My thoughts exactly. I've forgotten to set RDBASE before and had a few
tests fail. This is different. It was everything and it took me days to
get to a place where some of the base code was passing tests. Someone
mentioned that I need to build boost with the version of Python that I am
using. This is problem in an environment where people choose their own
adventure with modules. I have no guarantee that they won't chose Python
3.x when I've compiled everything with 2.7.7. That problem will be a good
to have when I get there. :)
If my present build doesn't pass everything, and it won't, I'll send you
the fun directly. :)
Thanks again Greg!
Matt
On Fri, Apr 15, 2016 at 9:34 PM, Greg Landrum <greg.land...@gmail.com>
wrote:
> Brian's suggestion to take a look at the cmake invocation in the travis
> file is a good one.
>
> Based on the number of failing tests, I think something more than just an
> RDBASE problem is wrong. The best way to track this down is by sending me
> the cmake command you ran, the output of running make, and the output of
> running ctest (after you run ctest you will find this in the directory
> Testing/Temporary/LastTest.log). Because this is pretty large and likely
> not of interest to others, it's probably best to send it directly to me or
> to create a gist and send the link to that.
>
> -greg
>
>
>
> On Sat, Apr 16, 2016 at 2:22 AM, Brian Kelley <fustiga...@gmail.com>
> wrote:
>
>> 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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>>
>>
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>> Applications Manager provides deep performance insights into multiple
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>> reduces your MTTR. Get your free trial!
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>
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