Re: openbabel-3.1* in Rawhide

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On Sat, Sep 25, 2021 at 08:07:20PM -0600, Jerry James wrote:
> On Sat, Sep 25, 2021 at 5:10 PM Alexander Ploumistos
> <alex.ploumistos@xxxxxxxxx> wrote:
> > I built the latest avogadro2 and avogadro2-libs from the srpm in your
> > copr for F34 and I hit some graphical glitches again. On Wayland,
> > Avogadro2 for X11 has a transparent canvas, whereas the other one (I
> > guess Wayland) doesn't, but as soon as I add a fourth atom to the
> > drawing, it crashes:
> >
> > /usr/include/c++/11/bits/stl_vector.h:1045: std::vector<_Tp,
> > _Alloc>::reference std::vector<_Tp,
> > _Alloc>::operator[](std::vector<_Tp, _Alloc>::size_type) [with _Tp =
> > Eigen::Matrix<double, 3, 1>; _Alloc =
> > std::allocator<Eigen::Matrix<double, 3, 1> >; std::vector<_Tp,
> > _Alloc>::reference = Eigen::Matrix<double, 3, 1>&; std::vector<_Tp,
> > _Alloc>::size_type = long unsigned int]: Assertion '__n <
> > this->size()' failed.
> > Aborted (core dumped)
> 
> I don't know if this is the same as the inchi-related abort, but that
> one is caused by this code, on lines 178-180 of molecule_smiles.cpp,
> in Molecule::ToInChI():
> 
>   std::string s = ostream.str();
>   s[s.length() - 1] = '\0'; // Abort happens here
>   return ( QString( s.c_str() ) );
> 
> The abort happens because s is the empty string, so s.length() == 0,
> and assigning to s[-1] just isn't a good idea.  I'm pretty sure that
> line isn't needed anyway.  Isn't s.c_str() guaranteed to provide a
> null-terminated C string?

Yes, this is guaranteed:

> Returns a pointer to an array that contains a null-terminated
> sequence of characters (i.e., a C-string) representing the current
> value of the string object.

Zbyszek
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