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 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
>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> 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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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!
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