Hi Greg,
I've been doing that too, and I am very happy that I've got the Java
wrappers built (v2016.03.1). I've got four Python operations that fail. I
can send the log from ctest -V if you'd like:
97% tests passed, 4 tests failed out of 133
Total Test time (real) = 464.59 sec
The following tests FAILED:
44 - pyChemReactions (Failed)
62 - pyForceFieldHelpers (Failed)
86 - pyGraphMolWrap (Failed)
133 - pythonTestDirChem (Failed)
Errors while running CTest
Thanks for everyone's help!
Matt
On Tue, Apr 19, 2016 at 4:23 AM, Greg Landrum <greg.land...@gmail.com>
wrote:
> It's great that you're almost there.
>
> The best way to help diagnose problems running the tests is to run ctest
> in verbose mode with "-V". Here's an example on my machine:
>
> glandrum@Otter:/scratch/RDKit_git/build$ echo $RDBASE
> /scratch/RDKit_git
> glandrum@Otter:/scratch/RDKit_git/build$ echo $LD_LIBRARY_PATH
> /scratch/RDKit_git/lib:/usr/local/pgsql/lib:
> glandrum@Otter:/scratch/RDKit_git/build$ ctest -V -R JavaAromat
> UpdateCTestConfiguration from
> :/scratch/RDKit_git/build/DartConfiguration.tcl
> UpdateCTestConfiguration from
> :/scratch/RDKit_git/build/DartConfiguration.tcl
> Test project /scratch/RDKit_git/build
> Constructing a list of tests
> Done constructing a list of tests
> Checking test dependency graph...
> Checking test dependency graph end
> test 99
> Start 99: JavaAromaticTests
>
> 99: Test command: /usr/bin/java
> "-Djava.library.path=/scratch/RDKit_git/Code/JavaWrappers/gmwrapper" "-cp"
> "/scratch/RDKit_git/External/java_lib/junit.jar:/scratch/RDKit_git/Code/JavaWrappers/gmwrapper/build-test:/scratch/RDKit_git/Code/JavaWrappers/gmwrapper/org.RDKit.jar"
> "org.RDKit.AromaticTests"
> 99: Test timeout computed to be: 9.99988e+06
> 99: JUnit version 4.10
> 99: ..
> 99: Time: 1.8
> 99:
> 99: OK (2 tests)
> 99:
> 1/1 Test #99: JavaAromaticTests ................ Passed 1.99 sec
>
> The following tests passed:
> JavaAromaticTests
>
> 100% tests passed, 0 tests failed out of 1
>
> Total Test time (real) = 2.00 sec
> glandrum@Otter:/scratch/RDKit_git/build$
>
>
> I do not have CLASSPATH set and I don't think it's necessary in order to
> be able to run the tests.
>
> -greg
>
>
>
>
> On Mon, Apr 18, 2016 at 11:47 PM, Matthew Lardy <mla...@gmail.com> wrote:
>
>> Hi Brian,
>>
>> Thanks! I gave it a whirl, but no improvement. In previous installs
>> I've specified the shared object directly, but there isn't a good reason
>> for me to do so. I've done a make install, so everything should be built
>> wherever it is supposed to go.
>>
>> I've missed something simple. I just don't see it yet,
>> Matt
>>
>>
>> On Mon, Apr 18, 2016 at 2:08 PM, Brian Kelley <fustiga...@gmail.com>
>> wrote:
>>
>>> > $RDBASE/Code/JavaWrappers/gmwrapper/libGraphMolWrap.so
>>>
>>> You probably need to drop the explicit .so, the library path is the path
>>> to the directory not to the .so itself.
>>>
>>> Here is what I normally use for testing ( note I usually build into an
>>> rdkit_build directory via: -DCMAKE_INSTALL_PREFIX=<path to
>>> rdkit_build> )
>>>
>>>
>>> RDBASE=`pwd`/../../rdkit LD_LIBRARY_PATH=`pwd`/rdkit_build/lib
>>> PYTHONPATH=`pwd`/rdkit_build/lib/python2.7/site-packages ctest
>>>
>>> On Mon, Apr 18, 2016 at 4:57 PM, Matthew Lardy <mla...@gmail.com> wrote:
>>>
>>>> A quick question, what should be set up for the environment for the
>>>> Java wrappers? I've got the following set:
>>>>
>>>> setenv RDBASE $WORKSPACE/RDKit-2016/rdkit-Release_2016_03
>>>> setenv PATH ${PATH}:$RDBASE/lib
>>>>
>>>> setenv CLASSPATH $RDBASE/Code/JavaWrappers/gmwrapper/org.RDKit.jar
>>>> setenv LD_LIBRARY_PATH
>>>> ${LD_LIBRARY_PATH}:$WORKSPACE/boost1.59/lib:$RDBASE/build/lib:$RDBASE/Code/JavaWrappers/gmwrapper/libGraphMolWrap.so
>>>> setenv PYTHONPATH ${PYTHONPATH}:$RDBASE
>>>>
>>>> The code builds without issue, save a few warnings. Here is the Java
>>>> error I am getting (during the tests):
>>>>
>>>> JUnit version 4.12
>>>> 119: Exception in thread "main" java.lang.NoClassDefFoundError:
>>>> org/hamcrest/SelfDescribing
>>>>
>>>> Is my CLASSPATH wrong? Did I forget a SO in my LD_LIBRARY_PATH?
>>>>
>>>> Thanks in advance!
>>>> Matt
>>>>
>>>>
>>>>
>>>> On Mon, Apr 18, 2016 at 9:56 AM, Matthew Lardy <mla...@gmail.com>
>>>> wrote:
>>>>
>>>>> 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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>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Rdkit-discuss mailing list
>>>>>>> Rdkit-discuss@lists.sourceforge.net
>>>>>>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> ------------------------------------------------------------------------------
>>>>>>> Find and fix application performance issues faster with Applications
>>>>>>> Manager
>>>>>>> Applications Manager provides deep performance insights into
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>>>>>>> your business applications. It resolves application problems quickly
>>>>>>> and
>>>>>>> reduces your MTTR. Get your free trial!
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>>>>>>> _______________________________________________
>>>>>>> Rdkit-discuss mailing list
>>>>>>> Rdkit-discuss@lists.sourceforge.net
>>>>>>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> Find and fix application performance issues faster with Applications
>>>> Manager
>>>> Applications Manager provides deep performance insights into multiple
>>>> tiers of
>>>> your business applications. It resolves application problems quickly and
>>>> reduces your MTTR. Get your free trial!
>>>> https://ad.doubleclick.net/ddm/clk/302982198;130105516;z
>>>> _______________________________________________
>>>> Rdkit-discuss mailing list
>>>> Rdkit-discuss@lists.sourceforge.net
>>>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>>>
>>>>
>>>
>>
>
------------------------------------------------------------------------------
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your business applications. It resolves application problems quickly and
reduces your MTTR. Get your free trial!
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