[Debichem-devel] Bug#979983: qcelemental downloads from the internet during the build

Adrian Bunk bunk at debian.org
Tue Jan 12 15:31:51 GMT 2021


Source: qcelemental
Version: 0.17.0+dfsg-2
Severity: serious
Tags: ftbfs

https://buildd.debian.org/status/fetch.php?pkg=qcelemental&arch=all&ver=0.17.0%2Bdfsg-2&stamp=1610282048&raw=0

...
   debian/rules override_dh_auto_test
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_test
I: pybuild base:232: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build; python3.9 -m pytest 
============================= test session starts ==============================
platform linux -- Python 3.9.1, pytest-6.0.2, py-1.10.0, pluggy-0.13.0
rootdir: /<<PKGBUILDDIR>>
plugins: cov-2.10.1
collected 998 items

qcelemental/molutil/test_molutil.py s..sss..sss.ss...s.................. [  3%]
.                                                                        [  3%]
qcelemental/tests/test_constants.py .................................... [  7%]
....x....                                                                [  8%]
qcelemental/tests/test_covalentradii.py .........................        [ 10%]
qcelemental/tests/test_datum.py .............                            [ 12%]
qcelemental/tests/test_importing.py ..........................           [ 14%]
qcelemental/tests/test_info.py ........................................  [ 18%]
qcelemental/tests/test_model_general.py ........                         [ 19%]
qcelemental/tests/test_model_results.py ................................ [ 22%]
.....                                                                    [ 23%]
qcelemental/tests/test_molecule.py .............s....s........s......... [ 26%]
.......s...........                                                      [ 28%]
qcelemental/tests/test_molparse_align_chiral.py ssssssssss               [ 29%]
qcelemental/tests/test_molparse_from_schema.py ............              [ 30%]
qcelemental/tests/test_molparse_from_string.py ......................... [ 33%]
........................................................................ [ 40%]
....                                                                     [ 41%]
qcelemental/tests/test_molparse_parse_nucleus_label.py .............     [ 42%]
qcelemental/tests/test_molparse_pubchem.py FFF...FFF                     [ 43%]
qcelemental/tests/test_molparse_reconcile_nucleus.py ................... [ 45%]
................................                                         [ 48%]
qcelemental/tests/test_molparse_to_schema.py ..............              [ 49%]
qcelemental/tests/test_molparse_to_string.py ........................... [ 52%]
....                                                                     [ 52%]
qcelemental/tests/test_molparse_validate_and_fill_chgmult.py ........... [ 54%]
........................................................                 [ 59%]
qcelemental/tests/test_periodictable.py ................................ [ 62%]
........................................................................ [ 70%]
............x                                                            [ 71%]
qcelemental/tests/test_testing.py ...................................... [ 75%]
......................                                                   [ 77%]
qcelemental/tests/test_units.py ........................................ [ 81%]
........................................................................ [ 88%]
...........                                                              [ 89%]
qcelemental/tests/test_utils.py ........................................ [ 93%]
..................sssssssssssssss                                        [ 96%]
qcelemental/tests/test_vanderwaalsradii.py ........................      [ 99%]
qcelemental/util/test_gph_uno_bipartite.py ssss                          [ 99%]
qcelemental/util/test_scipy_hungarian.py ..                              [100%]

=================================== FAILURES ===================================
...
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

matchobj = <re.Match object; span=(0, 11), match='PubChem:223'>

    def process_pubchem(matchobj):
        pubsearch = matchobj.group("pubsearch")
    
        # search pubchem for the provided string
        try:
            results = pubchem.get_pubchem_results(pubsearch)
        except Exception as e:
>           raise ValidationError(e.message)
E           qcelemental.exceptions.ValidationError: Input Error: 	PubchemError
E           <urlopen error [Errno 111] Connection refused>
E           	received when trying to open
E           	https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/223/property/IUPACName,MolecularFormula,Charge/JSON
E           	Check your internet connection, and the above URL, and try again.

qcelemental/molparse/from_string.py:309: ValidationError
----------------------------- Captured stdout call -----------------------------
	Searching PubChem database for CID 223
=============================== warnings summary ===============================
.pybuild/cpython3_3.9/build/qcelemental/tests/test_molparse_from_string.py: 10 warnings
  /usr/lib/python3/dist-packages/numpy/core/_asarray.py:83: VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-tuples-or ndarrays with different lengths or shapes) is deprecated. If you meant to do this, you must specify 'dtype=object' when creating the ndarray
    return array(a, dtype, copy=False, order=order)

-- Docs: https://docs.pytest.org/en/stable/warnings.html
=========================== short test summary info ============================
FAILED qcelemental/tests/test_molparse_pubchem.py::test_pubchem_4a - qcelemental.exceptions.ValidationError: Input Error: 	PubchemError
FAILED qcelemental/tests/test_molparse_pubchem.py::test_pubchem_4b - qcelemental.exceptions.ValidationError: Input Error: 	PubchemError
FAILED qcelemental/tests/test_molparse_pubchem.py::test_pubchem_4c - qcelemental.exceptions.ValidationError: Input Error: 	PubchemError
FAILED qcelemental/tests/test_molparse_pubchem.py::test_pubchem_multiout_g - qcelemental.exceptions.ValidationError: Input Error: 	PubchemError
FAILED qcelemental/tests/test_molparse_pubchem.py::test_pubchem_13h - qcelemental.exceptions.ValidationError: Input Error: 	PubchemError
FAILED qcelemental/tests/test_molparse_pubchem.py::test_pubchem_13i - qcelemental.exceptions.ValidationError: Input Error: 	PubchemError
====== 6 failed, 947 passed, 43 skipped, 2 xfailed, 10 warnings in 9.49s =======
E: pybuild pybuild:353: test: plugin distutils failed with: exit code=1: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build; python3.9 -m pytest 
dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p 3.9 returned exit code 13
make[1]: *** [debian/rules:9: override_dh_auto_test] Error 25



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