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October 17, 2016 20:19
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| Error compiling Cython file: | |
| ------------------------------------------------------------ | |
| ... | |
| cdef BondArray bondarray, bondarray_h | |
| cdef BondType btype = BondType() | |
| bondarray = self.thisptr.Bonds() | |
| bondarray_h = self.thisptr.BondsH() | |
| bondarray.insert(bondarray.end(), bondarray_h.begin(), bondarray_h.end()) | |
| ^ | |
| ------------------------------------------------------------ | |
| pytraj/topology/topology.pyx:672:28: Compiler crash in AnalyseExpressionsTransform | |
| ModuleNode.body = StatListNode(topology.pyx:2:0) | |
| StatListNode.stats[24] = StatListNode(topology.pyx:79:5) | |
| StatListNode.stats[0] = CClassDefNode(topology.pyx:79:5, | |
| as_name = 'Topology', | |
| class_name = 'Topology', | |
| module_name = '', | |
| visibility = 'private') | |
| CClassDefNode.body = StatListNode(topology.pyx:80:4) | |
| StatListNode.stats[51] = PropertyNode(topology.pyx:663:4, | |
| name = 'bonds') | |
| PropertyNode.body = StatListNode(topology.pyx:664:8) | |
| StatListNode.stats[0] = GeneratorDefNode(topology.pyx:664:8, | |
| doc = 'return bond iterator', | |
| is_generator = True, | |
| modifiers = [...]/0, | |
| name = '__get__', | |
| needs_closure = True, | |
| num_required_args = 1, | |
| py_wrapper_required = True, | |
| reqd_kw_flags_cname = '0', | |
| used = True) | |
| GeneratorDefNode.gbody = GeneratorBodyDefNode(topology.pyx:664:8, | |
| is_generator_body = True, | |
| modifiers = [...]/0, | |
| name = '__get__', | |
| py_wrapper_required = True, | |
| reqd_kw_flags_cname = '0') | |
| File 'Nodes.py', line 430, in analyse_expressions: StatListNode(topology.pyx:665:12) | |
| File 'Nodes.py', line 4741, in analyse_expressions: ExprStatNode(topology.pyx:672:28) | |
| File 'ExprNodes.py', line 519, in analyse_expressions: SimpleCallNode(topology.pyx:672:28, | |
| analysed = True, | |
| use_managed_ref = True) | |
| File 'ExprNodes.py', line 5122, in analyse_types: SimpleCallNode(topology.pyx:672:28, | |
| analysed = True, | |
| use_managed_ref = True) | |
| File 'ExprNodes.py', line 5176, in analyse_c_function_call: SimpleCallNode(topology.pyx:672:28, | |
| analysed = True, | |
| use_managed_ref = True) | |
| Compiler crash traceback from this point on: | |
| File "/u2/home/haichit/anaconda3/lib/python3.5/site-packages/Cython/Compiler/ExprNodes.py", line 5176, in analyse_c_function_call | |
| entry = PyrexTypes.best_match(args, alternatives, self.pos, env) | |
| File "/u2/home/haichit/anaconda3/lib/python3.5/site-packages/Cython/Compiler/PyrexTypes.py", line 4083, in best_match | |
| type = func_type.specialize(deductions), | |
| File "/u2/home/haichit/anaconda3/lib/python3.5/site-packages/Cython/Compiler/PyrexTypes.py", line 2747, in specialize | |
| [arg.specialize(values) for arg in self.args], | |
| File "/u2/home/haichit/anaconda3/lib/python3.5/site-packages/Cython/Compiler/PyrexTypes.py", line 2747, in <listcomp> | |
| [arg.specialize(values) for arg in self.args], | |
| File "/u2/home/haichit/anaconda3/lib/python3.5/site-packages/Cython/Compiler/PyrexTypes.py", line 3051, in specialize | |
| return CFuncTypeArg(self.name, self.type.specialize(values), self.pos, self.cname) | |
| File "/u2/home/haichit/anaconda3/lib/python3.5/site-packages/Cython/Compiler/PyrexTypes.py", line 3479, in specialize | |
| specialized.namespace = self.namespace.specialize(values) | |
| File "/u2/home/haichit/anaconda3/lib/python3.5/site-packages/Cython/Compiler/PyrexTypes.py", line 3489, in specialize | |
| T = values[self.templates[0]] | |
| KeyError: <Cython.Compiler.PyrexTypes.CppClassType object at 0x7feb11d7e8d0> |
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Reproduce error
git clone https://github.com/Amber-MD/pytraj cd pytraj cython pytraj/topology/topology.pyx --cplus