openbabel 2.3.1 doesn't compile in Mavericks

[gezelter@…]

The openbabel 2.3.1 port depends on eigen (which doesn't compile on Mavericks), and has a few C++11 oddities in include files that prevent compilation even with eigen3. The modified port file and 5 patches fix compilation on Mavericks and bump openbabel to 2.3.2.

[gezelter@…]

Portfile diff

[gezelter@…]

include/openbabel/alias.h patch

[gezelter@…]

include/openbabel/obmolecformat.h patch

[gezelter@…]

include/openbabel/reactions.h patch

[gezelter@…]

include/openbabel/shared_ptr.h patch

[gezelter@…]

src/ops/unique.cpp patch

[gezelter@…]

test/obtest.h patch

[ryandesign (Ryan Carsten Schmidt)]

The file attachment:Portfile-rrdtool.diff​ appears to be a diff for the port openbabel, not a diff for the port rrdtool....

[gezelter@…]

Replying to ryandesign@…:

The file attachment:Portfile-rrdtool.diff​ appears to be a diff for the port openbabel, not a diff for the port rrdtool....

Filename mistake on my part - it is indeed the Portfile diff for openbabel.

[SickTeddyBear]

Cc Me!

[ltalirz (Leopold Talirz)]

Cc Me!

[Mathias.Laurin+macports.org@…]

Cc Me!

[Mathias.Laurin+macports.org@…]

Replying to gezelter@…:

The openbabel 2.3.1 port depends on eigen (which doesn't compile on Mavericks), and has a few C++11 oddities in include files that prevent compilation even with eigen3. The modified port file and 5 patches fix compilation on Mavericks and bump openbabel to 2.3.2.

I have a patch-less solution. Matt Swain proposed a fix to the Open Babel mailing list on 31 Oct 2013 (he deserves the credit) and proposes that the tr1 oddities are due to the fact that Mavericks changes the default C++ library from libstdc++ to libc++ (I am quoting here).

Anyway, patched Portfile attached.

[Mathias.Laurin+macports.org@…]

Diff against open babel-2.3.1

[NicosPavlov]

Cc Me!

[NicosPavlov]

After the possibility of compiling again eigen version 2 on Mavericks (ticket #42969), it seems that the issues with c++ libraries are not eigen3-specific. However, while it is possible to compile with libstdc++, it is not considered good practice in Macports, as it can lead to conflicts in runtimes, and unexpected linking problems. Solving the issue to enable compilation with libc++ should be a preferred option.

It seems to me too that it could be possible to simplify slightly the patches, and since all changes are related to the same issue, they could be merged into one patch to make things simpler. Ideally, the port py-openbabel should also be upgraded to keep the two ports in sync.

I attach the corresponding files (merged patch, diffs, on Portfiles for openbabel and py-openbabel).

[NicosPavlov]

Patches committed in r122034 and r122035, along with update to 2.3.2 (ticket #42627)