Hi Don, I'm adding the rdkit-discuss mailing list to the "To" list.
On Mon, Jan 24, 2011 at 3:24 PM, Donald Keidel <[email protected]> wrote: > > I am trying to build RDKit_2010_09_1 with boost 1.44 on Ubuntu system > that is 64-bit running version 10.04. I am having problems with getting > all the tests to pass. I ahve searched the web for help for over a few > days now and have tried many different permutations of RDKit sources and > boost sources and still cannot get 100% test pass. I have also attached > my log file with the specific error messages when tests were run. This doesn't address the specific problems below, which I will comment on, but I would encourage you to use the most recent release (RDKit_2010_12_1) if possible. > > I have summarized what I have done belowIn /usr/local/ execute: > > sudo tar --bzip2 -xf boost_1_44_0.tar.bz2 > > 3. cd $BOOST (i.e. /usr/local/boost_1_44_0) > > 4. sudo ./bootstrap.sh > > the header files are installed to /usr/local/include, and the libraries > themselves are installed to /usr/local/lib. The above command should work, but for your future reference: the boost build process goes much more quickly if you only build the libraries that are required for the RDKit like this: ./bootstrap.sh --with-libraries=python,regex > 5. Building on 32 bit systems: sudo ./bjam install > Building on 64 bit systems: sudo ./bjam address-model=64 > cflags=-fPIC cxxflags=-fPIC install > > > result after building boost > ..... > ...failed updating 4 targets... > ...skipped 6 targets... > ...updated 8944 targets... It's not particularly nice that some targets failed to build, but based on the information below I don't think any of them are important for the RDKit. > I opened a new shell and changed my environment variables to: > > sudo rm -rf RDKit_2010_09_1 > > sudo tar -zxvf RDKit_2010_09_1.tgz I would suggest at this point doing a chown -R of the RDKit source directory so that you don't need to use sudo again. I think that a combination of permission and root-environment problems may explain some of the errors that occurred during testing. > RDBASE=/usr/local/RDKit_2010_09_1 > > export RDBASE > > PATH=/usr/local/RDKit_2010_09_1/bin:$PATH > > export PATH You no longer need to change your PATH for the RDKit > LD_LIBRARY_PATH=/usr/local/lib64:/usr/local/lib:$RDBASE/lib:$LD_LIBRARY_PATH > > export LD_LIBRARY_PATH > > BOOST=/usr/local/boost_1_44_0 > > export BOOST > > PYTHONPATH=$RDBASE:$PYTHONPATH > > export PYTHONPATH > > > rm -rf build > > sudo mkdir build > > cd build > > sudo cmake -DBoost_USE_STATIC_LIBS=OFF -DBOOST_ROOT=/usr/local .. I do not think the -DBoost_USE_STATIC_LIBS=OFF part should be required. Is there a specific reason you include it? > sudo make > sudo make install > > cd .. > > * create the databases used by the Python tests, requires sqlite3 > to be installed: Those two steps are no longer required (and are no longer in the INSTALL instructions). The corresponding .sqlite files are now included with the RDKit distribution. > cd build > > ctest (without sudo) > > 87% tests passed, 10 tests failed out of 76 > > Total Test time (real) = 35.76 sec > > The following tests FAILED: > Cannot create directory /usr/local/RDKit_2010_09_1/build/Testing/Temporary > Cannot create log file: LastTestsFailed.log > 24 - testDepictor (SEGFAULT) > 29 - testMolSupplier (SEGFAULT) > 30 - testMolWriter (SEGFAULT) > 45 - testMolTransforms (SEGFAULT) > 49 - testDistGeomHelpers (SEGFAULT) > 52 - pyMolAlign (Failed) > 61 - pyGraphMolWrap (Failed) > 70 - pythonTestDbCLI (Failed) > 71 - pythonTestDirML (Failed) > 76 - pythonTestDirChem (Failed) > Errors while running CTest As mentioned above, I suspect that these are permission problems, but some could be build problems. Please follow the tips above and retry the build and then see if you still have problems. Best Regards, -greg ------------------------------------------------------------------------------ Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)! Finally, a world-class log management solution at an even better price-free! Download using promo code Free_Logger_4_Dev2Dev. Offer expires February 28th, so secure your free ArcSight Logger TODAY! http://p.sf.net/sfu/arcsight-sfd2d _______________________________________________ Rdkit-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
