Command（make test） execution failed

wlhCNU commented 5 years ago

Hi，

 I encountered some problems in  execute the  command “make test”.  The error message is as follows, what might have caused the error ?

Thank you

lihui

###########################make test log################################### make test py.test ============================================================= test session starts ============================================================== platform linux -- Python 3.6.6, pytest-4.0.1, py-1.7.0, pluggy-0.8.0 rootdir: /export/wlh/01.software/pychopper, inifile: pytest.ini plugins: remotedata-0.3.1, openfiles-0.3.1 collected 3 items

pychopper/tests/test_detector.py .. [ 66%] pychopper/tests/test_integration.py F [100%]

=================================================================== FAILURES =================================================================== ___ TestIntegration.testIntegration ____

self =

def testIntegration(self):
    """ Integration test. """
    base = path.dirname(__file__)
    pkg_base = path.dirname(path.dirname(base))
    test_base = path.join(base, 'data')

    cdna_classifier = path.join(pkg_base, 'scripts', 'cdna_classifier.py')
    barcodes = path.join(test_base, 'barcodes.fas')
    input_fasta = path.join(test_base, 'ref.fas')
    output_fasta = path.join(test_base, 'test_output.fas')
    expected_output = path.join(test_base, 'expected_output.fas')

    subprocess.call([cdna_classifier, '-i', 'fasta', '-s', '95.0', '-b', barcodes, input_fasta, output_fasta])
    retval = subprocess.call(['cmp', output_fasta, expected_output])

  self.assertEqual(retval, 0)
E AssertionError: 2 != 0

pychopper/tests/test_integration.py:23: AssertionError ------------------------------------------------------------- Captured stderr call ------------------------------------------------------------- Traceback (most recent call last): File "/export/wlh/01.software/pychopper/scripts/cdna_classifier.py", line 9, in from pychopper import chopper File "/export/wlh/01.software/pychopper/pychopper/chopper.py", line 6, in from pychopper import seq_detect File "/export/wlh/01.software/pychopper/pychopper/seq_detect.py", line 5, in import parasail File "/export/wlh/01.software/anaconda3/lib/python3.6/site-packages/parasail-1.1.12-py3.6.egg/parasail/init.py", line 30, in _lib = ctypes.CDLL(_libname) File "/export//wlh/01.software/anaconda3/lib/python3.6/ctypes/init.py", line 348, in init self._handle = _dlopen(self._name, mode) OSError: libparasail.so: cannot open shared object file: No such file or directory cmp: /export//wlh/01.software/pychopper/pychopper/tests/data/test_output.fas: No such file or directory ===================================================== 1 failed, 2 passed in 73.85 seconds ====================================================== make: *** [test] Error 1 ################################################################################

bsipos commented 5 years ago

Hello,

It seems that the parasail l library (which is a dependency of pychopper) is not installed properly. Please try to reinstall it separately or install it from source.

SziKayLeung commented 5 years ago

Hello @bsipos

I had the exact same problem and re-installation of parasail semi-worked. However I'm not encountering the following error with "make test"

Any guidance would be greatly appreciated - thank you!

========================================================================= test session starts ========================================================================== platform linux -- Python 3.6.5, pytest-4.6.3, py-1.8.0, pluggy-0.12.0 rootdir: /gpfs/mrc0/projects/Research_Project-MRC148213/sl693/softwares/pychopper, inifile: pytest.ini, testpaths: pychopper collected 3 items

pychopper/tests/test_detector.py .. [ 66%] pychopper/tests/test_integration.py F [100%]

=============================================================================== FAILURES =============================================================================== ___ TestIntegration.testIntegration ____

self =

def testIntegration(self):
    """ Integration test. """
    base = path.dirname(__file__)
    pkg_base = path.dirname(path.dirname(base))
    test_base = path.join(base, 'data')

    cdna_classifier = path.join(pkg_base, 'scripts', 'cdna_classifier.py')
    barcodes = path.join(test_base, 'barcodes.fas')
    input_fasta = path.join(test_base, 'ref.fas')
    output_fasta = path.join(test_base, 'test_output.fas')
    expected_output = path.join(test_base, 'expected_output.fas')

    subprocess.call([cdna_classifier, '-i', 'fasta', '-s', '95.0', '-b', barcodes, input_fasta, output_fasta])
    retval = subprocess.call(['cmp', output_fasta, expected_output])

  self.assertEqual(retval, 0)
E AssertionError: 1 != 0

pychopper/tests/test_integration.py:23: AssertionError ------------------------------------------------------------------------- Captured stdout call ------------------------------------------------------------------------- /gpfs/mrc0/projects/Research_Project-MRC148213/sl693/softwares/pychopper/pychopper/tests/data/test_output.fas /gpfs/mrc0/projects/Research_Project-MRC148213/sl693/softwares/pychopper/pychopper/tests/data/expected_output.fas differ: char 11, line 1 ------------------------------------------------------------------------- Captured stderr call ------------------------------------------------------------------------- 98%|#########8| 4628/4703 [00:00<00:00, 516132.81it/s] ================================================================= 1 failed, 2 passed in 12.06 seconds ================================================================== make: *** [test] Error 1

nanoporetech / pychopper

Command（make test） execution failed #5