" --always-copy -U setuptools failed with error code 1
/usr/local/spring/spring_v0-85-1617/lib/python2.7/site-packages/pkg_resources/__init__.py:187: RuntimeWarning: You have iterated over the result of pkg_resources.parse_version. This is a legacy behavior which is inconsistent with the new version class introduced in setuptools 8.0. In most cases, conversion to a tuple is unnecessary. For comparison of versions, sort the Version instances directly. If you have another use case requiring the tuple, please file a bug with the setuptools project describing that need.
stacklevel=1,
Creating directory '/usr/local/spring/spring_v0-85-1617/develop-eggs'.
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4. Install latest Python dependencies for Spring
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Updating springpython.
----------------------------------------------------------------------------------
Install done. Check whether Spring was successfully installed by brief testing.
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..segmentclass --f parfile_32281.par --l segmentclass_test.log --d segmentclass_test
Program to classify excised in-plane rotated segments using SPARX's k-means clustering
Input parameters are read from parfile_32281.par
The following input parameters have been received:
Image input stack = /usr/local/spring/spring_v0-85-1617/test_segmentclass/test_segments.hdf
Class average stack = test_averages.hdf
Reference image option = False
Image reference stack = test_ref_segments.hdf
Spring database option = False
Database prepare option = False
spring.db file = ../spring.db
Class variance stack = test_variances.hdf
Eigenimage stack = test_eigenimages.hdf
Pixel size in Angstrom = 5.0
Estimated helix width and height in Angstrom = (450, 675)
Number of classes = 3
Number of iterations = 3
Keep intermediate files = False
Limit in-plane rotation = True
Delta in-plane rotation angle = 10.0
X and Y translation range in Angstrom = (20, 15)
High-pass filter option = False
Low-pass filter option = False
High and low-pass filter cutoffs in 1/Angstrom = (0.01, 0.06)
B-Factor = 0
Custom filter option = False
Custom-built filter file = test_filter_file.dat
Automatic filter option = False
Binning option = True
Binning factor = 2
MPI option = True
Number of CPUs = 8
Temporary directory = /usr/local/spring/spring_v0-85-1617/test_segmentclass
/usr/local/spring/spring_v0-85-1617/test_segmentclass/test_segments.hdf found
/usr/local/spring/spring_v0-85-1617/test_segmentclass found
Program to align segments from helical specimens with a restrained in-plane rotation of 0 or 180 +/- delta degrees
Input parameters are read from parfile_32345.par
The following input parameters have been received:
Image input stack = /usr/local/spring/spring_v0-85-1617/test_segmentclass/segmentclass_test/test_segments2binned.hdf
Image output stack = test_segments2binnedali.hdf
Number of iterations = 3
Reference option = True
Image reference stack = /usr/local/spring/spring_v0-85-1617/test_segmentclass/segmentclass_test/sxk_means00/averages.hdf
Update references = True
Aligned average stack = multi_ref_avg.hdf
Pixel size in Angstrom = 10.0
Estimated helix width and height in Angstrom = (450, 675)
Local refinement = False
Absolute X and Y translation limit in Angstrom = (20, 15)
Internal binning factor = 1
Limit in-plane rotation = True
Delta in-plane rotation angle = 10.0
X and Y translation range in Angstrom = (20, 15)
High-pass filter option = False
Low-pass filter option = False
High and low-pass filter cutoffs in 1/Angstrom = (0.01, 0.06)
B-Factor = 0
Custom filter option = False
Custom-built filter file = test_filter_file.dat
Automatic filter option = False
MPI option = True
Number of CPUs = 8
Temporary directory = /usr/local/spring/spring_v0-85-1617/test_segmentclass
/usr/local/spring/spring_v0-85-1617/test_segmentclass/segmentclass_test/test_segments2binned.hdf found
/usr/local/spring/spring_v0-85-1617/test_segmentclass/segmentclass_test/sxk_means00/averages.hdf found
/usr/local/spring/spring_v0-85-1617/test_segmentclass found
Program to align segments from helical specimens with a restrained in-plane rotation of 0 or 180 +/- delta degrees
Input parameters are read from parfile_32345.par
The following input parameters have been received:
Image input stack = /usr/local/spring/spring_v0-85-1617/test_segmentclass/segmentclass_test/test_segments2binned.hdf
Image output stack = test_segments2binnedali.hdf
Number of iterations = 3
Reference option = True
Image reference stack = /usr/local/spring/spring_v0-85-1617/test_segmentclass/segmentclass_test/sxk_means02/averages.hdf
Update references = True
Aligned average stack = multi_ref_avg.hdf
Pixel size in Angstrom = 10.0
Estimated helix width and height in Angstrom = (450, 675)
Local refinement = True
Absolute X and Y translation limit in Angstrom = (20, 15)
Internal binning factor = 1
Limit in-plane rotation = True
Delta in-plane rotation angle = 10.0
X and Y translation range in Angstrom = (20, 15)
High-pass filter option = False
Low-pass filter option = False
High and low-pass filter cutoffs in 1/Angstrom = (0.01, 0.06)
B-Factor = 0
Custom filter option = False
Custom-built filter file = test_filter_file.dat
Automatic filter option = False
MPI option = True
Number of CPUs = 8
Temporary directory = /usr/local/spring/spring_v0-85-1617/test_segmentclass
/usr/local/spring/spring_v0-85-1617/test_segmentclass/segmentclass_test/test_segments2binned.hdf found
/usr/local/spring/spring_v0-85-1617/test_segmentclass/segmentclass_test/sxk_means02/averages.hdf found
/usr/local/spring/spring_v0-85-1617/test_segmentclass found
Program to align segments from helical specimens with a restrained in-plane rotation of 0 or 180 +/- delta degrees
Input parameters are read from parfile_32345.par
The following input parameters have been received:
Image input stack = /usr/local/spring/spring_v0-85-1617/test_segmentclass/segmentclass_test/test_segments2binned.hdf
Image output stack = test_segments2binnedali.hdf
Number of iterations = 3
Reference option = True
Image reference stack = /usr/local/spring/spring_v0-85-1617/test_segmentclass/segmentclass_test/sxk_means03/averages.hdf
Update references = True
Aligned average stack = multi_ref_avg.hdf
Pixel size in Angstrom = 10.0
Estimated helix width and height in Angstrom = (450, 675)
Local refinement = True
Absolute X and Y translation limit in Angstrom = (20, 15)
Internal binning factor = 1
Limit in-plane rotation = True
Delta in-plane rotation angle = 10.0
X and Y translation range in Angstrom = (20, 15)
High-pass filter option = False
Low-pass filter option = False
High and low-pass filter cutoffs in 1/Angstrom = (0.01, 0.06)
B-Factor = 0
Custom filter option = False
Custom-built filter file = test_filter_file.dat
Automatic filter option = False
MPI option = True
Number of CPUs = 8
Temporary directory = /usr/local/spring/spring_v0-85-1617/test_segmentclass
/usr/local/spring/spring_v0-85-1617/test_segmentclass/segmentclass_test/test_segments2binned.hdf found
/usr/local/spring/spring_v0-85-1617/test_segmentclass/segmentclass_test/sxk_means03/averages.hdf found
/usr/local/spring/spring_v0-85-1617/test_segmentclass found
start analyzing..., ncov = 17002
test_segments.hdf=/usr/local/spring/spring_v0-85-1617/test_segmentclass/test_segments.hdf
test_averages.hdf=test_averages.hdf
False=False
test_ref_segments.hdf=test_ref_segments.hdf
False=False
False=False
../spring.db=../spring.db
test_variances.hdf=test_variances.hdf
test_eigenimages.hdf=test_eigenimages.hdf
5.0=5.0
(450, 675)=(450, 675)
3=3
3=3
False=False
True=True
10.0=10.0
(20, 15)=(20, 15)
False=False
False=False
(0.01, 0.06)=(0.01, 0.06)
0=0
False=False
test_filter_file.dat=test_filter_file.dat
False=False
True=True
2=2
True=True
8=8
/usr/local/spring/spring_v0-85-1617/test_segmentclass=/usr/local/spring/spring_v0-85-1617/test_segmentclass
..
----------------------------------------------------------------------
Ran 4 tests in 49.852s
OK
==================================================================================
Testing done. If 4 quick tests ran OK Spring was correctly installed.
Install done. Please type to add the following line to your .cshrc:
echo setenv PATH:/usr/local/spring/spring_v0-85-1617/bin:$PATH >> ~/.cshrc
or your favorite Bourne shell rc file (e.g. .bashrc, .zshrc):
echo export PATH:/usr/local/spring/spring_v0-85-1617/bin:$PATH >> ~/.bashrc
==================================================================================
...although ultimately the tests seem fine. But can one really disregard the errors in steps 1-3?
Thanks,