On Mon, May 28, 2012 at 3:08 AM, Noel O'Boyle <baoille...@gmail.com> wrote:
> > Now I've checked the tautomer tests, and it also fails with the "stock"
> > r4758, i.e. before I changed smilesformat.cpp.
> >
> > $ bin/test_tautomer
> >
> > /home/cjames/openbabel-2.3.x-r4758/source/test/tautomertest.cpp:76:
> > canonicalTautomers.size() == 1 [13 == 1] (FAIL)
>
> I think there's something wrong with your setup because if you go back
> in time on the dashboard you can see that the tests passed until last
> week. I typically run the tests with "ctest -R taut* -VV", which sets
> some environment variables and then runs the test from the correct
> directory with verbose output.
>
Hmmm ... something isn't adding up. I double-checked that I have an
unaltered OpenBabel source tree at revision 4758.
$ svn diff -r4758
$
I.e. it's a completely stock version of OpenBabel 2.3.x. I'm using Ubuntu
10.04 ("stable") release, fully updated. I don't have any environment
variables set that would affect OpenBabel. After "make install", I ran
"ctest -R '.*' -VV" and got lots of segfaults (see summary below).
I attached some output from valgrind below for one particular test
(cansmi), which seems to be typical. My first guess is that it's a problem
in the SMARTS matching system that's causing a double-free of memory.
Craig
The following tests passed:
spectrophore_Test
squareplanar_Test
tautomer_Test
tetrahedral_Test
tetranonplanar_Test
tetraplanar_Test
uniqueid_Test
atom_Test
bond_Test
datatest_Test
internalcoord_Test
invalidsmarts_Test
math_Test
smartsparse_Test
unitcell_Test
pytest_babel
pytest_sym
pytest_smartssym
pytest_fastsearch
pytest_unique
pytest_kekule
36% tests passed, 38 tests failed out of 59
Total Test time (real) = 136.52 sec
The following tests FAILED:
1 - automorphism_Test (SEGFAULT)
2 - builder_Test (SEGFAULT)
3 - canonconsistent_Test (SEGFAULT)
4 - canonstable_Test (SEGFAULT)
5 - cistrans_Test (SEGFAULT)
6 - graphsym_Test (SEGFAULT)
7 - implicitH_Test (SEGFAULT)
8 - lssr_Test (SEGFAULT)
9 - isomorphism_Test (SEGFAULT)
10 - rotor_Test (SEGFAULT)
11 - shuffle_Test (SEGFAULT)
12 - smiles_Test (SEGFAULT)
15 - stereo_Test (SEGFAULT)
16 - stereoperception_Test (SEGFAULT)
22 - inchiSamples.sdf_Test (SEGFAULT)
23 - inchiSamplesTechMan.sdf_Test (SEGFAULT)
24 - inchiSteffen_PubChem.smi_Test (SEGFAULT)
25 - aromatest_Test (SEGFAULT)
28 - cansmi_Test (SEGFAULT)
29 - charge-mmff94_Test (SEGFAULT)
30 - charge-gasteiger_Test (SEGFAULT)
31 - conversion_Test (SEGFAULT)
33 - ffgaff_Test (SEGFAULT)
34 - ffghemical_Test (SEGFAULT)
35 - ffmmff94_Test (SEGFAULT)
36 - ffuff_Test (SEGFAULT)
37 - formalcharge_Test (SEGFAULT)
38 - format_Test (SEGFAULT)
39 - formula_Test (SEGFAULT)
42 - invalidsmiles_Test (SEGFAULT)
43 - iterators_Test (SEGFAULT)
44 - logp_psa_Test (SEGFAULT)
46 - mol_Test (SEGFAULT)
47 - phmodel_Test (SEGFAULT)
48 - residue_Test (SEGFAULT)
49 - ringtest_Test (SEGFAULT)
50 - smartstest_Test (SEGFAULT)
52 - smilesmatch_Test (SEGFAULT)
Errors while running CTest
==25027== Invalid read of size 8
==25027== at 0x52FDB68: OpenBabel::FreePattern(OpenBabel::Pattern*)
(parsmart.cpp:544)
==25027== by 0x52FE433: OpenBabel::OBSmartsPattern::~OBSmartsPattern()
(parsmart.cpp:1787)
==25027== by 0x530C2EC: OpenBabel::OBPhModel::~OBPhModel() (phmodel.h:40)
==25027== by 0x4E6662F: __cxa_finalize (cxa_finalize.c:56)
==25027== by 0x520B865: ??? (in
/home/cjames/openbabel-2.3.x/lib/libopenbabel.so.4.0.0)
==25027== by 0x5371240: ??? (in
/home/cjames/openbabel-2.3.x/lib/libopenbabel.so.4.0.0)
==25027== by 0x4E66261: exit (exit.c:78)
==25027== by 0x4E4BC53: (below main) (libc-start.c:258)
==25027== Address 0x6398bd8 is 24 bytes inside a block of size 48 free'd
==25027== at 0x4C26DCF: operator delete(void*) (vg_replace_malloc.c:387)
==25027== by 0x52FE433: OpenBabel::OBSmartsPattern::~OBSmartsPattern()
(parsmart.cpp:1787)
==25027== by 0x530C2EC: OpenBabel::OBPhModel::~OBPhModel() (phmodel.h:40)
==25027== by 0x4E66261: exit (exit.c:78)
==25027== by 0x4E4BC53: (below main) (libc-start.c:258)
==25027==
==25027== Invalid read of size 8
==25027== at 0x52FDB6F: OpenBabel::FreePattern(OpenBabel::Pattern*)
(parsmart.cpp:544)
==25027== by 0x52FE433: OpenBabel::OBSmartsPattern::~OBSmartsPattern()
(parsmart.cpp:1787)
==25027== by 0x530C2EC: OpenBabel::OBPhModel::~OBPhModel() (phmodel.h:40)
==25027== by 0x4E6662F: __cxa_finalize (cxa_finalize.c:56)
==25027== by 0x520B865: ??? (in
/home/cjames/openbabel-2.3.x/lib/libopenbabel.so.4.0.0)
==25027== by 0x5371240: ??? (in
/home/cjames/openbabel-2.3.x/lib/libopenbabel.so.4.0.0)
==25027== by 0x4E66261: exit (exit.c:78)
==25027== by 0x4E4BC53: (below main) (libc-start.c:258)
==25027== Address 0x0 is not stack'd, malloc'd or (recently) free'd
==25027==
==25027==
==25027== Process terminating with default action of signal 11 (SIGSEGV)
==25027== Access not within mapped region at address 0x0
==25027== at 0x52FDB6F: OpenBabel::FreePattern(OpenBabel::Pattern*)
(parsmart.cpp:544)
==25027== by 0x52FE433: OpenBabel::OBSmartsPattern::~OBSmartsPattern()
(parsmart.cpp:1787)
==25027== by 0x530C2EC: OpenBabel::OBPhModel::~OBPhModel() (phmodel.h:40)
==25027== by 0x4E6662F: __cxa_finalize (cxa_finalize.c:56)
==25027== by 0x520B865: ??? (in
/home/cjames/openbabel-2.3.x/lib/libopenbabel.so.4.0.0)
==25027== by 0x5371240: ??? (in
/home/cjames/openbabel-2.3.x/lib/libopenbabel.so.4.0.0)
==25027== by 0x4E66261: exit (exit.c:78)
==25027== by 0x4E4BC53: (below main) (libc-start.c:258)
==25027== If you believe this happened as a result of a stack
==25027== overflow in your program's main thread (unlikely but
==25027== possible), you can try to increase the size of the
==25027== main thread stack using the --main-stacksize= flag.
==25027== The main thread stack size used in this run was 8388608.
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