Dear all.
I am trying to compile RDKit with boost from vcpkg which by standard use
latest which is boost 1.72, and link against python37.
All none python crests pass fine, but most python tests keeps failing for
me with something the "did not match C++ signature" error. Here is a
minimal example that fails:
In [7]: mol = Chem.MolFromSmiles('CCCC')
In [8]: mol.GetNumAtoms()
Out[8]: 4
In [9]: mol.Debug()
Atoms:
0 6 C chg: 0 deg: 1 exp: 1 imp: 3 hyb: 4 arom?: 0 chi: 0
1 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: 4 arom?: 0 chi: 0
2 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: 4 arom?: 0 chi: 0
3 6 C chg: 0 deg: 1 exp: 1 imp: 3 hyb: 4 arom?: 0 chi: 0
Bonds:
0 0->1 order: 1 conj?: 0 aromatic?: 0
1 1->2 order: 1 conj?: 0 aromatic?: 0
2 2->3 order: 1 conj?: 0 aromatic?: 0
In [10]: molh = Chem.AddHs(mol)
---------------------------------------------------------------------------
ArgumentError Traceback (most recent call last)
<ipython-input-10-9a58211410d1> in <module>
----> 1 molh = Chem.AddHs(mol)
ArgumentError: Python argument types in
rdkit.Chem.rdmolops.AddHs(Mol)
did not match C++ signature:
AddHs(RDKit::ROMol mol, bool explicitOnly=False, bool addCoords=False,
boost::python::api::object onlyOnAtoms=None, bool addResidueInfo=False)
Do you have any idea of why that is? My only suspiscion right now is if it
can because it is linking to the found numpy (which is in and conda
environment I am using for testing), if this is using another boost
version, can that be it?
my cmake call:
cmake -DPy_ENABLE_SHARED=1 \
-DPYTHON_EXECUTABLE=/home/hafnium/miniconda3/envs/py37/bin/python3 \
-DRDK_BUILD_COORDGEN_SUPPORT=OFF \
-DRDK_INSTALL_INTREE=OFF \
-DRDK_INSTALL_STATIC_LIBS=OFF \
-DRDK_BUILD_CPP_TESTS=ON \
-DRDK_USE_BOOST_IOSTREAMS=OFF \
-DBoost_NO_SYSTEM_PATHS=ON \
-DCMAKE_INSTALL_PREFIX=/home/hafnium/Hflabs-sync/HFgit/External/rdkit/rdkit-install
\
-DCMAKE_BUILD_TYPE=Release \
-DCMAKE_TOOLCHAIN_FILE=/home/hafnium/Hflabs-sync/vcpkg/scripts/buildsystems/vcpkg.cmake
\
..
The following tests FAILED:
17 - pyAlignment (Failed)
21 - pyForceFieldConstraints (Failed)
41 - pyDepictor (Failed)
62 - pyChemReactions (Failed)
63 - pyChemReactionEnumerations (Failed)
64 - pyChemReactionSanitize (Failed)
70 - pyFilterCatalog (Failed)
72 - pyFragCatalog (Failed)
87 - pyMolDescriptors (Child aborted)
88 - pyMolDescriptors3D (Failed)
93 - pyTestGenerator (Failed)
94 - pyTestMHFP (Failed)
96 - pyPartialCharges (Failed)
98 - pyMolTransforms (Failed)
103 - pyForceFieldHelpers (Failed)
105 - pyDistGeomHelpers (Failed)
107 - pyMolAlign (Failed)
109 - pyChemicalFeatures (Failed)
111 - pyShapeHelpers (Failed)
113 - pyMolCatalog (Failed)
117 - pyMolDraw2D (Failed)
119 - pyFMCS (Failed)
123 - pyMolHash (Failed)
125 - pyMMPA (Failed)
127 - pyReducedGraphs (Failed)
130 - pySubstructLibrary (Failed)
132 - pyRGroupDecomposition (Failed)
134 - pyMolInterchange (Failed)
137 - pyGraphMolWrap (Failed)
138 - pyTestConformerWrap (Failed)
139 - pyTestTrajectory (Failed)
140 - pyTestSGroups (Failed)
142 - pyTestPropertyLists (Failed)
151 - pyMolStandardize (Failed)
153 - pyScaffoldNetwork (Failed)
157 - pyMatCalc (Failed)
160 - pySimDivPickers (Failed)
161 - pyRanker (Failed)
163 - pyFeatures (Failed)
164 - pythonTestDbCLI (Failed)
165 - pythonTestDirML (Failed)
166 - pythonTestDirDataStructs (Failed)
168 - pythonTestDirSimDivFilters (Failed)
169 - pythonTestDirVLib (Failed)
170 - pythonTestDirChem (Failed)
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