Hi,
> - 2.3.2 and 2.3.90 : segfault (I have some gdb backtrace, hinting to
> mol2format.cpp or malloc.c, if anybody if able to read that output)
> - 2.2.3, 2.3.0 and 2.3.1: openbabel seems to be unable to open the file
> (although the C++ program can read it without any problem).
You might get more useful information if you run your program from
>> valgrind instead of gdb (or valgrind with option "--db-attach=yes" to
>> get the best of both).
>>
>>
>
I'm still stuck with the segfault error, so below is the valgring output,
but I'm not sure where I should look now (my C++ program? trying an other
version of libstdc++? looking for a bug in openbabel .cpp or .h files?), if
anybody may have a hint:
==4279== Invalid read of size 4
==4279== at 0x93665D: __dynamic_cast (in /usr/lib/libstdc++.so.6.0.13)
==4279== by 0x5CFBF05:
OpenBabel::MOL2Format::ReadMolecule(OpenBabel::OBBase*,
OpenBabel::OBConversion*) (base.h:278)
T* CastAndClear(bool clear=true)
{
T* pOb = dynamic_cast<T*>(this); # line 278
if(pOb && clear)// Clear only if this is of target class
Clear();
==4279== by 0x424D7B0: OpenBabel::OBConversion::Read(OpenBabel::OBBase*,
std::istream*) (obconversion.cpp:825)
pInStream->imbue(cNumericLocale);
bool success = pInFormat->ReadMolecule(pOb, this); # line 825
// return the C locale to the original one
obLocale.RestoreLocale();
==4279== by 0x424DB05:
OpenBabel::OBConversion::ReadFile(OpenBabel::OBBase*, std::string)
(obconversion.cpp:1003)
}
return Read(pOb,ifs); # line 1003
}
==4279== by 0x8082D40: main
==4279== Address 0xfffffff8 is not stack'd, malloc'd or (recently) free'd
gdb output at this step (compared to valgrind, is additionnally citing
"mol2format.cpp:72"):
#0 adjust_pointer<void> (src_ptr=0xbecb2c94, src_type=0x4340820,
dst_type=0x4340fe0, src2dst=0)
at ../../../../libstdc++-v3/libsupc++/tinfo.h:77
#1 __cxxabiv1::__dynamic_cast (src_ptr=0xbecb2c94, src_type=0x4340820,
dst_type=0x4340fe0, src2dst=0)
at ../../../../libstdc++-v3/libsupc++/dyncast.cc:56
#2 0x05cfbf06 in CastAndClear<OpenBabel::OBMol> (this=0x5d00488,
pOb=0xbecb2c94, pConv=0xbecb2a9c)
at /opt/OPENBABEL/openbabel-2.3.2/src/include/openbabel/base.h:278
#3 OpenBabel::MOL2Format::ReadMolecule (this=0x5d00488, pOb=0xbecb2c94,
pConv=0xbecb2a9c)
at /opt/OPENBABEL/openbabel-2.3.2/src/src/formats/mol2format.cpp:72
#4 0x0424d7b1 in OpenBabel::OBConversion::Read (this=0xbecb2a9c,
pOb=0xbecb2c94, pin=0x56283a0)
at /opt/OPENBABEL/openbabel-2.3.2/src/src/obconversion.cpp:825
#5 0x0424db06 in OpenBabel::OBConversion::ReadFile (this=0xbecb2a9c,
pOb=0xbecb2c94, filePath="1lrh_0-NLA-1.mol2")
at /opt/OPENBABEL/openbabel-2.3.2/src/src/obconversion.cpp:1003
#6 0x08082d41 in main ()
==4279==
==4279==
==4279== Process terminating with default action of signal 11 (SIGSEGV)
==4279== Access not within mapped region at address 0xFFFFFFF8
==4279== at 0x93665D: __dynamic_cast (in /usr/lib/libstdc++.so.6.0.13)
==4279== by 0x5CFBF05:
OpenBabel::MOL2Format::ReadMolecule(OpenBabel::OBBase*,
OpenBabel::OBConversion*) (base.h:278)
==4279== by 0x424D7B0: OpenBabel::OBConversion::Read(OpenBabel::OBBase*,
std::istream*) (obconversion.cpp:825)
==4279== by 0x424DB05:
OpenBabel::OBConversion::ReadFile(OpenBabel::OBBase*, std::string)
(obconversion.cpp:1003)
==4279== by 0x8082D40: main
Many thanks,
Regards,
Pascal
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