Hi Huw,
On Fri, Nov 15, 2013 at 1:31 PM, Huw Jones <[email protected]> wrote:
> Hi again,
>
> I wanted to take advantage of the newer DrawingOptions so updated my
> homebrew formula to the latest version kindly created by Eddie Cao which
> works great.
>
> As a result of the libraries update I needed to rebuild the Postgres
> cartridge so grabbed the latest build from GitHub.
>
> I’ve been trying to compile this but there’s a hitch:
>
> Undefined symbols for architecture x86_64:
> "RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&,
> std::__1::vector<std::__1::pair<int, int>,
> std::__1::allocator<std::__1::pair<int, int> > >&, bool, bool, bool)",
> referenced from:
> _molcmp in adapter.o
> _MolSubstruct in adapter.o
> "RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&,
> std::__1::vector<std::__1::vector<std::__1::pair<int, int>,
> std::__1::allocator<std::__1::pair<int, int> > >,
> std::__1::allocator<std::__1::vector<std::__1::pair<int, int>,
> std::__1::allocator<std::__1::pair<int, int> > > > >&, bool, bool, bool,
> bool)", referenced from:
> _MolSubstructCount in adapter.o
> ld: symbol(s) not found for architecture x86_64
> clang: error: linker command failed with exit code 1 (use -v to see
> invocation)
>
> Normally if I see this type of error I assume it’s an issue with the
> version of PostgreSQL and it’s libraries but in this instance it appears
> not to be.
>
> I did some reading and I don’t know if this is an issue:
>
>
> http://stackoverflow.com/questions/19637164/c-linking-error-after-upgrading-to-mac-os-x-10-9-xcode-5-0-1
>
> I tried this (although wasn’t sure if I placed the flags in the
> appropriate section in the makefile). I also tried compiling with the -m32
> flag set but was still unsuccessful.
>
> I don’t know if anyone has experienced anything similar or is aware of a
> solution? If this is a known issue I’ll happily revert as it does seem like
> OSX upgrades are a bit of a nightmare for compatibility.
>
This is actually due to a change that I made to the github source at the
end of the week. If you're building the cartridge using the github head,
then you need to be sure that the RDKit build you're using is also using
the github head. You can do this with homebrew using: "brew install --HEAD
rdkit"
Best,
-greg
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