mirror of
https://github.com/rdkit/rdkit.git
synced 2026-06-03 21:44:30 +08:00
Fix some build warnings (#6618)
* fixes a copy constructor issue:
In copy constructor ‘boost::shared_ptr<T>::shared_ptr(const boost::shared_ptr<T>&) [with T = RDKit::ROMol]’,
inlined from ‘PyObject* RDKit::RunReactant(ChemicalReaction*, T, unsigned int) [with T = boost::python::api::object]’ at /tmp/rdkit_builder/rdkit/Code/GraphMol/ChemReactions/Wrap/rdChemReactions.cpp:129:14:
/usr/include/boost/smart_ptr/shared_ptr.hpp:416:66: warning: ‘*(const boost::shared_ptr<RDKit::ROMol>*)((char*)&<unnamed> + offsetof(boost::python::extract<boost::shared_ptr<RDKit::ROMol> >,boost::python::extract<boost::shared_ptr<RDKit::ROMol> >::<unnamed>.boost::python::converter::extract_rvalue<boost::shared_ptr<RDKit::ROMol> >::m_data.boost::python::converter::rvalue_from_python_data<boost::shared_ptr<RDKit::ROMol> >::<unnamed>.boost::python::converter::rvalue_from_python_storage<boost::shared_ptr<RDKit::ROMol> >::storage)).boost::shared_ptr<RDKit::ROMol>::px’ may be used uninitialized [-Wmaybe-uninitialized]
416 | shared_ptr( shared_ptr const & r ) BOOST_SP_NOEXCEPT : px( r.px ), pn( r.pn )
| ~~^~
/tmp/rdkit_builder/rdkit/Code/GraphMol/ChemReactions/Wrap/rdChemReactions.cpp: In function ‘PyObject* RDKit::RunReactant(ChemicalReaction*, T, unsigned int) [with T = boost::python::api::object]’:
/tmp/rdkit_builder/rdkit/Code/GraphMol/ChemReactions/Wrap/rdChemReactions.cpp:129:30: note: ‘<anonymous>’ declared here
129 | ROMOL_SPTR react = python::extract<ROMOL_SPTR>(reactant);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/boost/smart_ptr/shared_ptr.hpp:17:
In copy constructor ‘boost::detail::shared_count::shared_count(const boost::detail::shared_count&)’,
inlined from ‘boost::shared_ptr<T>::shared_ptr(const boost::shared_ptr<T>&) [with T = RDKit::ROMol]’ at /usr/include/boost/smart_ptr/shared_ptr.hpp:416:72,
inlined from ‘PyObject* RDKit::RunReactant(ChemicalReaction*, T, unsigned int) [with T = boost::python::api::object]’ at /tmp/rdkit_builder/rdkit/Code/GraphMol/ChemReactions/Wrap/rdChemReactions.cpp:129:14:
/usr/include/boost/smart_ptr/detail/shared_count.hpp:438:67: warning: ‘((const boost::detail::shared_count*)((char*)&<unnamed> + offsetof(boost::python::extract<boost::shared_ptr<RDKit::ROMol> >,boost::python::extract<boost::shared_ptr<RDKit::ROMol> >::<unnamed>.boost::python::converter::extract_rvalue<boost::shared_ptr<RDKit::ROMol> >::m_data.boost::python::converter::rvalue_from_python_data<boost::shared_ptr<RDKit::ROMol> >::<unnamed>.boost::python::converter::rvalue_from_python_storage<boost::shared_ptr<RDKit::ROMol> >::storage)))[1].boost::detail::shared_count::pi_’ may be used uninitialized [-Wmaybe-uninitialized]
438 | shared_count(shared_count const & r) BOOST_SP_NOEXCEPT: pi_(r.pi_)
| ~~^~~
/tmp/rdkit_builder/rdkit/Code/GraphMol/ChemReactions/Wrap/rdChemReactions.cpp: In function ‘PyObject* RDKit::RunReactant(ChemicalReaction*, T, unsigned int) [with T = boost::python::api::object]’:
/tmp/rdkit_builder/rdkit/Code/GraphMol/ChemReactions/Wrap/rdChemReactions.cpp:129:30: note: ‘<anonymous>’ declared here
129 | ROMOL_SPTR react = python::extract<ROMOL_SPTR>(reactant);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
* Fixes a (weird) allocation warning in GCC 12
In file included from /usr/include/c++/12/bits/alloc_traits.h:33,
from /usr/include/c++/12/ext/alloc_traits.h:34,
from /usr/include/c++/12/bits/basic_string.h:39,
from /usr/include/c++/12/string:53,
from /usr/include/c++/12/bits/locale_classes.h:40,
from /usr/include/c++/12/bits/ios_base.h:41,
from /usr/include/c++/12/streambuf:41,
from /usr/include/c++/12/bits/streambuf_iterator.h:35,
from /usr/include/c++/12/iterator:66,
from /usr/include/boost/iterator/iterator_traits.hpp:10,
from /usr/include/boost/range/iterator_range_core.hpp:26,
from /usr/include/boost/range/iterator_range.hpp:13,
from /usr/include/boost/iostreams/traits.hpp:38,
from /usr/include/boost/iostreams/detail/call_traits.hpp:15,
from /usr/include/boost/iostreams/detail/adapter/device_adapter.hpp:22,
from /usr/include/boost/iostreams/tee.hpp:18,
from /tmp/rdkit_builder/rdkit/Code/RDGeneral/RDLog.h:17,
from /tmp/rdkit_builder/rdkit/Code/GraphMol/ChemTransforms/testChemTransforms.cpp:11:
In function ‘void std::_Construct(_Tp*, _Args&& ...) [with _Tp = pair<int, int>; _Args = {const pair<int, int>&}]’,
inlined from ‘_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = const pair<int, int>*; _ForwardIterator = pair<int, int>*]’ at /usr/include/c++/12/bits/stl_uninitialized.h:120:21,
inlined from ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = const std::pair<int, int>*; _ForwardIterator = std::pair<int, int>*; bool _TrivialValueTypes = false]’ at /usr/include/c++/12/bits/stl_uninitialized.h:137:32,
inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = const pair<int, int>*; _ForwardIterator = pair<int, int>*]’ at /usr/include/c++/12/bits/stl_uninitialized.h:185:15,
inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = const pair<int, int>*; _ForwardIterator = pair<int, int>*; _Tp = pair<int, int>]’ at /usr/include/c++/12/bits/stl_uninitialized.h:372:37,
inlined from ‘void std::vector<_Tp, _Alloc>::_M_range_insert(iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = const std::pair<int, int>*; _Tp = std::pair<int, int>; _Alloc = std::allocator<std::pair<int, int> >]’ at /usr/include/c++/12/bits/vector.tcc:808:38,
inlined from ‘std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, std::initializer_list<_Tp>) [with _Tp = std::pair<int, int>; _Alloc = std::allocator<std::pair<int, int> >]’ at /usr/include/c++/12/bits/stl_vector.h:1409:17,
inlined from ‘void testReplaceCoreMatchVectMultipleMappingToCore()’ at /tmp/rdkit_builder/rdkit/Code/GraphMol/ChemTransforms/testChemTransforms.cpp:974:17:
/usr/include/c++/12/bits/stl_construct.h:119:7: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’ writing 56 bytes into a region of size 48 overflows the destination [-Wstringop-overflow=]
119 | ::new((void*)__p) _Tp(std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/x86_64-linux-gnu/c++/12/bits/c++allocator.h:33,
from /usr/include/c++/12/bits/allocator.h:46,
from /usr/include/c++/12/string:41:
In member function ‘_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = std::pair<int, int>]’,
inlined from ‘static _Tp* std::allocator_traits<std::allocator<_CharT> >::allocate(allocator_type&, size_type) [with _Tp = std::pair<int, int>]’ at /usr/include/c++/12/bits/alloc_traits.h:464:28,
inlined from ‘std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = std::pair<int, int>; _Alloc = std::allocator<std::pair<int, int> >]’ at /usr/include/c++/12/bits/stl_vector.h:378:33,
inlined from ‘void std::vector<_Tp, _Alloc>::_M_range_insert(iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = const std::pair<int, int>*; _Tp = std::pair<int, int>; _Alloc = std::allocator<std::pair<int, int> >]’ at /usr/include/c++/12/bits/vector.tcc:799:40,
inlined from ‘std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, std::initializer_list<_Tp>) [with _Tp = std::pair<int, int>; _Alloc = std::allocator<std::pair<int, int> >]’ at /usr/include/c++/12/bits/stl_vector.h:1409:17,
inlined from ‘void testReplaceCoreMatchVectMultipleMappingToCore()’ at /tmp/rdkit_builder/rdkit/Code/GraphMol/ChemTransforms/testChemTransforms.cpp:974:17:
/usr/include/c++/12/bits/new_allocator.h:137:55: note: at offset [8, 56] into destination object of size 56 allocated by ‘operator new’
137 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp)));
| ^
* finalForce maybe uninitialized in inlined copy constructor
* failure is being used uninitialized
* MaeWriter::write overrides a method of the base class without being marked 'override'
This one is annoying because it happens in an exported header, so it propagates
to any code using the header!
* otq is never used
* fix implicitly declared assignment operator warning
* variables in catch statements that are never used
* fix type (sign) mismatch warning
* drop duplicate export macro
This commit is contained in:
Ric
GitHub
@@ -278,7 +278,7 @@ int ForceField::minimize(unsigned int snapshotFreq,
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unsigned int numIters = 0;
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unsigned int dim = this->d_numPoints * d_dimension;
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double finalForce;
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double finalForce = 0.0;
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auto *points = new double[dim];
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this->scatter(points);
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@@ -123,10 +123,9 @@ PyObject *RunReactants(ChemicalReaction *self, T reactants,
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return res;
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}
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template <typename T>
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PyObject *RunReactant(ChemicalReaction *self, T reactant,
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PyObject *RunReactant(ChemicalReaction *self, python::object reactant,
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unsigned int reactionIdx) {
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ROMOL_SPTR react = python::extract<ROMOL_SPTR>(reactant);
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auto react = python::extract<ROMOL_SPTR>(reactant);
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std::vector<MOL_SPTR_VECT> mols;
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@@ -562,9 +561,7 @@ Sample Usage:
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"the products as a tuple of tuples. If maxProducts is not zero,"
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" stop the reaction when maxProducts have been generated "
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"[default=1000]")
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.def("RunReactant",
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(PyObject * (*)(RDKit::ChemicalReaction *, python::object, unsigned))
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RDKit::RunReactant,
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.def("RunReactant", RDKit::RunReactant,
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"apply the reaction to a single reactant")
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.def("RunReactantInPlace", RDKit::RunReactantInPlace,
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(python::arg("self"), python::arg("reactant"),
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@@ -970,9 +970,7 @@ void testReplaceCoreMatchVectMultipleMappingToCore() {
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// 3 dummies in core map to single N in molecule
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core = "C1([*:1])C([*:2])C([*:3])C1"_smiles;
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mol = "C1C2C3N2C13"_smiles;
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mapping.clear();
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mapping.insert(mapping.end(),
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{{0, 4}, {1, 3}, {2, 2}, {3, 3}, {4, 1}, {5, 3}, {6, 0}});
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mapping.assign({{0, 4}, {1, 3}, {2, 2}, {3, 3}, {4, 1}, {5, 3}, {6, 0}});
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result.reset(replaceCore(*mol.get(), *core.get(), mapping, false));
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smi = MolToSmiles(*result.get(), true);
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TEST_ASSERT("[1*]N([2*])[3*]" == smi);
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@@ -1072,13 +1070,13 @@ void testMurckoDecomp() {
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{"OC2C(C)C21C(N)C1C", "C2CC12CC1"}, // Spiro
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{"C1CC1C(=O)OC", "C1CC1"}, // Carbonyl outside scaffold
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{"C1CC1C=C", "C1CC1"}, // Double bond outside scaffold
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{"C1CC1C=CC1CC1C=CNNCO", "C1CC1C=CC1CC1"}, // Double bond in scaffold
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{"C1CC1C=CC1CC1C=CNNCO", "C1CC1C=CC1CC1"}, // Double bond in scaffold
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{"CC1CC1C(N)C1C(N)C1", "C1CC1CC1CC1"},
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{"C1CC1S(=O)C1CC1C=CNNCO", "C1CC1S(=O)C1CC1"}, // S=O group in scaffold
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{"O=SCNC1CC1S(=O)C1CC1C=CNNCO",
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"C1CC1S(=O)C1CC1"}, // S=O group outside scaffold
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"C1CC1S(=O)C1CC1"}, // S=O group outside scaffold
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{"C1CC1S(=O)(=O)C1CC1C=CNNCO",
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"C1CC1S(=O)(=O)C1CC1"}, // SO2 group in scaffold
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"C1CC1S(=O)(=O)C1CC1"}, // SO2 group in scaffold
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{"O=S(CNCNC)(=O)CNC1CC1S(=O)(=O)C1CC1C=CNNCO",
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"C1CC1S(=O)(=O)C1CC1"}, // SO2 group outside scaffold
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{"C1CC1C=NO", "C1CC1"}, // Hydroxamide
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@@ -37,9 +37,9 @@ RDKIT_DESCRIPTORS_EXPORT double PMI1(const ROMol&, int confId = -1,
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bool force = false);
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const std::string PMI1Version = "1.0.0";
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//! second principal moment of inertia
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RDKIT_DESCRIPTORS_EXPORT RDKIT_DESCRIPTORS_EXPORT double PMI2(
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const ROMol&, int confId = -1, bool useAtomicMasses = true,
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bool force = false);
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RDKIT_DESCRIPTORS_EXPORT double PMI2(const ROMol&, int confId = -1,
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bool useAtomicMasses = true,
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bool force = false);
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const std::string PMI2Version = "1.0.0";
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//! Third (largest) principal moment of inertia
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RDKIT_DESCRIPTORS_EXPORT double PMI3(const ROMol&, int confId = -1,
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@@ -395,7 +395,7 @@ class RDKIT_FILEPARSERS_EXPORT MaeWriter : public MolWriter {
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const STR_VECT &propNames = STR_VECT());
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//! \brief write a new molecule to the file.
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void write(const ROMol &mol, int confId = defaultConfId);
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void write(const ROMol &mol, int confId = defaultConfId) override;
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//! \brief flush the ostream
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void flush() override;
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@@ -84,8 +84,6 @@ TEST_CASE("tautomer basics") {
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REQUIRE(mol);
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ExtendedQueryMol xqm =
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std::unique_ptr<TautomerQuery>(TautomerQuery::fromMol(*mol));
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const TautomerQuery &otq =
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*std::get<ExtendedQueryMol::TautomerQuery_T>(xqm.xqmol);
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SECTION("substructure matching and serialization") {
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ExtendedQueryMol xqm2(xqm.toBinary());
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@@ -65,6 +65,8 @@ class MolBundle : public RDProps {
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MolBundle(const std::string &pkl) { initFromString(pkl); }
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virtual ~MolBundle() {}
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MolBundle &operator=(const MolBundle &other) = default;
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//! returns our molecules
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virtual const std::vector<boost::shared_ptr<ROMol>> &getMols() const {
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return d_mols;
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@@ -443,7 +443,7 @@ TautomerEnumeratorResult TautomerEnumerator::enumerate(const ROMol &mol) const {
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MolOps::SANITIZE_SETCONJUGATION |
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MolOps::SANITIZE_SETHYBRIDIZATION |
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MolOps::SANITIZE_ADJUSTHS);
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} catch (const KekulizeException &ke) {
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} catch (const KekulizeException &) {
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continue;
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}
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#ifdef VERBOSE_ENUMERATION
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@@ -1009,7 +1009,7 @@ void testSetProps(ROMol &mol) {
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for (auto &bond : mol.bonds()) {
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_testSetProps(*bond, std::string("bond_") + std::to_string(bond->getIdx()));
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}
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for (int conf_idx = 0; conf_idx < mol.getNumConformers(); ++conf_idx) {
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for (unsigned conf_idx = 0; conf_idx < mol.getNumConformers(); ++conf_idx) {
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_testSetProps(mol.getConformer(conf_idx),
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"conf_" + std::to_string(conf_idx));
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}
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@@ -24,7 +24,6 @@
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#include <boost/utility/typed_in_place_factory.hpp>
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#include <RDGeneral/BoostEndInclude.h>
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//#include <tbxx/error_utils.hpp>
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#include <RDGeneral/Invariant.h>
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#include <RDGeneral/Exceptions.h>
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@@ -459,7 +458,7 @@ class streambuf : public std::basic_streambuf<char> {
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boost::optional<off_type> seekoff_without_calling_python(
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off_type off, std::ios_base::seekdir way, std::ios_base::openmode which) {
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boost::optional<off_type> const failure;
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boost::optional<off_type> const failure = off_type(-1);
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// Buffer range and current position
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off_type buf_begin, buf_end, buf_cur, upper_bound;
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@@ -65,7 +65,7 @@ void test1() {
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bool ok = false;
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try {
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readAmberTrajectory(fName, coords, mol->getNumAtoms());
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} catch (ValueErrorException &e) {
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} catch (ValueErrorException &) {
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ok = true;
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}
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TEST_ASSERT(ok);
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@@ -74,7 +74,7 @@ void test1() {
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ok = false;
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try {
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readAmberTrajectory(fName, coords, mol->getNumAtoms());
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} catch (ValueErrorException &e) {
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} catch (ValueErrorException &) {
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// std::cout << e.what() << std::endl;
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ok = true;
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}
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