Double check all of your environment variables. I saw a similar error occur
due to a typo in my LD_LIBRARY_PATH settings.
-Kirk
On Thu, Jan 6, 2011 at 12:28 PM, Igor Filippov [Contr]
<[email protected]>wrote:
> Dear Kirk and Greg,
>
> I have got RDKit to compile!!!
> Unfortunately almost all of the tests are failing when I run ctest - any
> hints would be very welcome:
>
>
> Linking CXX shared module ../../../rdkit/Chem/rdChemicalFeatures.so
> [100%] Built target rdChemicalFeatures
> [r...@mgcct25 build]# sqlite3 $RDBASE/Data/RDTests.sqlt <
> $RDBASE/rdkit/Dbase/test_data/RDTests.sqlite
> SQL error: table basic_2class already exists
> SQL error: table ferro_noquant already exists
> SQL error: table ferro_noquant_realact already exists
> SQL error: table ferro_quant already exists
> SQL error: table float_2class already exists
> SQL error: table simple_mols already exists
> SQL error: table simple_mols_fps already exists
> SQL error: table simple_mols1 already exists
> SQL error: table simple_mols1_fp already exists
> SQL error: table ten_elements already exists
> SQL error: table ten_elements_dups already exists
> SQL error: table bit_ensemble_test already exists
> SQL error: table fromtext already exists
> SQL error: table fromtext2 already exists
> SQL error: table StorageTest already exists
> SQL error: column id is not unique
> SQL error: column id is not unique
> SQL error: column id is not unique
> SQL error: table simple_combined already exists
> [r...@mgcct25 build]# sqlite3 $RDBASE/Data/RDData.sqlt <
> $RDBASE/rdkit/Dbase/test_data/RDData.sqlite
> SQL error: table atomic_data already exists
> SQL error: table lsd_data already exists
> SQL error: table source_notes already exists
> [r...@mgcct25 build]# ctest
> Start processing tests
> Test project /root/RDKit_2010_09_1/build
> 1/ 76 Testing testDict ***Failed
> 2/ 76 Testing testDataStructs ***Failed
> 3/ 76 Testing pyBV ***Failed
> 4/ 76 Testing pyDiscreteValueVect ***Failed
> 5/ 76 Testing pySparseIntVect ***Failed
> 6/ 76 Testing testTransforms ***Failed
> 7/ 76 Testing testGrid ***Failed
> 8/ 76 Testing testPyGeometry ***Failed
> 9/ 76 Testing testMatrices ***Failed
> 10/ 76 Testing testAlignment ***Failed
> 11/ 76 Testing pyAlignment ***Failed
> 12/ 76 Testing testOptimizer ***Failed
> 13/ 76 Testing testForceField ***Failed
> 14/ 76 Testing testDistGeom ***Failed
> 15/ 76 Testing pyDistGeom ***Failed
> 16/ 76 Testing graphmolTest1 ***Failed
> 17/ 76 Testing graphmolcpTest ***Failed
> 18/ 76 Testing graphmolqueryTest ***Failed
> 19/ 76 Testing graphmolMolOpsTest ***Failed
> 20/ 76 Testing graphmoltestCanon ***Failed
> 21/ 76 Testing graphmoltestChirality ***Failed
> 22/ 76 Testing graphmoltestPickler ***Failed
> 23/ 76 Testing graphmolIterTest ***Failed
> 24/ 76 Testing testDepictor ***Failed
> 25/ 76 Testing pyDepictor ***Failed
> 26/ 76 Testing smiTest1 ***Failed
> 27/ 76 Testing smaTest1 ***Failed
> 28/ 76 Testing fileParsersTest1 ***Failed
> 29/ 76 Testing testMolSupplier ***Failed
> 30/ 76 Testing testMolWriter ***Failed
> 31/ 76 Testing testTplParser ***Failed
> 32/ 76 Testing testMol2ToMol ***Failed
> 33/ 76 Testing testSubstructMatch ***Failed
> 34/ 76 Testing testReaction ***Failed
> 35/ 76 Testing pyChemReactions ***Failed
> 36/ 76 Testing testChemTransforms ***Failed
> 37/ 76 Testing testSubgraphs1 ***Failed
> 38/ 76 Testing testSubgraphs2 ***Failed
> 39/ 76 Testing testFragCatalog ***Failed
> 40/ 76 Testing pyFragCatalog ***Failed
> 41/ 76 Testing testDescriptors ***Failed
> 42/ 76 Testing pyMolDescriptors ***Failed
> 43/ 76 Testing testFingerprints ***Failed
> 44/ 76 Testing pyPartialCharges ***Failed
> 45/ 76 Testing testMolTransforms ***Failed
> 46/ 76 Testing pyMolTransforms ***Failed
> 47/ 76 Testing testForceFieldHelpers ***Failed
> 48/ 76 Testing pyForceFieldHelpers ***Failed
> 49/ 76 Testing testDistGeomHelpers ***Failed
> 50/ 76 Testing pyDistGeom ***Failed
> 51/ 76 Testing testMolAlign ***Failed
> 52/ 76 Testing pyMolAlign ***Failed
> 53/ 76 Testing testFeatures ***Failed
> 54/ 76 Testing pyChemicalFeatures ***Failed
> 55/ 76 Testing testShapeHelpers ***Failed
> 56/ 76 Testing pyShapeHelpers ***Failed
> 57/ 76 Testing testMolCatalog ***Failed
> 58/ 76 Testing pyMolCatalog ***Failed
> 59/ 76 Testing testSLNParse ***Failed
> 60/ 76 Testing pySLNParse ***Failed
> 61/ 76 Testing pyGraphMolWrap ***Failed
> 62/ 76 Testing pyTestConformerWrap ***Failed
> 63/ 76 Testing testQuery ***Failed
> 64/ 76 Testing testMatCalc ***Failed
> 65/ 76 Testing pyMatCalc ***Failed
> 66/ 76 Testing pyCMIM ***Failed
> 67/ 76 Testing pyRanker ***Failed
> 68/ 76 Testing testChemicalFeatures ***Failed
> 69/ 76 Testing pyFeatures ***Failed
> 70/ 76 Testing pythonTestDbCLI ***Failed
> 71/ 76 Testing pythonTestDirML ***Failed
> 72/ 76 Testing pythonTestDirDataStructs Passed
> 73/ 76 Testing pythonTestDirDbase Passed
> 74/ 76 Testing pythonTestDirSimDivFilters Passed
> 75/ 76 Testing pythonTestDirVLib Passed
> 76/ 76 Testing pythonTestDirChem ***Failed
>
> 5% tests passed, 72 tests failed out of 76
>
> The following tests FAILED:
> 1 - testDict (Failed)
> 2 - testDataStructs (Failed)
> 3 - pyBV (Failed)
> 4 - pyDiscreteValueVect (Failed)
> 5 - pySparseIntVect (Failed)
> 6 - testTransforms (Failed)
> 7 - testGrid (Failed)
> 8 - testPyGeometry (Failed)
> 9 - testMatrices (Failed)
> 10 - testAlignment (Failed)
> 11 - pyAlignment (Failed)
> 12 - testOptimizer (Failed)
> 13 - testForceField (Failed)
> 14 - testDistGeom (Failed)
> 15 - pyDistGeom (Failed)
> 16 - graphmolTest1 (Failed)
> 17 - graphmolcpTest (Failed)
> 18 - graphmolqueryTest (Failed)
> 19 - graphmolMolOpsTest (Failed)
> 20 - graphmoltestCanon (Failed)
> 21 - graphmoltestChirality (Failed)
> 22 - graphmoltestPickler (Failed)
> 23 - graphmolIterTest (Failed)
> 24 - testDepictor (Failed)
> 25 - pyDepictor (Failed)
> 26 - smiTest1 (Failed)
> 27 - smaTest1 (Failed)
> 28 - fileParsersTest1 (Failed)
> 29 - testMolSupplier (Failed)
> 30 - testMolWriter (Failed)
> 31 - testTplParser (Failed)
> 32 - testMol2ToMol (Failed)
> 33 - testSubstructMatch (Failed)
> 34 - testReaction (Failed)
> 35 - pyChemReactions (Failed)
> 36 - testChemTransforms (Failed)
> 37 - testSubgraphs1 (Failed)
> 38 - testSubgraphs2 (Failed)
> 39 - testFragCatalog (Failed)
> 40 - pyFragCatalog (Failed)
> 41 - testDescriptors (Failed)
> 42 - pyMolDescriptors (Failed)
> 43 - testFingerprints (Failed)
> 44 - pyPartialCharges (Failed)
> 45 - testMolTransforms (Failed)
> 46 - pyMolTransforms (Failed)
> 47 - testForceFieldHelpers (Failed)
> 48 - pyForceFieldHelpers (Failed)
> 49 - testDistGeomHelpers (Failed)
> 50 - pyDistGeom (Failed)
> 51 - testMolAlign (Failed)
> 52 - pyMolAlign (Failed)
> 53 - testFeatures (Failed)
> 54 - pyChemicalFeatures (Failed)
> 55 - testShapeHelpers (Failed)
> 56 - pyShapeHelpers (Failed)
> 57 - testMolCatalog (Failed)
> 58 - pyMolCatalog (Failed)
> 59 - testSLNParse (Failed)
> 60 - pySLNParse (Failed)
> 61 - pyGraphMolWrap (Failed)
> 62 - pyTestConformerWrap (Failed)
> 63 - testQuery (Failed)
> 64 - testMatCalc (Failed)
> 65 - pyMatCalc (Failed)
> 66 - pyCMIM (Failed)
> 67 - pyRanker (Failed)
> 68 - testChemicalFeatures (Failed)
> 69 - pyFeatures (Failed)
> 70 - pythonTestDbCLI (Failed)
> 71 - pythonTestDirML (Failed)
> 76 - pythonTestDirChem (Failed)
> Errors while running CTest
> [r...@mgcct25 build]#
>
>
> On Thu, 2011-01-06 at 12:26 -0500, [email protected] wrote:
> > Igor,
> >
> > I am very happy to hear that the script is helpful. And, yes,
> > installation on CentOS 5.5 is a pain. The problem actually resides in
> > the fact that the major CentOS and RHEL releases are very dated once
> > they are released. GCC is my biggest complaint as the standard version
> > on the current CentOS is known to have a major bug that causes the
> > Boost compile and therefore RDKit compile to fail. I believe that the
> > new RHEL 6 is somewhat better - based on Fedora 12 and 13 - and the
> > upcoming CentOS 6 will obviously be better as well. Unfortunately,
> > this is what we have to work with. Alternatively, I have also
> > installed RDKit on Fedora 14 with no need for any updates to any other
> > package. One step and I was done. The good news is that future
> > releases of RDKit should go somewhat painlessly. I was able to install
> > the current beta package by simply compiling the RDKit code. After 2
> > minutes of hands on time, 15 minutes of waiting, and RDKit was up and
> > running.
> >
> > If you run into any problems, please post them so that we can
> > (hopefully) help and others can benefit in the future.
> >
> > -Kirk
> >
> >
> >
> > On Jan 6, 2011 10:11am, "Igor Filippov [Contr]" <[email protected]>
> > wrote:
> > > Dear Kirk,
> > >
> > >
> > >
> > > Thank you so much! I'm in the process of compiling gcc-4.5.1 right
> > now,
> > >
> > > having got gmp, mpc, and mpfr built with the older version of gcc.
> > >
> > > Your instructions have to be preserved for the others, I can't
> > believe
> > >
> > > I'm the only one using CentOs/RHEL on a server/compute node.
> > >
> > >
> > >
> > > Greg, don't take it as a slam but compiling the Linux kernel is a
> > walk
> > >
> > > in a park compared to a recent RDkit. I'm working on it second day
> > and
> > >
> > > I'm barely half-way through the process of installing dependencies.
> > Even
> > >
> > > without python the version of gcc which comes with CentOs 5 (4.1.2)
> > >
> > > cannot compile RDKit.
> > >
> > > On the other hand the RPM packages for Fedora have been painless to
> > >
> > > install, how nice it would be to have the RDKit RPMs for CentOs!
> > >
> > >
> > >
> > > Best,
> > >
> > > Igor
> > >
> > >
> > >
> > > On Wed, 2011-01-05 at 17:41 -0500, Robert DeLisle wrote:
> > >
> > > > I have been able to reproducibly build RDKit on CentOS 5.5, but it
> > >
> > > > required a significant amount of updating of the build components.
> > >
> > > > The attached walk-through script should get you there. I do not
> > >
> > > > recall ever seeing that particular error, however.
> > >
> > > >
> > >
> > > > -Kirk
> > >
> > > >
> > >
> > > >
> > >
> > > >
> > >
> > > >
> > >
> > > > On Wed, Jan 5, 2011 at 1:15 PM, Igor Filippov [Contr]
> > >
> > > > [email protected]> wrote:
> > >
> > > > Dear All,
> > >
> > > >
> > >
> > > > Has anyone successfully compiled RDKit on CentOs 5? I'm
> > >
> > > > running into the
> > >
> > > > following error message:
> > >
> > > > [ 15%] Building CXX object
> > >
> > > >
> > >
> > > >
> > Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/rdAlignment.cpp.o
> > >
> > > >
> > >
> > > >
> >
> /root/RDKit_2010_09_1/Code/Numerics/Alignment/Wrap/rdAlignment.cpp:14:31:
> error: numpy/arrayobject.h: No such file or directory
> > >
> > > >
> > >
> > > > On CentOs 5 arrayobject.h is part of python-numeric
> > package
> > >
> > > > and it's
> > >
> > > > located in:
> > >
> > > > /usr/include/python2.4/Numeric/arrayobject.h
> > >
> > > >
> > >
> > > > I'm attempting to compile RDKit_2010_09_1, using boost
> > version
> > >
> > > > 1.39.0,
> > >
> > > > x86_64 system.
> > >
> > > >
> > >
> > > > Regards,
> > >
> > > > Igor
> > >
> > > >
> > >
> > > >
> > >
> > > >
> > >
> > > >
> > >
> > > >
> > >
> > > >
> >
> ------------------------------------------------------------------------------
> > >
> > > > Learn how Oracle Real Application Clusters (RAC) One Node
> > >
> > > > allows customers
> > >
> > > > to consolidate database storage, standardize their
> > database
> > >
> > > > environment, and,
> > >
> > > > should the need arise, upgrade to a full multi-node Oracle
> > RAC
> > >
> > > > database
> > >
> > > > without downtime or disruption
> > >
> > > > http://p.sf.net/sfu/oracle-sfdevnl
> > >
> > > > _______________________________________________
> > >
> > > > Rdkit-discuss mailing list
> > >
> > > > [email protected]
> > >
> > > > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
> > >
> > > >
> > >
> > >
> > >
> > >
> > >
>
>
>
------------------------------------------------------------------------------
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to consolidate database storage, standardize their database environment, and,
should the need arise, upgrade to a full multi-node Oracle RAC database
without downtime or disruption
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