[Debichem-devel] Bug#796854: openbabel: transition needed for g++-5 ABIs

[Simon McVittie]

Source: openbabel
Version: 2.3.2+dfsg-2.1
Severity: serious
Justification: breaks reverse-dependencies
Tags: patch

Background[1]: libstdc++6 introduces a new ABI to conform to the
C++11 standard, but keeps the old ABI to not break existing binaries.
Packages which are built with g++-5 from experimental (not the one
from testing/unstable) are using the new ABI.  Libraries built from
this source package export some of the new __cxx11 or B5cxx11 symbols,
dropping other symbols.  If these symbols are part of the API of
the library, then this rebuild with g++-5 will trigger a transition
for the library.

In the case of openbabel, std::string appears in header files that
get installed, so it seems very likely that a transition is needed.
The transition consists of renaming the library package
containing libopenbabel.so.4 from "libopenbabel4" to "libopenbabel4v5".
A patch is available in Ubuntu,
<http://patches.ubuntu.com/o/openbabel/openbabel_2.3.2+dfsg-2.1ubuntu1.patch>.

These follow-up transitions for libstdc++ are not going through exactly
the normal transition procedure, because many entangled transitions are
going on at the same time, and the usual ordered transition procedure
does not scale that far. When all the libraries on which openbabel depends
have started their transitions if required, openbabel should do the same,
closing this bug; the release team will deal with binNMUs as needed.

In the case of openbabel, libwxgtk3.0-dev has already started its
transition, and libeigen3-dev appears to be unaffected, so openbabel
is ready for its rename now.

The package might be NMU'd in the near future, with a patch very similar
to the one in Ubuntu, if its maintainers do not respond; the release
team have declared a 2 day NMU delay[2] for packages involved in the
libstdc++ transition, in order to get unstable back to a usable state
in a finite time.

    S

[1] https://wiki.debian.org/GCC5#libstdc.2B-.2B-_ABI_transition
[2] https://lists.debian.org/debian-devel-announce/2015/08/msg00000.html