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, rkdeli...@gmail.com 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]" <ig...@helix.nih.gov> > 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] > > > > > ig...@helix.nih.gov> 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 > > > > > Rdkit-discuss@lists.sourceforge.net > > > > > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > > > > > > > > > > > > > > > ------------------------------------------------------------------------------ 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 Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss