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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