... ok
NumpyDoc: mdtraj.trajectory.load_hdf ... ok
NumpyDoc: mdtraj.trajectory.load_dcd ... ok
NumpyDoc: mdtraj.trajectory.load_binpos ... ok
NumpyDoc: mdtraj.trajectory.load ... ok
NumpyDoc: mdtraj.trajectory.Trajectory.slice ... ok
NumpyDoc: mdtraj.trajectory.Trajectory.save_xtc ... ok
NumpyDoc: mdtraj.trajectory.Trajectory.save_trr ... ok
MDTraj.test.test_trajectory.test_hdf0 ... ok
MDTraj.test.test_trajectory.test_hdf1 ... ok
MDTraj.test.test_trajectory.test_hdf1 ... ok
MDTraj.test.test_trajectory.test_hdf2 ... ok
MDTraj.test.test_trajectory.test_hdf2 ... ok
MDTraj.test.test_trajectory.test_hdf2 ... ok
MDTraj.test.test_trajectory.test_slice ... ok
MDTraj.test.test_trajectory.test_slice ... ok
MDTraj.test.test_trajectory.test_slice ... ok
MDTraj.test.test_trajectory.test_xtc ... ok
MDTraj.test.test_trajectory.test_xtc ... ok
MDTraj.test.test_trajectory.test_xtc ... ok
MDTraj.test.test_trajectory.test_xtc ... ok
MDTraj.test.test_trajectory.test_dcd ... /usr/local/lib/python2.6/dist-packages/mdtraj-0.0.0-py2.6-linux-i686.egg/mdtraj/utils/arrays.py:52: TypeCastPerformanceWarning: Casting dtype=int32 to <type 'numpy.float32'>
TypeCastPerformanceWarning)
ok
MDTraj.test.test_trajectory.test_dcd ... ok
MDTraj.test.test_trajectory.test_dcd ... ok
MDTraj.test.test_trajectory.test_dcd ... ok
MDTraj.test.test_trajectory.test_binpos ... ok
MDTraj.test.test_trajectory.test_binpos ... ok
MDTraj.test.test_trajectory.test_binpos ... ok
MDTraj.test.test_trajectory.test_binpos ... ok
MDTraj.test.test_trr.test1 ... ok
MDTraj.test.test_trr.test2 ... ok
NumpyDoc: mdtraj.xtc.write ... ok
NumpyDoc: mdtraj.xtc.read ... ok
MDTraj.test.test_xtc.test_read_chunk1 ... ok
MDTraj.test.test_xtc.test_read_chunk1 ... ok
MDTraj.test.test_xtc.test_read_chunk1 ... ok
MDTraj.test.test_xtc.test_read_chunk1 ... ok
MDTraj.test.test_xtc.test_read_chunk1 ... ok
MDTraj.test.test_xtc.test_read_chunk10 ... ok
MDTraj.test.test_xtc.test_read_chunk10 ... ok
MDTraj.test.test_xtc.test_read_chunk10 ... ok
MDTraj.test.test_xtc.test_read_chunk10 ... ok
MDTraj.test.test_xtc.test_read_chunk10 ... ok
MDTraj.test.test_xtc.test_read_chunk1000 ... ok
MDTraj.test.test_xtc.test_read_chunk1000 ... ok
MDTraj.test.test_xtc.test_read_chunk1000 ... ok
MDTraj.test.test_xtc.test_read_chunk1000 ... ok
MDTraj.test.test_xtc.test_read_chunk1000 ... ok
MDTraj.test.test_xtc.test_write_0 ... ok
MDTraj.test.test_xtc.test_write_1 ... /usr/local/lib/python2.6/dist-packages/mdtraj-0.0.0-py2.6-linux-i686.egg/mdtraj/utils/arrays.py:52: TypeCastPerformanceWarning: Casting dtype=float64 to <type 'numpy.float32'>
TypeCastPerformanceWarning)
ok


Ran 100 tests in 2.209s

OK
dermen@faust:~/mdtraj$


----- Original Message -----
From: "Robert McGibbon" [email protected]
To: "rmcgibbo/mdtraj" [email protected]
Cc: "Derek Mendez" [email protected]
Sent: Monday, December 3, 2012 5:54:49 PM
Subject: Re: [mdtraj] get the following error when installing under ubuntu (#7)

Also, can you try running the tests in mdtraj, and post the output? $ cd mdtraj
$ easy_install nose
$ nosetests


Reply to this email directly or view it on GitHub .

Reply to this email directly or view it on GitHub.


Reply to this email directly or view it on GitHub .

from mdtraj.

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