Run test ERROR: python -m unittest discover ; The following error is reported. Can the clipper still be used normally

[geng-lee]

The following error is reported. Can the clipper still be used normally

python -m unittest discover

python -m unittest discover
.F....ERROR:root:Poisson cutoff failled float() argument must be a string or a number, not 'NoneType'
.WARNING:py.warnings:/backup/home/changxing/anaconda3/envs/clipper3/lib/python3.7/subprocess.py:883: ResourceWarning: subprocess 15250 is still running
ResourceWarning, source=self)

WARNING:py.warnings:/backup/home/changxing/anaconda3/envs/clipper3/lib/python3.7/site-packages/pybedtools/bedtool.py:401: ResourceWarning: unclosed file <_io.BufferedReader name=34>
decode_output=decode_output,

WARNING:py.warnings:/backup/home/changxing/anaconda3/envs/clipper3/lib/python3.7/site-packages/pybedtools/bedtool.py:1416: ResourceWarning: unclosed file <_io.BufferedReader name=32>
for i in iterable:

53
22
0
0
.WARNING:py.warnings:/backup/home/changxing/anaconda3/envs/clipper3/lib/python3.7/subprocess.py:883: ResourceWarning: subprocess 15293 is still running
ResourceWarning, source=self)

53
22
0
0
.WARNING:py.warnings:/backup/home/changxing/anaconda3/envs/clipper3/lib/python3.7/subprocess.py:689: ResourceWarning: unclosed file <_io.BufferedReader name=32>
_cleanup()

WARNING:py.warnings:/backup/home/changxing/anaconda3/envs/clipper3/lib/python3.7/subprocess.py:689: ResourceWarning: unclosed file <_io.BufferedReader name=34>
_cleanup()

WARNING:py.warnings:/backup/home/changxing/anaconda3/envs/clipper3/lib/python3.7/subprocess.py:883: ResourceWarning: subprocess 15342 is still running
ResourceWarning, source=self)

WARNING:py.warnings:/backup/home/changxing/anaconda3/envs/clipper3/lib/python3.7/subprocess.py:689: ResourceWarning: unclosed file <_io.BufferedReader name=32>
_cleanup()

WARNING:py.warnings:/backup/home/changxing/anaconda3/envs/clipper3/lib/python3.7/subprocess.py:689: ResourceWarning: unclosed file <_io.BufferedReader name=34>
_cleanup()

..testing find sectionds
.[(0, 2), (31, 63)]
....[2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 11.0, 11.0, 11.0, 11.0, 11.0, 11.0, 11.0, 11.0, 11.0, 11.0, 11.0, 11.0, 11.0, 11.0, 11.0, 11.0, 11.0, 11.0, 11.0, 11.0, 11.0, 11.0, 11.0, 11.0, 11.0, 9.0, 9.0, 9.0, 9.0, 9.0, 9.0, 9.0, 9.0, 0, 0, 0]
..[0.06060606060606061, 0.06060606060606061, 0.06060606060606061, 0.06060606060606061, 0.06060606060606061, 0.06060606060606061, 0.06060606060606061, 0.06060606060606061, 0.33333333333333326, 0.33333333333333326, 0.33333333333333326, 0.33333333333333326, 0.33333333333333326, 0.33333333333333326, 0.33333333333333326, 0.33333333333333326, 0.33333333333333326, 0.33333333333333326, 0.33333333333333326, 0.33333333333333326, 0.33333333333333326, 0.33333333333333326, 0.33333333333333326, 0.33333333333333326, 0.33333333333333326, 0.33333333333333326, 0.33333333333333326, 0.33333333333333326, 0.33333333333333326, 0.33333333333333326, 0.33333333333333326, 0.33333333333333326, 0.33333333333333326, 0.2727272727272727, 0.2727272727272727, 0.2727272727272727, 0.2727272727272727, 0.2727272727272727, 0.2727272727272727, 0.2727272727272727, 0.2727272727272727, 0.0, 0.0, 0.0]
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..............[(31, 32, 31), (82, 85, 84), (85, 90, 87), (90, 98, 95), (98, 109, 105), (109, 117, 111), (118, 119, 118), (121, 122, 121), (124, 126, 125), (128, 130, 128), (130, 135, 131)]
.E

ERROR: test_check_for_index (test_utils.Test)
Performs unit tests on check_for_index function

Traceback (most recent call last):
File "/backup/home/changxing/personal/LG/software/clipper-2.0.1/clipper/test/test_utils.py", line 27, in test_check_for_index
handle = clipper.test_file("test_peakfinder.py")
File "/backup/home/changxing/anaconda3/envs/clipper3/lib/python3.7/site-packages/clipper/init.py", line 30, in test_file
raise ValueError("%s does not exist" % (fn))
ValueError: /backup/home/changxing/anaconda3/envs/clipper3/lib/python3.7/site-packages/clipper/test/data/test_peakfinder.py does not exist

======================================================================
FAIL: test_get_FDR_cutoff_mean (test_call_peak.Test)
Performs unit tests on get_FDR_cutoff_mean function

Traceback (most recent call last):
File "/backup/home/changxing/personal/LG/software/clipper-2.0.1/clipper/test/test_call_peak.py", line 57, in test_get_FDR_cutoff_mean
self.assertAlmostEqual(result, 11, 2) # sometimes output 1
AssertionError: 12 != 11 within 2 places (1 difference)

---

Ran 36 tests in 28.989s

FAILED (failures=1, errors=1)

[ziyili20]

I have the same error. Really hope if someone and provide a suggestion.

[neurbio]

Same error with the test. Any suggestion?

[neurbio]

Same error with the test. Any suggestion?

Seems problem with samtools. RAN
cd /root/anaconda3/envs/clipper3/lib
ln -s libcrypto.so.1.1 libcrypto.so.1.0.0

The error is gone. However, test run still shows fail. Any help?

FAIL: test_get_FDR_cutoff_mean (test_call_peak.Test)
Performs unit tests on get_FDR_cutoff_mean function

Traceback (most recent call last):
File "/clipper/clipper/test/test_call_peak.py", line 57, in test_get_FDR_cutoff_mean
self.assertAlmostEqual(result, 11, 2) # sometimes output 1
AssertionError: 12 != 11 within 2 places (1 difference)

---

Ran 36 tests in 25.394s

FAILED (failures=1)