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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