Make sure /usr/local/lib appears before /usr/lib64 in your LD_LIBRARY_PATH. It
seems python import loads the system boost rather than your custom boost.
-Eddie
On Nov 15, 2010, at 2:44 PM, Robert DeLisle wrote:
> It must be something in the release version of RDKit. I just grabbed the SVN
> version, put it in the same location, followed the same procedures, and it
> has just compiled fine without any other changes on my part.
>
> Greg - any ideas what the difference is here? Not that it matters given that
> the SVN is working, but just for curiosity's sake.
>
> Sadly, now I get this from with Python:
>
>
> >>> from rdkit import Chem
> Traceback (most recent call last):
> File "<stdin>", line 1, in <module>
> File "/opt/RDKit_svn_20101115/rdkit/Chem/__init__.py", line 18, in <module>
> from rdkit import rdBase
> ImportError: /usr/lib64/libboost_python.so.2: undefined symbol:
> PyUnicodeUCS4_FromEncodedObject
>
>
>
> -Kirk
>
>
>
>
>
> On Mon, Nov 15, 2010 at 3:28 PM, Robert DeLisle <[email protected]> wrote:
> 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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