Getting the right version of boost can be tricky. You can see our normal cmake
incantation here as well as how we set RDBASE for tests
https://github.com/rdkit/rdkit/blob/master/.travis.yml
Note the
-D Boost_NO_SYSTEM_PATHS=ON
When running cmake, otherwise cmake can get very confused.
----
Brian Kelley
> On Apr 15, 2016, at 6:26 PM, Matthew Lardy <mla...@gmail.com> wrote:
>
> I'll add, that remembering that cmake and ccmake can produce different
> outcomes I've gone back to trying cmake. But I can't overwrite the variables
> in cmake. Here are the results from trying to specify them:
>
> Manually-specified variables were not used by the project:
>
> BOOST_DIR
> BOOST_INCLUDE_DIR
> BOOST_LIBRARY_DIR
> BOOST_PYTHON_LIBRARY_DEBUG
> BOOST_PYTHON_LIBRARY_RELEASE
> BOOST_REGEX_LIBRARY_DEBUG
> BOOST_REGEX_LIBRARY_RELEASE
> BOOST_SERIALIZATION_LIBRARY_DEBUG
> BOOST_SERIALIZATION_LIBRARY_RELEASE
> BOOST_SYSTEM_LIBRARY_DEBUG
> BOOST_SYSTEM_LIBRARY_RELEASE
> BOOST_THREAD_LIBRARY_DEBUG
> BOOST_THREAD_LIBRARY_RELEASE
>
> cmake, as per it's usual, picked up an ancient version of boost (which I want
> to override). I can get around this with ccmake, but nothing that I compile
> can pass all of the tests. If someone knows what these variables (shown in
> ccmake) are called, I'd love to know.
>
> Thanks in advance!
> Matthew
>
>
>> On Fri, Apr 15, 2016 at 2:58 PM, Matthew Lardy <mla...@gmail.com> wrote:
>> Hi all,
>>
>> If someone has an insight I would love to hear it about how best to build
>> RDKit from scratch.
>>
>> I am using the following to build the 2015.03 release:
>> RedHat Linux version 6.4
>> gcc version 4.4.7 20120313 (Red Hat 4.4.7-11) (GCC)
>> swig version 3.0.8
>> cmake version 3.0.0
>> boost version 1.53.0 (I've also tried boost 1.59.0)
>> python version 2.7.7
>>
>> I use ccmake and alter the things which need to be altered (as cmake always
>> grabs the wrong things for me). My build compiles nicely, and without
>> errors. But the tests are a mess. Here is the summary of my build:
>>
>> 26% tests passed, 87 tests failed out of 118
>>
>> I've put the details of the tests, in the hope that someone sees a pattern
>> that I do not, below.
>>
>> Before someone recommends a clean install that is not possible. I also do
>> not have root, so I can't just wipe the machine and start over. I cannot
>> use an RPM, so that is out too. Any ideas are welcome!
>>
>> Thanks,
>> Matthew
>>
>> The following tests FAILED:
>> 2 - testDataStructs (OTHER_FAULT)
>> 3 - pyBV (Failed)
>> 4 - pyDiscreteValueVect (Failed)
>> 5 - pySparseIntVect (Failed)
>> 7 - testGrid (OTHER_FAULT)
>> 8 - testPyGeometry (Failed)
>> 11 - pyAlignment (Failed)
>> 14 - testMMFFForceField (OTHER_FAULT)
>> 15 - pyForceFieldConstraints (Failed)
>> 17 - pyDistGeom (Failed)
>> 18 - graphmolTest1 (OTHER_FAULT)
>> 21 - graphmolMolOpsTest (SEGFAULT)
>> 23 - graphmoltestChirality (OTHER_FAULT)
>> 24 - graphmoltestPickler (OTHER_FAULT)
>> 26 - hanoiTest (OTHER_FAULT)
>> 28 - testDepictor (OTHER_FAULT)
>> 29 - pyDepictor (Failed)
>> 32 - fileParsersTest1 (OTHER_FAULT)
>> 33 - testMolSupplier (OTHER_FAULT)
>> 34 - testMolWriter (OTHER_FAULT)
>> 35 - testTplParser (OTHER_FAULT)
>> 36 - testMol2ToMol (OTHER_FAULT)
>> 38 - testReaction (OTHER_FAULT)
>> 40 - pyChemReactions (Failed)
>> 41 - testChemTransforms (OTHER_FAULT)
>> 44 - testFragCatalog (OTHER_FAULT)
>> 45 - pyFragCatalog (Failed)
>> 46 - testDescriptors (OTHER_FAULT)
>> 47 - pyMolDescriptors (Failed)
>> 48 - testFingerprints (OTHER_FAULT)
>> 50 - pyPartialCharges (Failed)
>> 51 - testMolTransforms (OTHER_FAULT)
>> 52 - pyMolTransforms (Failed)
>> 53 - testMMFFForceFieldHelpers (OTHER_FAULT)
>> 54 - testUFFForceFieldHelpers (OTHER_FAULT)
>> 55 - pyForceFieldHelpers (Failed)
>> 56 - testDistGeomHelpers (OTHER_FAULT)
>> 57 - pyDistGeom (Failed)
>> 58 - testMolAlign (OTHER_FAULT)
>> 59 - pyMolAlign (Failed)
>> 60 - testFeatures (OTHER_FAULT)
>> 61 - pyChemicalFeatures (Failed)
>> 62 - testShapeHelpers (OTHER_FAULT)
>> 63 - pyShapeHelpers (Failed)
>> 65 - pyMolCatalog (Failed)
>> 66 - moldraw2DTest1 (OTHER_FAULT)
>> 67 - pyMolDraw2D (Failed)
>> 69 - pyFMCS (Failed)
>> 72 - pyMolHash (Failed)
>> 74 - pySLNParse (Failed)
>> 75 - pyGraphMolWrap (Failed)
>> 76 - pyTestConformerWrap (Failed)
>> 79 - pyMatCalc (Failed)
>> 80 - pySimDivPickers (Failed)
>> 81 - pyRanker (Failed)
>> 83 - pyFeatures (Failed)
>> 84 - JavaAromaticTests (Failed)
>> 85 - JavaAtomPairsTests (Failed)
>> 86 - JavaBasicMoleculeTests (Failed)
>> 87 - JavaBasicMolecule2Tests (Failed)
>> 88 - JavaChemAtomTests (Failed)
>> 89 - JavaChemBondTests (Failed)
>> 90 - JavaChemReactionTests (Failed)
>> 91 - JavaChemSmartsTests (Failed)
>> 92 - JavaChemTests (Failed)
>> 93 - JavaChemv2Tests (Failed)
>> 94 - JavaConformerTests (Failed)
>> 95 - JavaDescriptorTests (Failed)
>> 96 - JavaDistanceGeometryTests (Failed)
>> 97 - JavaErrorHandlingTests (Failed)
>> 98 - JavaFingerprintsTests (Failed)
>> 99 - JavaForceFieldsTests (Failed)
>> 100 - JavaHManipulationsTests (Failed)
>> 101 - JavaLipinskiTests (Failed)
>> 102 - JavaPicklingTests (Failed)
>> 103 - JavaSmilesCreationTests (Failed)
>> 104 - JavaSmilesDetailsTests (Failed)
>> 105 - JavaSmilesTests (Failed)
>> 106 - JavaSuppliersTests (Failed)
>> 107 - JavaWrapperTests (Failed)
>> 108 - JavaChemTransformsTests (Failed)
>> 109 - JavaFMCSTests (Failed)
>> 110 - JavaPDBTests (Failed)
>> 111 - JavaAlignTests (Failed)
>> 112 - pythonTestDbCLI (Failed)
>> 113 - pythonTestDirML (Failed)
>> 118 - pythonTestDirChem (Failed)
>> Errors while running CTest
>
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