On Sun, May 20, 2012 at 10:19 AM, Noel O'Boyle <baoille...@gmail.com> wrote:
> Can you provide some small example code that triggers this?
>
I've been trying to find a simple example but haven't yet. I'll keep
working on it.
Craig
>
> - Noel
>
> On 16 May 2012 02:08, Craig James <cja...@emolecules.com> wrote:
>
>> This looks like a bug but I wanted to post it here before adding it to
>> the bug database. It's using some memory after freeing it.
>>
>> This is output from valgrind. The first stack trace reports the invalid
>> free, and the second stack trace shows the code that freed the memory
>> earlier.
>>
>> Craig
>>
>> ==23964== Invalid read of size 8
>> ==23964== at 0x4FD4375: OpenBabel::OBCisTransStereo::IsValid() const
>> (cistrans.cpp:89)
>> ==23964== by 0x4FD616E:
>> OpenBabel::OBCisTransStereo::GetConfig(OpenBabel::OBStereo::Shape) const
>> (cistrans.cpp:125)
>> ==23964== by 0x4EB4560:
>> OpenBabel::CanonicalLabelsImpl::CalcCanonicalLabels(OpenBabel::OBMol*,
>> std::vector<unsigned int, std::allocator<unsigned int> > const&, std\
>> ::vector<unsigned int, std::allocator<unsigned int> >&,
>> std::vector<OpenBabel::OBStereoUnit,
>> std::allocator<OpenBabel::OBStereoUnit> > const&, OpenBabel::OBBitVec con\
>> st&, OpenBabel::OBStereoFacade*, int, bool) (canon.cpp:1534)
>> ==23964== by 0x4EA96EB: OpenBabel::CanonicalLabels(OpenBabel::OBMol*,
>> std::vector<unsigned int, std::allocator<unsigned int> > const&,
>> std::vector<unsigned int, st\
>> d::allocator<unsigned int> >&, OpenBabel::OBBitVec const&, int, bool)
>> (canon.cpp:1735)
>> ==23964== by 0x9F0F41E:
>> OpenBabel::OBMol2Cansmi::CreateFragCansmiString(OpenBabel::OBMol&,
>> OpenBabel::OBBitVec&, bool, char*) (smilesformat.cpp:3802)
>> ==23964== by 0x9F1053E:
>> OpenBabel::CreateCansmiString(OpenBabel::OBMol&, char*,
>> OpenBabel::OBBitVec&, bool, OpenBabel::OBConversion*)
>> (smilesformat.cpp:4025)
>> ==23964== by 0x9F11C2A:
>> OpenBabel::SMIBaseFormat::WriteMolecule(OpenBabel::OBBase*,
>> OpenBabel::OBConversion*) (smilesformat.cpp:4091)
>> ==23964== by 0x4F5F7C9:
>> OpenBabel::OBConversion::Write(OpenBabel::OBBase*, std::ostream*)
>> (obconversion.cpp:833)
>> ==23964== by 0x4F61944:
>> OpenBabel::OBConversion::WriteString(OpenBabel::OBBase*, bool)
>> (obconversion.cpp:856)
>> ==23964== by 0x40D1CE: AddRingGroups (in
>> /home/cjames/emi/src/trunk/postgres_chmoogle/chemistry/test/smi2keywords)
>> ==23964== by 0x40DB7E: chmoogle_ring_keywords (in
>> /home/cjames/emi/src/trunk/postgres_chmoogle/chemistry/test/smi2keywords)
>> ==23964== by 0x407543: chmoogle_ichem_keywords (in
>> /home/cjames/emi/src/trunk/postgres_chmoogle/chemistry/test/smi2keywords)
>> ==23964== Address 0x158bf178 is 40 bytes inside a block of size 88 free'd
>> ==23964== at 0x4C26DCF: operator delete(void*)
>> (vg_replace_malloc.c:387)
>> ==23964== by 0x4E924D5: OpenBabel::OBBase::DeleteData(unsigned int)
>> (base.cpp:199)
>> ==23964== by 0x4EA97A9: OpenBabel::CanonicalLabels(OpenBabel::OBMol*,
>> std::vector<unsigned int, std::allocator<unsigned int> > const&,
>> std::vector<unsigned int, st\
>> d::allocator<unsigned int> >&, OpenBabel::OBBitVec const&, int, bool)
>> (canon.cpp:1718)
>> ==23964== by 0x9F0F41E:
>> OpenBabel::OBMol2Cansmi::CreateFragCansmiString(OpenBabel::OBMol&,
>> OpenBabel::OBBitVec&, bool, char*) (smilesformat.cpp:3802)
>> ==23964== by 0x9F1053E:
>> OpenBabel::CreateCansmiString(OpenBabel::OBMol&, char*,
>> OpenBabel::OBBitVec&, bool, OpenBabel::OBConversion*)
>> (smilesformat.cpp:4025)
>> ==23964== by 0x9F11C2A:
>> OpenBabel::SMIBaseFormat::WriteMolecule(OpenBabel::OBBase*,
>> OpenBabel::OBConversion*) (smilesformat.cpp:4091)
>> ==23964== by 0x4F5F7C9:
>> OpenBabel::OBConversion::Write(OpenBabel::OBBase*, std::ostream*)
>> (obconversion.cpp:833)
>> ==23964== by 0x4F61944:
>> OpenBabel::OBConversion::WriteString(OpenBabel::OBBase*, bool)
>> (obconversion.cpp:856)
>> ==23964== by 0x40D1CE: AddRingGroups (in
>> /home/cjames/emi/src/trunk/postgres_chmoogle/chemistry/test/smi2keywords)
>> ==23964== by 0x40DB7E: chmoogle_ring_keywords (in
>> /home/cjames/emi/src/trunk/postgres_chmoogle/chemistry/test/smi2keywords)
>> ==23964== by 0x407543: chmoogle_ichem_keywords (in
>> /home/cjames/emi/src/trunk/postgres_chmoogle/chemistry/test/smi2keywords)
>> ==23964== by 0x405604: main (smi2keywords.c:44)
>>
>>
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