Comments (5)
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
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
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
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/binUsing /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
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/binUsing /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 .
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Related Issues (20)
- mdtraj pip install error HOT 2
- Feature suggestion: guess bonds HOT 4
- DeprecationWarning: invalid escape sequence '\g' HOT 2
- ValueError: invalid literal for int() with base 16: HOT 1
- Build docs in CI HOT 9
- Build docs HOT 2
- mdtraj 1.9.9 and python 3.11.3 HOT 7
- Lammpstrj bounding box origin (shifts) in case os "scaled" coordinates representation HOT 2
- shrake-rupley error quits instead of raising error HOT 4
- xrdlib deprecation warning
- mdconvert dcd -> xtc breaks time field HOT 3
- Get velocity of atom from HDF5 trajectory. HOT 1
- Compiling in PPC64le HOT 2
- RMSD method HOT 3
- Support for velocities (& forces) in trajectory I/O HOT 9
- MDTraj reader not compatible with latest GSD
- bond angle computation results in 'nan' HOT 4
- Memory leak in NetCDF reporter HOT 2
- Drop old hard-coded version checks
- Compatibility with CMS topology files
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