Source: cinfony Version: 1.2-4 X-Debbugs-CC: debian...@lists.debian.org User: debian...@lists.debian.org Usertags: regression
Dear maintainers, With a recent upload of cinfony the autopkgtest of cinfony fails in testing when that autopkgtest is run with the binary packages of cinfony from unstable. It passes when run with only packages from testing. In tabular form: pass fail cinfony from testing 1.2-4 all others from testing from testing I copied some of the output at the bottom of this report. Currently this regression is blocking the migration to testing [1]. Can you please investigate the situation and fix it? If needed, please change the bug's severity. More information about this bug and the reason for filing it can be found on https://wiki.debian.org/ContinuousIntegration/RegressionEmailInformation Paul [1] https://qa.debian.org/excuses.php?package=cinfony https://ci.debian.net/data/autopkgtest/testing/amd64/c/cinfony/2857991/log.gz ====================================================================== ERROR: testDraw (__main__.TestWebel) Create a 2D depiction ---------------------------------------------------------------------- Traceback (most recent call last): File "testall.py", line 520, in testDraw filename="%s.png" % self.toolkit.__name__) File "/usr/lib/python2.7/dist-packages/cinfony/webel.py", line 305, in draw imagedata = nci(_quo(self.smiles), "image") File "/usr/lib/python2.7/dist-packages/cinfony/webel.py", line 74, in server resp = urllib2.urlopen(url) File "/usr/lib/python2.7/urllib2.py", line 154, in urlopen return opener.open(url, data, timeout) File "/usr/lib/python2.7/urllib2.py", line 435, in open response = meth(req, response) File "/usr/lib/python2.7/urllib2.py", line 548, in http_response 'http', request, response, code, msg, hdrs) File "/usr/lib/python2.7/urllib2.py", line 467, in error result = self._call_chain(*args) File "/usr/lib/python2.7/urllib2.py", line 407, in _call_chain result = func(*args) File "/usr/lib/python2.7/urllib2.py", line 654, in http_error_302 return self.parent.open(new, timeout=req.timeout) File "/usr/lib/python2.7/urllib2.py", line 429, in open response = self._open(req, data) File "/usr/lib/python2.7/urllib2.py", line 447, in _open '_open', req) File "/usr/lib/python2.7/urllib2.py", line 407, in _call_chain result = func(*args) File "/usr/lib/python2.7/urllib2.py", line 1241, in https_open context=self._context) File "/usr/lib/python2.7/urllib2.py", line 1198, in do_open raise URLError(err) URLError: <urlopen error [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:727)> ====================================================================== ERROR: testRFoutputfile (__main__.TestWebel) Test the Outputfile class ---------------------------------------------------------------------- Traceback (most recent call last): File "testall.py", line 536, in testRFoutputfile outputfile.write(mol) File "/usr/lib/python2.7/dist-packages/cinfony/webel.py", line 158, in write output = molecule.write(self.format) File "/usr/lib/python2.7/dist-packages/cinfony/webel.py", line 281, in write output = nci(_quo(self.smiles), "file?format=%s" % format).rstrip() File "/usr/lib/python2.7/dist-packages/cinfony/webel.py", line 74, in server resp = urllib2.urlopen(url) File "/usr/lib/python2.7/urllib2.py", line 154, in urlopen return opener.open(url, data, timeout) File "/usr/lib/python2.7/urllib2.py", line 435, in open response = meth(req, response) File "/usr/lib/python2.7/urllib2.py", line 548, in http_response 'http', request, response, code, msg, hdrs) File "/usr/lib/python2.7/urllib2.py", line 467, in error result = self._call_chain(*args) File "/usr/lib/python2.7/urllib2.py", line 407, in _call_chain result = func(*args) File "/usr/lib/python2.7/urllib2.py", line 654, in http_error_302 return self.parent.open(new, timeout=req.timeout) File "/usr/lib/python2.7/urllib2.py", line 429, in open response = self._open(req, data) File "/usr/lib/python2.7/urllib2.py", line 447, in _open '_open', req) File "/usr/lib/python2.7/urllib2.py", line 407, in _call_chain result = func(*args) File "/usr/lib/python2.7/urllib2.py", line 1241, in https_open context=self._context) File "/usr/lib/python2.7/urllib2.py", line 1198, in do_open raise URLError(err) URLError: <urlopen error [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:727)> ====================================================================== ERROR: testRFsingletofile (__main__.TestWebel) Test the molecule.write() method ---------------------------------------------------------------------- Traceback (most recent call last): File "testall.py", line 264, in testRFsingletofile mol.write("smi", "testoutput.txt") File "/usr/lib/python2.7/dist-packages/cinfony/webel.py", line 285, in write raise IOError("%s already exists. Use 'overwrite=True' to overwrite it." % filename) IOError: testoutput.txt already exists. Use 'overwrite=True' to overwrite it. ====================================================================== ERROR: testRSconversiontoMOL (__main__.TestWebel) Convert to mol ---------------------------------------------------------------------- Traceback (most recent call last): File "testall.py", line 555, in testRSconversiontoMOL as_mol = self.mols[0].write("mol") File "/usr/lib/python2.7/dist-packages/cinfony/webel.py", line 281, in write output = nci(_quo(self.smiles), "file?format=%s" % format).rstrip() File "/usr/lib/python2.7/dist-packages/cinfony/webel.py", line 74, in server resp = urllib2.urlopen(url) File "/usr/lib/python2.7/urllib2.py", line 154, in urlopen return opener.open(url, data, timeout) File "/usr/lib/python2.7/urllib2.py", line 435, in open response = meth(req, response) File "/usr/lib/python2.7/urllib2.py", line 548, in http_response 'http', request, response, code, msg, hdrs) File "/usr/lib/python2.7/urllib2.py", line 467, in error result = self._call_chain(*args) File "/usr/lib/python2.7/urllib2.py", line 407, in _call_chain result = func(*args) File "/usr/lib/python2.7/urllib2.py", line 654, in http_error_302 return self.parent.open(new, timeout=req.timeout) File "/usr/lib/python2.7/urllib2.py", line 429, in open response = self._open(req, data) File "/usr/lib/python2.7/urllib2.py", line 447, in _open '_open', req) File "/usr/lib/python2.7/urllib2.py", line 407, in _call_chain result = func(*args) File "/usr/lib/python2.7/urllib2.py", line 1241, in https_open context=self._context) File "/usr/lib/python2.7/urllib2.py", line 1198, in do_open raise URLError(err) URLError: <urlopen error [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:727)> ---------------------------------------------------------------------- Ran 30 tests in 23.884s FAILED (errors=4) ....................E.E.============================== *** Open Babel Warning in WriteMolecule No 2D or 3D coordinates exist. Stereochemical information will be stored using an Open Babel extension. To generate 2D or 3D coordinates instead use --gen2D or --gen3D. .============================== *** Open Babel Error in ReadMolecule &*)(%)($) contained a character '&' which is invalid in SMILES ........ ====================================================================== ERROR: testRFoutputfile (__main__.TestIronable) Test the Outputfile class ---------------------------------------------------------------------- Traceback (most recent call last): File "testall.py", line 276, in testRFoutputfile self.assertRaises(ValueError, self.toolkit.Outputfile, "noel", "testoutput.txt") File "/usr/lib/python2.7/unittest/case.py", line 473, in assertRaises callableObj(*args, **kwargs) File "/usr/lib/python2.7/dist-packages/cinfony/pybel.py", line 222, in __init__ raise IOError("%s already exists. Use 'overwrite=True' to overwrite it." % self.filename) IOError: testoutput.txt already exists. Use 'overwrite=True' to overwrite it. ====================================================================== ERROR: testRFsingletofile (__main__.TestIronable) Test the molecule.write() method ---------------------------------------------------------------------- Traceback (most recent call last): File "testall.py", line 264, in testRFsingletofile mol.write("smi", "testoutput.txt") File "/usr/lib/python2.7/dist-packages/cinfony/pybel.py", line 417, in write raise IOError("%s already exists. Use 'overwrite=True' to overwrite it." % filename) IOError: testoutput.txt already exists. Use 'overwrite=True' to overwrite it. ---------------------------------------------------------------------- Ran 33 tests in 0.464s FAILED (errors=2) ..................E.E.......... ====================================================================== ERROR: testRFoutputfile (__main__.TestIndigo) Test the Outputfile class ---------------------------------------------------------------------- Traceback (most recent call last): File "testall.py", line 276, in testRFoutputfile self.assertRaises(ValueError, self.toolkit.Outputfile, "noel", "testoutput.txt") File "/usr/lib/python2.7/unittest/case.py", line 473, in assertRaises callableObj(*args, **kwargs) File "/usr/lib/python2.7/dist-packages/cinfony/indy.py", line 178, in __init__ raise IOError, "%s already exists. Use 'overwrite=True' to overwrite it." % self.filename IOError: testoutput.txt already exists. Use 'overwrite=True' to overwrite it. ====================================================================== ERROR: testRFsingletofile (__main__.TestIndigo) Test the molecule.write() method ---------------------------------------------------------------------- Traceback (most recent call last): File "testall.py", line 264, in testRFsingletofile mol.write("smi", "testoutput.txt") File "/usr/lib/python2.7/dist-packages/cinfony/indy.py", line 292, in write raise IOError, "%s already exists. Use 'overwrite=True' to overwrite it." % filename IOError: testoutput.txt already exists. Use 'overwrite=True' to overwrite it. ---------------------------------------------------------------------- Ran 31 tests in 0.041s FAILED (errors=2) TESTING TestWebel == == == == == == == == == == TESTING TestIronable == == == == == == == == == == TESTING TestIndigo == == == == == == == == == == Failed tests exist
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