Yep, I've defintely done that. I've even gone so far as to wipe out the
directory entirely and start with a fresh RDKit directory. I also looked
into the cache file and seen that the library directories appear to be set
as /usr/local/lib and /user/local/lib64, but one the error occurs, it refers
to /usr/lib64. I can't seem to find any reason for this.
-Kirk
On Mon, Nov 15, 2010 at 3:26 PM, Eddie Cao <[email protected]> wrote:
> Have you tried to remove the CMake cache file before rerun cmake?
>
> rm -f CMakeCache.txt
>
> After rerun cmake, take a look at that file again and make sure things like
> Boost_INCLUDE_DIR and Boost_LIBRARY_DIRS all point to /usr/local/include
> and /usr/local/lib, etc.
>
> Eddie
>
>
> On Nov 15, 2010, at 12:45 PM, Robert DeLisle wrote:
>
> > I've been working to build RDKit on Centos 5, and I'm hitting a very
> common error. Unfortunately, none of the standard fixes have helped.
> >
> > Details:
> >
> > The error that I'm seeing is this:
> >
> > [ 82%] Building CXX object
> Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/SLNParse.cpp.o
> > [ 83%] Building CXX object
> Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o
> > [ 83%] Building CXX object
> Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/sln.tab.cpp.o
> > [ 84%] Building CXX object
> Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/lex.yysln.cpp.o
> > Linking CXX shared library libSLNParse.so
> > /usr/bin/ld: /usr/lib/../lib64/libboost_regex.a(instances.o): relocation
> R_X86_64_32 against
> `boost::object_cache<boost::re_detail::cpp_regex_traits_base<char>,
> boost::re_detail::cpp_regex_traits_implementation<char>
> >::do_get(boost::re_detail::cpp_regex_traits_base<char> const&, unsigned
> long)::s_data' can not be used when making a shared object; recompile with
> -fPIC
> > /usr/lib/../lib64/libboost_regex.a: could not read symbols: Bad value
> > collect2: ld returned 1 exit status
> > make[2]: *** [Code/GraphMol/SLNParse/libSLNParse.so] Error 1
> > make[1]: *** [Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/all] Error 2
> > make: *** [all] Error 2
> >
> >
> > I've taken the standard steps of building Python (v2.7) with the -fPIC
> flag. Specficially, I attached CFLAGS=-fPIC to configure in the Python
> build. This solved the first instance of this type of error occuring at
> about 3%.
> >
> > I've also tried the two fixes for Boost with the following command line
> to build RDKit:
> >
> > cmake -DBOOST_ROOT=/usr/local -DBoost_USE_STATIC_LIBS=OFF ..
> >
> >
> > I still get this error, and I notice that the Boost libraries that are
> being referred to are actually the system installation in usr/lib64 and not
> those that I've build in /usr/local/lib. It would seem that I can't seem to
> force make to look in the right location.
> >
> > Any tips are greatly apprciated.
> >
> > -Kirk
> >
> >
> >
> >
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> >
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>
>
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