#3 Unit tests fail
When I build ghmm and run the unit tests, several tests fail -- Are these problematic?
$ make check
Making all in .
make[1]: Entering directory `/home/makerpm/rpmbuild/BUILD/ghmm/ghmmwrapper'
make[1]: Nothing to be done for `all-am'.
make[1]: Leaving directory `/home/makerpm/rpmbuild/BUILD/ghmm/ghmmwrapper'
CFLAGS="-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic -fasynchronous-unwind-tables" /usr/bin/python setup.py build
running build
running build_py
running build_ext
Making check in .
make[1]: Entering directory `/home/makerpm/rpmbuild/BUILD/ghmm/ghmmwrapper'
make[1]: Nothing to be done for `check-am'.
make[1]: Leaving directory `/home/makerpm/rpmbuild/BUILD/ghmm/ghmmwrapper'
PYTHONPATH=./build/lib.linux-i686-2.5/: LD_LIBRARY_PATH=../ghmm/.libs: /usr/bin/python ghmmunittests.py
...............F..............I/O warning : failed to load external entity "/usr/share/ghmm/ghmm.dtd.1.0"
I/O warning : failed to load external entity "/usr/share/ghmm/ghmm.dtd.1.0"
...................FF..FI/O warning : failed to load external entity "/usr/share/ghmm/ghmm.dtd.1.0"
I/O warning : failed to load external entity "/usr/share/ghmm/ghmm.dtd.1.0"
.I/O warning : failed to load external entity "/usr/share/ghmm/ghmm.dtd.1.0"
I/O warning : failed to load external entity "/usr/share/ghmm/ghmm.dtd.1.0"
....................................F........................I/O warning : failed to load external entity "/usr/share/ghmm/ghmm.dtd.1.0"
EI/O warning : failed to load external entity "/usr/share/ghmm/ghmm.dtd.1.0"
E
======================================================================
ERROR: testReadHMMed (__main__.XMLIOTests)
----------------------------------------------------------------------
Traceback (most recent call last):
File "ghmmunittests.py", line 1763, in testReadHMMed
model = ghmm.HMMOpen('testdata/multexon-4.xml')
File "/home/makerpm/rpmbuild/BUILD/ghmm/ghmmwrapper/ghmm.py", line 1262, in __call__
return self.openOldXML(fileName)
File "/home/makerpm/rpmbuild/BUILD/ghmm/ghmmwrapper/ghmm.py", line 1336, in openOldXML
from ghmm_gato import xmlutil
File "/home/makerpm/rpmbuild/BUILD/ghmm/ghmmwrapper/ghmm_gato/xmlutil.py", line 38, in <module>
import EditObjectAttributesDialog
File "/home/makerpm/rpmbuild/BUILD/ghmm/ghmmwrapper/ghmm_gato/EditObjectAttributesDialog.py", line 38, in <module>
from Tkinter import *
ImportError: No module named Tkinter
======================================================================
ERROR: testWriteReadXML (__main__.XMLIOTests)
----------------------------------------------------------------------
Traceback (most recent call last):
File "ghmmunittests.py", line 1774, in testWriteReadXML
model2 = ghmm.HMMOpen('testdata/discrete.xml')
File "/home/makerpm/rpmbuild/BUILD/ghmm/ghmmwrapper/ghmm.py", line 1262, in __call__
return self.openOldXML(fileName)
File "/home/makerpm/rpmbuild/BUILD/ghmm/ghmmwrapper/ghmm.py", line 1336, in openOldXML
from ghmm_gato import xmlutil
File "/home/makerpm/rpmbuild/BUILD/ghmm/ghmmwrapper/ghmm_gato/xmlutil.py", line 38, in <module>
import EditObjectAttributesDialog
File "/home/makerpm/rpmbuild/BUILD/ghmm/ghmmwrapper/ghmm_gato/EditObjectAttributesDialog.py", line 38, in <module>
from Tkinter import *
ImportError: No module named Tkinter
======================================================================
FAIL: testprobfunctions (__main__.ContinuousMixtureHMM2Tests)
----------------------------------------------------------------------
Traceback (most recent call last):
File "ghmmunittests.py", line 1387, in testprobfunctions
self.assertAlmostEqual(lp, -14.990634258963)
AssertionError: -17.865712264614888 != -14.990634258963 within 7 places
======================================================================
FAIL: testforward (__main__.GaussianEmissionHMMTests)
----------------------------------------------------------------------
Traceback (most recent call last):
File "ghmmunittests.py", line 1049, in testforward
[0.81096817099594998, 0.0, 0.18903182900404999]])
AssertionError: [[1.0, 0.0, 0.0], [0.0, 1.0, 0.0], [0.70600966368231, 0.0, 0.29399033631769]] != [[1.0, 0.0, 0.0], [0.0, 1.0, 0.0], [0.81096817099594998, 0.0, 0.18903182900404999]]
======================================================================
FAIL: testloglikelihoods (__main__.GaussianEmissionHMMTests)
----------------------------------------------------------------------
Traceback (most recent call last):
File "ghmmunittests.py", line 1057, in testloglikelihoods
self.assertEqual(str(res), '[-138.66374870816287]' )
AssertionError: '[-139.72681085125927]' != '[-138.66374870816287]'
======================================================================
FAIL: testviterbi (__main__.GaussianEmissionHMMTests)
----------------------------------------------------------------------
Traceback (most recent call last):
File "ghmmunittests.py", line 1062, in testviterbi
self.assertEqual(str(res), '([0, 1, 0, 1, 0, 1, 2, 2, 1, 0, 1, 2, 0, 1, 2, 1, 2, 2, 0, 1], -33.575966803792092)')
AssertionError: '([0, 1, 0, 1, 0, 1, 2, 0, 1, 2, 0, 1, 2, 2, 0, 1, 0, 1, 0, 1], -32.376495625079315)' != '([0, 1, 0, 1, 0, 1, 2, 2, 1, 0, 1, 2, 0, 1, 2, 1, 2, 2, 0, 1], -33.575966803792092)'
======================================================================
FAIL: testprobfunctions (__main__.MultivariateMixtureHMMTests)
----------------------------------------------------------------------
Traceback (most recent call last):
File "ghmmunittests.py", line 1669, in testprobfunctions
self.assertAlmostEqual(lp, -115.70197178468406)
AssertionError: -150.14447234804231 != -115.70197178468406 within 7 places
----------------------------------------------------------------------
Ran 118 tests in 15.444s
FAILED (failures=5, errors=2)
make: *** [check] Error 1