testInit
ft1.1: gtrackcore.test.memmap.TestOutputDirectory.TestOutputDirectory.testInit
Profiling report (cumulative time)
--- PROFILE (SORTED BY CUMULATIVE TIME)---
Sun Aug 27 20:23:56 2017 /Users/sveinugu/PycharmProjects/nose-html-output/results_profiles/2017_08_27_20_23_55/gtrackcore.test.memmap.TestOutputDirectory.TestOutputDirectory.testInit/test.cprof
585 function calls (579 primitive calls) in 0.005 seconds
Ordered by: cumulative time
ncalls tottime percall cumtime percall filename:lineno(function)
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--- END PROFILE ---
Profiling report (internal time)
--- PROFILE (SORTED BY INTERNAL TIME)---
Sun Aug 27 20:23:56 2017 /Users/sveinugu/PycharmProjects/nose-html-output/results_profiles/2017_08_27_20_23_55/gtrackcore.test.memmap.TestOutputDirectory.TestOutputDirectory.testInit/test.cprof
585 function calls (579 primitive calls) in 0.005 seconds
Ordered by: internal time
ncalls tottime percall cumtime percall filename:lineno(function)
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--- END PROFILE ---
Call-graph (pruned, colored by cumulative time)
Call-graph (pruned, colored by internal time)
Call-graph (not pruned, colored by cumulative time)
Traceback (most recent call last):
File "/Users/sveinugu/miniconda2/lib/python2.7/unittest/case.py", line 329, in run
testMethod()
File "/Users/sveinugu/PycharmProjects/gtrackcore/gtrackcore/test/memmap/TestOutputDirectory.py", line 100, in testInit
self._assertInit(['start'], True)
File "/Users/sveinugu/PycharmProjects/gtrackcore/gtrackcore/test/memmap/TestOutputDirectory.py", line 79, in _assertInit
self.assertTrue(s.od._indexFiles is not None)
File "/Users/sveinugu/miniconda2/lib/python2.7/unittest/case.py", line 422, in assertTrue
raise self.failureException(msg)
AssertionError: False is not true
testWriteElement
pt1.2: gtrackcore.test.memmap.TestOutputDirectory.TestOutputDirectory.testWriteElement
Profiling report (cumulative time)
--- PROFILE (SORTED BY CUMULATIVE TIME)---
Sun Aug 27 20:23:56 2017 /Users/sveinugu/PycharmProjects/nose-html-output/results_profiles/2017_08_27_20_23_55/gtrackcore.test.memmap.TestOutputDirectory.TestOutputDirectory.testWriteElement/test.cprof
370 function calls (364 primitive calls) in 0.002 seconds
Ordered by: cumulative time
ncalls tottime percall cumtime percall filename:lineno(function)
1 0.000 0.000 0.002 0.002 <string>:1(<module>)
1 0.000 0.000 0.002 0.002 /Users/sveinugu/miniconda2/lib/python2.7/unittest/case.py:392(__call__)
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1 0.000 0.000 0.001 0.001 /Users/sveinugu/PycharmProjects/gtrackcore/gtrackcore/test/memmap/TestOutputDirectory.py:104(testWriteElement)
8 0.000 0.000 0.001 0.000 /Users/sveinugu/PycharmProjects/gtrackcore/gtrackcore/test/common/Asserts.py:20(assertEqual)
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--- END PROFILE ---
Profiling report (internal time)
--- PROFILE (SORTED BY INTERNAL TIME)---
Sun Aug 27 20:23:56 2017 /Users/sveinugu/PycharmProjects/nose-html-output/results_profiles/2017_08_27_20_23_55/gtrackcore.test.memmap.TestOutputDirectory.TestOutputDirectory.testWriteElement/test.cprof
370 function calls (364 primitive calls) in 0.002 seconds
Ordered by: internal time
ncalls tottime percall cumtime percall filename:lineno(function)
8 0.000 0.000 0.000 0.000 /Users/sveinugu/PycharmProjects/gtrackcore/gtrackcore/test/common/Asserts.py:32(_assertIsNan)
3 0.000 0.000 0.000 0.000 {posix.mkdir}
24 0.000 0.000 0.000 0.000 /Users/sveinugu/PycharmProjects/gtrackcore/gtrackcore/input/core/GenomeElement.py:68(__getattr__)
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3 0.000 0.000 0.000 0.000 {posix.listdir}
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1 0.000 0.000 0.000 0.000 /Users/sveinugu/PycharmProjects/gtrackcore/gtrackcore/preprocess/memmap/OutputDirectory.py:29(writeElement)
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--- END PROFILE ---
Call-graph (pruned, colored by cumulative time)
Call-graph (pruned, colored by internal time)
Call-graph (not pruned, colored by cumulative time)
testLen
pt2.1: gtrackcore.test.memmap.TestOutputFile.TestOutputFile.testLen
Profiling report (cumulative time)
--- PROFILE (SORTED BY CUMULATIVE TIME)---
Sun Aug 27 20:23:56 2017 /Users/sveinugu/PycharmProjects/nose-html-output/results_profiles/2017_08_27_20_23_55/gtrackcore.test.memmap.TestOutputFile.TestOutputFile.testLen/test.cprof
118 function calls (115 primitive calls) in 0.001 seconds
Ordered by: cumulative time
ncalls tottime percall cumtime percall filename:lineno(function)
1 0.000 0.000 0.001 0.001 <string>:1(<module>)
1 0.000 0.000 0.001 0.001 /Users/sveinugu/miniconda2/lib/python2.7/unittest/case.py:392(__call__)
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1 0.000 0.000 0.001 0.001 /Users/sveinugu/PycharmProjects/gtrackcore/gtrackcore/test/memmap/TestOutputFile.py:207(testLen)
1 0.000 0.000 0.001 0.001 /Users/sveinugu/PycharmProjects/gtrackcore/gtrackcore/test/memmap/TestOutputFile.py:18(__init__)
1 0.000 0.000 0.001 0.001 {posix.tempnam}
1 0.000 0.000 0.001 0.001 /Users/sveinugu/miniconda2/lib/python2.7/warnings.py:25(_show_warning)
1 0.000 0.000 0.001 0.001 /Users/sveinugu/miniconda2/lib/python2.7/warnings.py:40(formatwarning)
1 0.000 0.000 0.001 0.001 /Users/sveinugu/miniconda2/lib/python2.7/linecache.py:13(getline)
1 0.000 0.000 0.001 0.001 /Users/sveinugu/miniconda2/lib/python2.7/linecache.py:33(getlines)
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1 0.000 0.000 0.000 0.000 /Users/sveinugu/PycharmProjects/gtrackcore/gtrackcore/test/common/Asserts.py:32(_assertIsNan)
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2 0.000 0.000 0.000 0.000 {open}
3 0.000 0.000 0.000 0.000 {posix.stat}
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1 0.000 0.000 0.000 0.000 /Users/sveinugu/miniconda2/lib/python2.7/site-packages/htmlprofiler/htmloutput.py:485(addSuccess)
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1 0.000 0.000 0.000 0.000 /Users/sveinugu/miniconda2/lib/python2.7/unittest/case.py:279(__str__)
6 0.000 0.000 0.000 0.000 {isinstance}
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--- END PROFILE ---
Profiling report (internal time)
--- PROFILE (SORTED BY INTERNAL TIME)---
Sun Aug 27 20:23:56 2017 /Users/sveinugu/PycharmProjects/nose-html-output/results_profiles/2017_08_27_20_23_55/gtrackcore.test.memmap.TestOutputFile.TestOutputFile.testLen/test.cprof
118 function calls (115 primitive calls) in 0.001 seconds
Ordered by: internal time
ncalls tottime percall cumtime percall filename:lineno(function)
1 0.001 0.001 0.001 0.001 {method 'readlines' of 'file' objects}
1 0.000 0.000 0.001 0.001 {posix.tempnam}
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2 0.000 0.000 0.000 0.000 {open}
3 0.000 0.000 0.000 0.000 {posix.stat}
1 0.000 0.000 0.000 0.000 /Users/sveinugu/PycharmProjects/gtrackcore/gtrackcore/preprocess/memmap/OutputFile.py:23(__init__)
1 0.000 0.000 0.000 0.000 /Users/sveinugu/PycharmProjects/gtrackcore/gtrackcore/test/common/Asserts.py:32(_assertIsNan)
1 0.000 0.000 0.000 0.000 {numpy.core.multiarray.zeros}
1 0.000 0.000 0.001 0.001 /Users/sveinugu/miniconda2/lib/python2.7/warnings.py:40(formatwarning)
2 0.000 0.000 0.000 0.000 {method 'write' of 'file' objects}
1 0.000 0.000 0.001 0.001 /Users/sveinugu/miniconda2/lib/python2.7/unittest/case.py:295(run)
1 0.000 0.000 0.000 0.000 /Users/sveinugu/miniconda2/lib/python2.7/site-packages/nose/case.py:153(shortDescription)
1 0.000 0.000 0.001 0.001 /Users/sveinugu/PycharmProjects/gtrackcore/gtrackcore/test/memmap/TestOutputFile.py:18(__init__)
1 0.000 0.000 0.000 0.000 /Users/sveinugu/PycharmProjects/gtrackcore/gtrackcore/test/memmap/TestOutputFile.py:77(tearDown)
1 0.000 0.000 0.000 0.000 /Users/sveinugu/miniconda2/lib/python2.7/unittest/runner.py:57(addSuccess)
1 0.000 0.000 0.001 0.001 /Users/sveinugu/miniconda2/lib/python2.7/linecache.py:13(getline)
1 0.000 0.000 0.001 0.001 /Users/sveinugu/PycharmProjects/gtrackcore/gtrackcore/test/memmap/TestOutputFile.py:207(testLen)
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4/3 0.000 0.000 0.000 0.000 {len}
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1 0.000 0.000 0.000 0.000 /Users/sveinugu/miniconda2/lib/python2.7/site-packages/nose/proxy.py:175(stopTest)
1 0.000 0.000 0.000 0.000 /Users/sveinugu/miniconda2/lib/python2.7/site-packages/nose/proxy.py:162(addSuccess)
8 0.000 0.000 0.000 0.000 {getattr}
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1 0.000 0.000 0.000 0.000 /Users/sveinugu/miniconda2/lib/python2.7/posixpath.py:120(dirname)
1 0.000 0.000 0.001 0.001 /Users/sveinugu/miniconda2/lib/python2.7/warnings.py:25(_show_warning)
1 0.000 0.000 0.001 0.001 /Users/sveinugu/miniconda2/lib/python2.7/linecache.py:33(getlines)
1 0.000 0.000 0.000 0.000 /Users/sveinugu/miniconda2/lib/python2.7/site-packages/htmlprofiler/htmloutput.py:485(addSuccess)
4/3 0.000 0.000 0.000 0.000 /Users/sveinugu/miniconda2/lib/python2.7/site-packages/nose/plugins/manager.py:98(__call__)
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--- END PROFILE ---
Call-graph (pruned, colored by cumulative time)
Call-graph (pruned, colored by internal time)
Call-graph (not pruned, colored by cumulative time)
testWrite
pt2.2: gtrackcore.test.memmap.TestOutputFile.TestOutputFile.testWrite
Profiling report (cumulative time)
--- PROFILE (SORTED BY CUMULATIVE TIME)---
Sun Aug 27 20:23:56 2017 /Users/sveinugu/PycharmProjects/nose-html-output/results_profiles/2017_08_27_20_23_55/gtrackcore.test.memmap.TestOutputFile.TestOutputFile.testWrite/test.cprof
315 function calls (313 primitive calls) in 0.026 seconds
Ordered by: cumulative time
ncalls tottime percall cumtime percall filename:lineno(function)
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1 0.000 0.000 0.026 0.026 /Users/sveinugu/PycharmProjects/gtrackcore/gtrackcore/test/memmap/TestOutputFile.py:203(testWrite)
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4 0.020 0.005 0.021 0.005 /Users/sveinugu/miniconda2/lib/python2.7/site-packages/numpy/core/memmap.py:202(__new__)
2 0.000 0.000 0.012 0.006 /Users/sveinugu/PycharmProjects/gtrackcore/gtrackcore/preprocess/memmap/OutputFile.py:90(close)
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--- END PROFILE ---
Profiling report (internal time)
--- PROFILE (SORTED BY INTERNAL TIME)---
Sun Aug 27 20:23:56 2017 /Users/sveinugu/PycharmProjects/nose-html-output/results_profiles/2017_08_27_20_23_55/gtrackcore.test.memmap.TestOutputFile.TestOutputFile.testWrite/test.cprof
315 function calls (313 primitive calls) in 0.026 seconds
Ordered by: internal time
ncalls tottime percall cumtime percall filename:lineno(function)
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--- END PROFILE ---
Call-graph (pruned, colored by cumulative time)
Call-graph (pruned, colored by internal time)
Call-graph (not pruned, colored by cumulative time)
testWriteElement
pt2.3: gtrackcore.test.memmap.TestOutputFile.TestOutputFile.testWriteElement
Profiling report (cumulative time)
--- PROFILE (SORTED BY CUMULATIVE TIME)---
Sun Aug 27 20:23:56 2017 /Users/sveinugu/PycharmProjects/nose-html-output/results_profiles/2017_08_27_20_23_55/gtrackcore.test.memmap.TestOutputFile.TestOutputFile.testWriteElement/test.cprof
3482 function calls (2976 primitive calls) in 0.168 seconds
Ordered by: cumulative time
ncalls tottime percall cumtime percall filename:lineno(function)
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--- END PROFILE ---
Profiling report (internal time)
--- PROFILE (SORTED BY INTERNAL TIME)---
Sun Aug 27 20:23:56 2017 /Users/sveinugu/PycharmProjects/nose-html-output/results_profiles/2017_08_27_20_23_55/gtrackcore.test.memmap.TestOutputFile.TestOutputFile.testWriteElement/test.cprof
3482 function calls (2976 primitive calls) in 0.168 seconds
Ordered by: internal time
ncalls tottime percall cumtime percall filename:lineno(function)
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--- END PROFILE ---
Call-graph (pruned, colored by cumulative time)
Call-graph (pruned, colored by internal time)
Call-graph (not pruned, colored by cumulative time)
testWriteElementPartial
pt2.4: gtrackcore.test.memmap.TestOutputFile.TestOutputFile.testWriteElementPartial
Profiling report (cumulative time)
--- PROFILE (SORTED BY CUMULATIVE TIME)---
Sun Aug 27 20:23:56 2017 /Users/sveinugu/PycharmProjects/nose-html-output/results_profiles/2017_08_27_20_23_55/gtrackcore.test.memmap.TestOutputFile.TestOutputFile.testWriteElementPartial/test.cprof
1038 function calls (948 primitive calls) in 0.052 seconds
Ordered by: cumulative time
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Profiling report (internal time)
--- PROFILE (SORTED BY INTERNAL TIME)---
Sun Aug 27 20:23:56 2017 /Users/sveinugu/PycharmProjects/nose-html-output/results_profiles/2017_08_27_20_23_55/gtrackcore.test.memmap.TestOutputFile.TestOutputFile.testWriteElementPartial/test.cprof
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Ordered by: internal time
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--- END PROFILE ---
Call-graph (pruned, colored by cumulative time)
Call-graph (pruned, colored by internal time)
Call-graph (not pruned, colored by cumulative time)
testWriteIndexes
ft3.1:
Profiling report (cumulative time)
--- PROFILE (SORTED BY CUMULATIVE TIME)---
Sun Aug 27 20:23:56 2017 /Users/sveinugu/PycharmProjects/nose-html-output/results_profiles/2017_08_27_20_23_55/gtrackcore.test.memmap.TestOutputIndexFilePair.TestOutputIndexFilePair.testWriteIndexes/test.cprof
261 function calls in 0.002 seconds
Ordered by: cumulative time
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Profiling report (internal time)
--- PROFILE (SORTED BY INTERNAL TIME)---
Sun Aug 27 20:23:56 2017 /Users/sveinugu/PycharmProjects/nose-html-output/results_profiles/2017_08_27_20_23_55/gtrackcore.test.memmap.TestOutputIndexFilePair.TestOutputIndexFilePair.testWriteIndexes/test.cprof
261 function calls in 0.002 seconds
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Call-graph (pruned, colored by cumulative time)
Call-graph (pruned, colored by internal time)
Call-graph (not pruned, colored by cumulative time)
Traceback (most recent call last):
File "/Users/sveinugu/miniconda2/lib/python2.7/unittest/case.py", line 329, in run
testMethod()
File "/Users/sveinugu/PycharmProjects/gtrackcore/gtrackcore/test/memmap/TestOutputIndexFilePair.py", line 63, in testWriteIndexes
self._assertWriteIndexes([1, 1, 1], [1, 1, 1], [-1], [], 300)
File "/Users/sveinugu/PycharmProjects/gtrackcore/gtrackcore/test/memmap/TestOutputIndexFilePair.py", line 55, in _assertWriteIndexes
of.writeIndexes()
File "/Users/sveinugu/PycharmProjects/gtrackcore/gtrackcore/preprocess/memmap/OutputIndexFilePair.py", line 16, in writeIndexes
a = 1 + 'a'
TypeError: unsupported operand type(s) for +: 'int' and 'str'