[Debichem-devel] Bug#939064: cinfony: autopkgtest regression: SSL: CERTIFICATE_VERIFY_FAILED

Paul Gevers elbrus at debian.org
Sat Aug 31 19:40:25 BST 2019


Source: cinfony
Version: 1.2-4
X-Debbugs-CC: debian-ci at lists.debian.org
User: debian-ci at 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

-------------- next part --------------
A non-text attachment was scrubbed...
Name: signature.asc
Type: application/pgp-signature
Size: 488 bytes
Desc: OpenPGP digital signature
URL: <http://alioth-lists.debian.net/pipermail/debichem-devel/attachments/20190831/8c742bd5/attachment.sig>


More information about the Debichem-devel mailing list