That helped, thanks! Didn't realize 'make install' was needed after
building the wrappers - I had built without the wrappers first, trying to
detect problems iteratively.
So now I'm able to use the wrappers in Java but noticed not all "core
functionality" is covered by the wrappers. Specifically, I'm looking for a
way to access
rdkit.Chem.MolStandardize.rdMolStandardize
from Java. I could not find any matching Java class nor function. Is this
functionality supported via the Java wrappers ?
Thanks & Regards,
Thomas
On Wed, Apr 22, 2020 at 11:55 AM Tim Dudgeon <tdudgeon...@gmail.com> wrote:
> Have a look in 'Code/JavaWrappers/gmwrapper/' not
> 'build/Code/JavaWrappers/gmwrapper/' ?
>
> Tim
> On 22/04/2020 10:36, Thomas Eckert wrote:
>
> Hi folks,
>
> Trying to build RDKit + JavaWrappers from scratch but, in the end, the JAR
> files are missing.
>
> Working on a freshly installed Ubuntu 19.10 and followed the steps
> described at [1]. All dependencies installed via Ubuntu's apt, no manually
> installed libs.
>
> Cloned the RDKit sources to
> /home/thomas/git/rdkit
> and set env variables
> RDBASE=/home/thomas/git/rdkit
> LD_LIBRARY_PATH=/home/thomas/git/rdkit/lib:/lib/x86_64-linux-gnu/
>
> Using this 'cmake' command
> cmake -DRDK_BUILD_PYTHON_WRAPPERS=OFF -DRDK_BUILD_SWIG_WRAPPERS=ON ..
> I get OK looking output except for
> CMake Warning (dev) at /usr/share/cmake-3.13/Modules/UseSWIG.cmake:564
> (message):
> Policy CMP0078 is not set. Run "cmake --help-policy CMP0078" for
> policy
> details. Use the cmake_policy command to set the policy and
> suppress this
> warning.
> Call Stack (most recent call first):
> Code/JavaWrappers/gmwrapper/CMakeLists.txt:109 (SWIG_ADD_LIBRARY)
> This warning is for project developers. Use -Wno-dev to suppress it.
> but as the warning states, this seems to be fine for non-rdkit-dev users,
> so I just carry on.
>
> 'make' then runs happily with a few warnings on the first build but no
> errors are reported. It even states
> (...)
> [ 99%] Built target GraphMolWrap_swig_compilation
> [ 99%] Built target GraphMolWrap
> [100%] building jar
> [100%] Built target GraphMolWrapJar
> [100%] building test classes
> [100%] Built target BuildJavaWrapperTests
> which seems to mean the JavaWrappers were built. However this is then the
> case
> ~/git/rdkit/build$ ls -lha Code/JavaWrappers/gmwrapper/
> total 16M
> drwxr-xr-x 3 thomas thomas 4,0K Apr 22 11:15 .
> drwxr-xr-x 4 thomas thomas 4,0K Apr 22 11:15 ..
> drwxr-xr-x 7 thomas thomas 4,0K Apr 22 11:15 CMakeFiles
> -rw-r--r-- 1 thomas thomas 2,6K Apr 22 10:47 cmake_install.cmake
> -rw-r--r-- 1 thomas thomas 13K Apr 22 10:47 CTestTestfile.cmake
> -rwxr-xr-x 1 thomas thomas 16M Apr 22 10:49 libGraphMolWrap.so
> -rw-r--r-- 1 thomas thomas 13K Apr 22 10:47 Makefile
> so no JAR files to be found even though the shared library mentioned in
> "Building the Java wrappers" at [1] is there.
>
> Thus I ran the tests
> /git/rdkit/build$ ctest
> Test project /home/thomas/git/rdkit/build
> (...)
> 73% tests passed, 39 tests failed out of 143
>
> Total Test time (real) = 98.60 sec
>
> The following tests FAILED:
> 105 - JavaAromaticTests (Failed)
> 106 - JavaAtomPairsTests (Failed)
> 107 - JavaBasicMoleculeTests (Failed)
> 108 - JavaBasicMolecule2Tests (Failed)
> 109 - JavaChemAtomTests (Failed)
> 110 - JavaChemBondTests (Failed)
> 111 - JavaChemReactionTests (Failed)
> 112 - JavaChemSmartsTests (Failed)
> 113 - JavaChemTests (Failed)
> 114 - JavaChemv2Tests (Failed)
> 115 - JavaConformerTests (Failed)
> 116 - JavaDescriptorTests (Failed)
> 117 - JavaDistanceGeometryTests (Failed)
> 118 - JavaErrorHandlingTests (Failed)
> 119 - JavaFingerprintsTests (Failed)
> 120 - JavaForceFieldsTests (Failed)
> 121 - JavaHManipulationsTests (Failed)
> 122 - JavaLipinskiTests (Failed)
> 123 - JavaPicklingTests (Failed)
> 124 - JavaSmilesCreationTests (Failed)
> 125 - JavaSmilesDetailsTests (Failed)
> 126 - JavaSmilesTests (Failed)
> 127 - JavaSuppliersTests (Failed)
> 128 - JavaTrajectoryTests (Failed)
> 129 - JavaWrapperTests (Failed)
> 130 - JavaChemTransformsTests (Failed)
> 131 - JavaFMCSTests (Failed)
> 132 - JavaPDBTests (Failed)
> 133 - JavaSequenceTests (Failed)
> 134 - JavaAlignTests (Failed)
> 135 - JavaMolQueryTests (Failed)
> 136 - JavaFilterCatalogTests (Failed)
> 137 - JavaSubstructLibraryTests (Failed)
> 138 - JavaRGroupDecompositionTests (Failed)
> 139 - JavaScaffoldNetworkTests (Failed)
> 140 - JavaMolHashTest (Failed)
> 141 - JavaDiversityPickerTests (Failed)
> 142 - JavaBitOpsTests (Failed)
> 143 - MolStandardizeTest (Failed)
> Errors while running CTest
>
> At this point I cannot find anything in the documentation to proceed
> further. I'm not familiar with most of the stack used with/for RDKit
> either, so I don't know where to look. Any hints on where to look or what
> to check ?
>
> Regards,
> Thomas
>
> [1] https://www.rdkit.org/docs/Install.html#building-from-source
>
>
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