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
>> >
>> >
>> >
>> >
>> ------------------------------------------------------------------------------
>> > Centralized Desktop Delivery: Dell and VMware Reference Architecture
>> > Simplifying enterprise desktop deployment and management using
>> > Dell EqualLogic storage and VMware View: A highly scalable, end-to-end
>> > client virtualization framework. Read more!
>> >
>> http://p.sf.net/sfu/dell-eql-dev2dev_______________________________________________
>> > Rdkit-discuss mailing list
>> > [email protected]
>> > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>
>>
>
------------------------------------------------------------------------------
Centralized Desktop Delivery: Dell and VMware Reference Architecture
Simplifying enterprise desktop deployment and management using
Dell EqualLogic storage and VMware View: A highly scalable, end-to-end
client virtualization framework. Read more!
http://p.sf.net/sfu/dell-eql-dev2dev
_______________________________________________
Rdkit-discuss mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
