Re: [Rdkit-devel] "symbol(s) not found" on Mac OS X 10.7.3

[James S. <jsw...@gm...>]

Sorry for the red herring, Andrew.

FWIW, per the comment in CMakeLists.txt, I was able to reproduce the error
on GCC 4.4.3 on our corporate ubuntu distribution by removing the -O0 flag.
 Experimentation revealed that building Dict.cpp with -O1 links
successfully, so I assume the particular optimization that is eliding these
symbols is in O2 or beyond.

Best,
James

On Wed, Aug 22, 2012 at 11:56 PM, Greg Landrum <gre...@gm...>wrote:

> Hi Andrew,
>
> On Wed, Aug 22, 2012 at 12:17 PM, Andrew Dalke
> <da...@da...> wrote:
> > On Aug 17, 2012, at 11:35 AM, Greg Landrum wrote:
> >> Here is, hopefully, the last update on this topic. Apologies for the
> verbosity.
> >
> > I'm trying to build the latests from the new repository. Here's
> > the message I get:
> >
> > [  4%] Building CXX object
> Code/RDGeneral/CMakeFiles/testDict.dir/testDict.cpp.o
> > Linking CXX executable testDict
> > ld: warning: path '/usr/lib/libpython2.7.dylib' following -L not a
> directory
> > Undefined symbols for architecture x86_64:
> >   "boost::any RDKit::Dict::toany<std::vector<std::vector<int,
> std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int>
> > > > >(std::vector<std::vector<int, std::allocator<int> >,
> std::allocator<std::vector<int, std::allocator<int> > > >) const",
> referenced from:
> >       void RDKit::Dict::setVal<std::vector<std::vector<int,
> std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int>
> > > > >(std::string const&, std::vector<std::vector<int,
> std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int>
> > > >&) in testDict.cpp.o
> >   "std::vector<int, std::allocator<int> >
> RDKit::Dict::fromany<std::vector<int, std::allocator<int> > >(boost::any
> const&) const", referenced from:
> >       void RDKit::Dict::getVal<std::vector<int, std::allocator<int> >
> >(std::string const&, std::vector<int, std::allocator<int> >&) const in
> testDict.cpp.o
> >   "boost::any RDKit::Dict::toany<std::vector<int, std::allocator<int> >
> >(std::vector<int, std::allocator<int> >) const", referenced from:
> >       void RDKit::Dict::setVal<std::vector<int, std::allocator<int> >
> >(std::string const&, std::vector<int, std::allocator<int> >&) in
> testDict.cpp.o
> >   "int RDKit::Dict::fromany<int>(boost::any const&) const", referenced
> from:
> >       void RDKit::Dict::getVal<int>(std::string const&, int&) const in
> testDict.cpp.o
> >   "boost::any RDKit::Dict::toany<int>(int) const", referenced from:
> >       void RDKit::Dict::setVal<int>(std::string const&, int&) in
> testDict.cpp.o
> > ld: symbol(s) not found for architecture x86_64
> > clang: error: linker command failed with exit code 1 (use -v to see
> invocation)
> >
>
> Nikolas Fechner, who has a MacBookPro running Lion, and I just got
> this figured out.
> There's a test at line 4 of $RDBASE/Code/RDGeneral/CMakeLists.txt:
>
> if(CMAKE_COMPILER_IS_GNUCXX OR CMAKE_COMPILER_IS_CLANG)
> # Dict.cpp behaves badly if compiled with optimization under g++
> SET_SOURCE_FILES_PROPERTIES(Dict.cpp PROPERTIES COMPILE_FLAGS -O0)
> endif()
>
> apparently neither of those two variables is set under Lion. The
> "fix", which I will check in later today, is:
>
> if(NOT MSVC)
> # Dict.cpp behaves badly if compiled with optimization under g++
> SET_SOURCE_FILES_PROPERTIES(Dict.cpp PROPERTIES COMPILE_FLAGS -O0)
> endif()
>
> After making this change we were able to complete an RDKit build on
> Niko's machine.
>
> I will try to remember to do a longer explanation of why the above is
> necessary later, but right now I have to run to a meeting.
>
> Hope this helps,
> -greg
>
>
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