Can you provide some small example code that triggers this?
- 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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