Re: [Rdkit-discuss] One last build error

[Peter Harley]

Greg Landrum wrote:
Hi Peter,

On Mon, Sep 8, 2008 at 12:26 AM, Peter Harley <pj...@cam.ac.uk> wrote:
  
I'm trying to build RDKit for the first time, on linux. I've managed to
reduce the number of errors I'm getting down to just one now. Any help
in figuring out what I've missed would be great.

failed gcc.compile.c++
Geometry/Wrap/bin/gcc-4.2.3/release/threading-multi/Point.o
        

There should have been some kind of error message (probably a fairly
long one) just before this. Can you please send that?
  
Sure:

gcc.compile.c++ Geometry/Wrap/bin/gcc-4.2.3/release/threading-multi/Point.o
/home/pete/Archive/boost_1_36_0/boost/python/operators.hpp: In static 
member function ‘static PyObject* 
boost::python::detail::operator_l<op_sub>::apply<L, R>::execute(typename 
boost::python::detail::unwrap_wrapper_<L>::type&, const typename 
boost::python::detail::unwrap_wrapper_<R>::type&) [with L = 
RDGeom::Point3D, R = RDGeom::Point3D]’:
/home/pete/Archive/boost_1_36_0/boost/python/operators.hpp:152: 
instantiated from ‘void boost::python::detail::operator_<id, L, 
R>::visit(ClassT&) const [with ClassT = 
boost::python::class_<RDGeom::Point3D, 
boost::python::detail::not_specified, 
boost::python::detail::not_specified, 
boost::python::detail::not_specified>, 
boost::python::detail::operator_id id = op_sub, L = 
boost::python::self_ns::self_t, R = boost::python::self_ns::self_t]’
/home/pete/Archive/boost_1_36_0/boost/python/def_visitor.hpp:31: 
instantiated from ‘static void 
boost::python::def_visitor_access::visit(const V&, classT&) [with V = 
boost::python::def_visitor<boost::python::detail::operator_<op_sub, 
boost::python::self_ns::self_t, boost::python::self_ns::self_t> >, 
classT = boost::python::class_<RDGeom::Point3D, 
boost::python::detail::not_specified, 
boost::python::detail::not_specified, 
boost::python::detail::not_specified>]’
/home/pete/Archive/boost_1_36_0/boost/python/def_visitor.hpp:67: 
instantiated from ‘void 
boost::python::def_visitor<DerivedVisitor>::visit(classT&) const [with 
classT = boost::python::class_<RDGeom::Point3D, 
boost::python::detail::not_specified, 
boost::python::detail::not_specified, 
boost::python::detail::not_specified>, DerivedVisitor = 
boost::python::detail::operator_<op_sub, boost::python::self_ns::self_t, 
boost::python::self_ns::self_t>]’
/home/pete/Archive/boost_1_36_0/boost/python/class.hpp:225: instantiated 
from ‘boost::python::class_<T, X1, X2, X3>& boost::python::class_<T, X1, 
X2, X3>::def(const boost::python::def_visitor<Derived>&) [with Derived = 
boost::python::detail::operator_<op_sub, boost::python::self_ns::self_t, 
boost::python::self_ns::self_t>, W = RDGeom::Point3D, X1 = 
boost::python::detail::not_specified, X2 = 
boost::python::detail::not_specified, X3 = 
boost::python::detail::not_specified]’
Geometry/Wrap/Point.cpp:128: instantiated from here
/home/pete/Archive/boost_1_36_0/boost/python/operators.hpp:213: error: 
no match for ‘operator-’ in ‘l - r’
./Geometry/point.h:142: note: candidates are: RDGeom::Point3D 
RDGeom::Point3D::operator-() const
/home/pete/Archive/boost_1_36_0/boost/python/operators.hpp: In static 
member function ‘static PyObject* 
boost::python::detail::operator_l<op_add>::apply<L, R>::execute(typename 
boost::python::detail::unwrap_wrapper_<L>::type&, const typename 
boost::python::detail::unwrap_wrapper_<R>::type&) [with L = 
RDGeom::Point3D, R = RDGeom::Point3D]’:
/home/pete/Archive/boost_1_36_0/boost/python/operators.hpp:152: 
instantiated from ‘void boost::python::detail::operator_<id, L, 
R>::visit(ClassT&) const [with ClassT = 
boost::python::class_<RDGeom::Point3D, 
boost::python::detail::not_specified, 
boost::python::detail::not_specified, 
boost::python::detail::not_specified>, 
boost::python::detail::operator_id id = op_add, L = 
boost::python::self_ns::self_t, R = boost::python::self_ns::self_t]’
/home/pete/Archive/boost_1_36_0/boost/python/def_visitor.hpp:31: 
instantiated from ‘static void 
boost::python::def_visitor_access::visit(const V&, classT&) [with V = 
boost::python::def_visitor<boost::python::detail::operator_<op_add, 
boost::python::self_ns::self_t, boost::python::self_ns::self_t> >, 
classT = boost::python::class_<RDGeom::Point3D, 
boost::python::detail::not_specified, 
boost::python::detail::not_specified, 
boost::python::detail::not_specified>]’
/home/pete/Archive/boost_1_36_0/boost/python/def_visitor.hpp:67: 
instantiated from ‘void 
boost::python::def_visitor<DerivedVisitor>::visit(classT&) const [with 
classT = boost::python::class_<RDGeom::Point3D, 
boost::python::detail::not_specified, 
boost::python::detail::not_specified, 
boost::python::detail::not_specified>, DerivedVisitor = 
boost::python::detail::operator_<op_add, boost::python::self_ns::self_t, 
boost::python::self_ns::self_t>]’
/home/pete/Archive/boost_1_36_0/boost/python/class.hpp:225: instantiated 
from ‘boost::python::class_<T, X1, X2, X3>& boost::python::class_<T, X1, 
X2, X3>::def(const boost::python::def_visitor<Derived>&) [with Derived = 
boost::python::detail::operator_<op_add, boost::python::self_ns::self_t, 
boost::python::self_ns::self_t>, W = RDGeom::Point3D, X1 = 
boost::python::detail::not_specified, X2 = 
boost::python::detail::not_specified, X3 = 
boost::python::detail::not_specified]’
Geometry/Wrap/Point.cpp:130: instantiated from here
/home/pete/Archive/boost_1_36_0/boost/python/operators.hpp:212: error: 
no match for ‘operator+’ in ‘l + r’
/home/pete/Archive/boost_1_36_0/boost/python/operators.hpp: In static 
member function ‘static PyObject* 
boost::python::detail::operator_l<op_sub>::apply<L, R>::execute(typename 
boost::python::detail::unwrap_wrapper_<L>::type&, const typename 
boost::python::detail::unwrap_wrapper_<R>::type&) [with L = 
RDGeom::Point2D, R = RDGeom::Point2D]’:
/home/pete/Archive/boost_1_36_0/boost/python/operators.hpp:152: 
instantiated from ‘void boost::python::detail::operator_<id, L, 
R>::visit(ClassT&) const [with ClassT = 
boost::python::class_<RDGeom::Point2D, 
boost::python::detail::not_specified, 
boost::python::detail::not_specified, 
boost::python::detail::not_specified>, 
boost::python::detail::operator_id id = op_sub, L = 
boost::python::self_ns::self_t, R = boost::python::self_ns::self_t]’
/home/pete/Archive/boost_1_36_0/boost/python/def_visitor.hpp:31: 
instantiated from ‘static void 
boost::python::def_visitor_access::visit(const V&, classT&) [with V = 
boost::python::def_visitor<boost::python::detail::operator_<op_sub, 
boost::python::self_ns::self_t, boost::python::self_ns::self_t> >, 
classT = boost::python::class_<RDGeom::Point2D, 
boost::python::detail::not_specified, 
boost::python::detail::not_specified, 
boost::python::detail::not_specified>]’
/home/pete/Archive/boost_1_36_0/boost/python/def_visitor.hpp:67: 
instantiated from ‘void 
boost::python::def_visitor<DerivedVisitor>::visit(classT&) const [with 
classT = boost::python::class_<RDGeom::Point2D, 
boost::python::detail::not_specified, 
boost::python::detail::not_specified, 
boost::python::detail::not_specified>, DerivedVisitor = 
boost::python::detail::operator_<op_sub, boost::python::self_ns::self_t, 
boost::python::self_ns::self_t>]’
/home/pete/Archive/boost_1_36_0/boost/python/class.hpp:225: instantiated 
from ‘boost::python::class_<T, X1, X2, X3>& boost::python::class_<T, X1, 
X2, X3>::def(const boost::python::def_visitor<Derived>&) [with Derived = 
boost::python::detail::operator_<op_sub, boost::python::self_ns::self_t, 
boost::python::self_ns::self_t>, W = RDGeom::Point2D, X1 = 
boost::python::detail::not_specified, X2 = 
boost::python::detail::not_specified, X3 = 
boost::python::detail::not_specified]’
Geometry/Wrap/Point.cpp:170: instantiated from here
/home/pete/Archive/boost_1_36_0/boost/python/operators.hpp:213: error: 
no match for ‘operator-’ in ‘l - r’
./Geometry/point.h:333: note: candidates are: RDGeom::Point2D 
RDGeom::Point2D::operator-() const
/home/pete/Archive/boost_1_36_0/boost/python/operators.hpp: In static 
member function ‘static PyObject* 
boost::python::detail::operator_l<op_add>::apply<L, R>::execute(typename 
boost::python::detail::unwrap_wrapper_<L>::type&, const typename 
boost::python::detail::unwrap_wrapper_<R>::type&) [with L = 
RDGeom::Point2D, R = RDGeom::Point2D]’:
/home/pete/Archive/boost_1_36_0/boost/python/operators.hpp:152: 
instantiated from ‘void boost::python::detail::operator_<id, L, 
R>::visit(ClassT&) const [with ClassT = 
boost::python::class_<RDGeom::Point2D, 
boost::python::detail::not_specified, 
boost::python::detail::not_specified, 
boost::python::detail::not_specified>, 
boost::python::detail::operator_id id = op_add, L = 
boost::python::self_ns::self_t, R = boost::python::self_ns::self_t]’
/home/pete/Archive/boost_1_36_0/boost/python/def_visitor.hpp:31: 
instantiated from ‘static void 
boost::python::def_visitor_access::visit(const V&, classT&) [with V = 
boost::python::def_visitor<boost::python::detail::operator_<op_add, 
boost::python::self_ns::self_t, boost::python::self_ns::self_t> >, 
classT = boost::python::class_<RDGeom::Point2D, 
boost::python::detail::not_specified, 
boost::python::detail::not_specified, 
boost::python::detail::not_specified>]’
/home/pete/Archive/boost_1_36_0/boost/python/def_visitor.hpp:67: 
instantiated from ‘void 
boost::python::def_visitor<DerivedVisitor>::visit(classT&) const [with 
classT = boost::python::class_<RDGeom::Point2D, 
boost::python::detail::not_specified, 
boost::python::detail::not_specified, 
boost::python::detail::not_specified>, DerivedVisitor = 
boost::python::detail::operator_<op_add, boost::python::self_ns::self_t, 
boost::python::self_ns::self_t>]’
/home/pete/Archive/boost_1_36_0/boost/python/class.hpp:225: instantiated 
from ‘boost::python::class_<T, X1, X2, X3>& boost::python::class_<T, X1, 
X2, X3>::def(const boost::python::def_visitor<Derived>&) [with Derived = 
boost::python::detail::operator_<op_add, boost::python::self_ns::self_t, 
boost::python::self_ns::self_t>, W = RDGeom::Point2D, X1 = 
boost::python::detail::not_specified, X2 = 
boost::python::detail::not_specified, X3 = 
boost::python::detail::not_specified]’
Geometry/Wrap/Point.cpp:172: instantiated from here
/home/pete/Archive/boost_1_36_0/boost/python/operators.hpp:212: error: 
no match for ‘operator+’ in ‘l + r’
/home/pete/Archive/boost_1_36_0/boost/python/operators.hpp: In static 
member function ‘static PyObject* 
boost::python::detail::operator_l<op_sub>::apply<L, R>::execute(typename 
boost::python::detail::unwrap_wrapper_<L>::type&, const typename 
boost::python::detail::unwrap_wrapper_<R>::type&) [with L = 
RDGeom::PointND, R = RDGeom::PointND]’:
/home/pete/Archive/boost_1_36_0/boost/python/operators.hpp:152: 
instantiated from ‘void boost::python::detail::operator_<id, L, 
R>::visit(ClassT&) const [with ClassT = 
boost::python::class_<RDGeom::PointND, 
boost::python::detail::not_specified, 
boost::python::detail::not_specified, 
boost::python::detail::not_specified>, 
boost::python::detail::operator_id id = op_sub, L = 
boost::python::self_ns::self_t, R = boost::python::self_ns::self_t]’
/home/pete/Archive/boost_1_36_0/boost/python/def_visitor.hpp:31: 
instantiated from ‘static void 
boost::python::def_visitor_access::visit(const V&, classT&) [with V = 
boost::python::def_visitor<boost::python::detail::operator_<op_sub, 
boost::python::self_ns::self_t, boost::python::self_ns::self_t> >, 
classT = boost::python::class_<RDGeom::PointND, 
boost::python::detail::not_specified, 
boost::python::detail::not_specified, 
boost::python::detail::not_specified>]’
/home/pete/Archive/boost_1_36_0/boost/python/def_visitor.hpp:67: 
instantiated from ‘void 
boost::python::def_visitor<DerivedVisitor>::visit(classT&) const [with 
classT = boost::python::class_<RDGeom::PointND, 
boost::python::detail::not_specified, 
boost::python::detail::not_specified, 
boost::python::detail::not_specified>, DerivedVisitor = 
boost::python::detail::operator_<op_sub, boost::python::self_ns::self_t, 
boost::python::self_ns::self_t>]’
/home/pete/Archive/boost_1_36_0/boost/python/class.hpp:225: instantiated 
from ‘boost::python::class_<T, X1, X2, X3>& boost::python::class_<T, X1, 
X2, X3>::def(const boost::python::def_visitor<Derived>&) [with Derived = 
boost::python::detail::operator_<op_sub, boost::python::self_ns::self_t, 
boost::python::self_ns::self_t>, W = RDGeom::PointND, X1 = 
boost::python::detail::not_specified, X2 = 
boost::python::detail::not_specified, X3 = 
boost::python::detail::not_specified]’
Geometry/Wrap/Point.cpp:211: instantiated from here
/home/pete/Archive/boost_1_36_0/boost/python/operators.hpp:213: error: 
no match for ‘operator-’ in ‘l - r’
/home/pete/Archive/boost_1_36_0/boost/python/operators.hpp: In static 
member function ‘static PyObject* 
boost::python::detail::operator_l<op_add>::apply<L, R>::execute(typename 
boost::python::detail::unwrap_wrapper_<L>::type&, const typename 
boost::python::detail::unwrap_wrapper_<R>::type&) [with L = 
RDGeom::PointND, R = RDGeom::PointND]’:
/home/pete/Archive/boost_1_36_0/boost/python/operators.hpp:152: 
instantiated from ‘void boost::python::detail::operator_<id, L, 
R>::visit(ClassT&) const [with ClassT = 
boost::python::class_<RDGeom::PointND, 
boost::python::detail::not_specified, 
boost::python::detail::not_specified, 
boost::python::detail::not_specified>, 
boost::python::detail::operator_id id = op_add, L = 
boost::python::self_ns::self_t, R = boost::python::self_ns::self_t]’
/home/pete/Archive/boost_1_36_0/boost/python/def_visitor.hpp:31: 
instantiated from ‘static void 
boost::python::def_visitor_access::visit(const V&, classT&) [with V = 
boost::python::def_visitor<boost::python::detail::operator_<op_add, 
boost::python::self_ns::self_t, boost::python::self_ns::self_t> >, 
classT = boost::python::class_<RDGeom::PointND, 
boost::python::detail::not_specified, 
boost::python::detail::not_specified, 
boost::python::detail::not_specified>]’
/home/pete/Archive/boost_1_36_0/boost/python/def_visitor.hpp:67: 
instantiated from ‘void 
boost::python::def_visitor<DerivedVisitor>::visit(classT&) const [with 
classT = boost::python::class_<RDGeom::PointND, 
boost::python::detail::not_specified, 
boost::python::detail::not_specified, 
boost::python::detail::not_specified>, DerivedVisitor = 
boost::python::detail::operator_<op_add, boost::python::self_ns::self_t, 
boost::python::self_ns::self_t>]’
/home/pete/Archive/boost_1_36_0/boost/python/class.hpp:225: instantiated 
from ‘boost::python::class_<T, X1, X2, X3>& boost::python::class_<T, X1, 
X2, X3>::def(const boost::python::def_visitor<Derived>&) [with Derived = 
boost::python::detail::operator_<op_add, boost::python::self_ns::self_t, 
boost::python::self_ns::self_t>, W = RDGeom::PointND, X1 = 
boost::python::detail::not_specified, X2 = 
boost::python::detail::not_specified, X3 = 
boost::python::detail::not_specified]’
Geometry/Wrap/Point.cpp:213: instantiated from here
/home/pete/Archive/boost_1_36_0/boost/python/operators.hpp:212: error: 
no match for ‘operator+’ in ‘l + r’
/home/pete/Archive/boost_1_36_0/boost/python/converter/pyobject_type.hpp: 
In static member function ‘static bool 
boost::python::converter::pyobject_type<Object, 
pytype>::check(PyObject*) [with Object = boost::python::tuple, 
PyTypeObject* pytype = (& PyTuple_Type)]’:
/home/pete/Archive/boost_1_36_0/boost/python/converter/obj_mgr_arg_from_python.hpp:69: 
instantiated from ‘bool 
boost::python::converter::object_manager_value_arg_from_python<T>::convertible() 
const [with T = boost::python::tuple]’
/home/pete/Archive/boost_1_36_0/boost/preprocessor/iteration/detail/local.hpp:37: 
instantiated from ‘PyObject* 
boost::python::detail::caller_arity<2u>::impl<F, Policies, 
Sig>::operator()(PyObject*, PyObject*) [with F = void 
(*)(RDGeom::PointND&, boost::python::tuple), Policies = 
boost::python::default_call_policies, Sig = boost::mpl::vector3<void, 
RDGeom::PointND&, boost::python::tuple>]’
/home/pete/Archive/boost_1_36_0/boost/python/object/py_function.hpp:38: 
instantiated from ‘PyObject* 
boost::python::objects::caller_py_function_impl<Caller>::operator()(PyObject*, 
PyObject*) [with Caller = boost::python::detail::caller<void 
(*)(RDGeom::PointND&, boost::python::tuple), 
boost::python::default_call_policies, boost::mpl::vector3<void, 
RDGeom::PointND&, boost::python::tuple> >]’
Geometry/Wrap/Point.cpp:250: instantiated from here
/home/pete/Archive/boost_1_36_0/boost/python/converter/pyobject_type.hpp:21: 
warning: dereferencing type-punned pointer will break strict-aliasing rules
./RDGeneral/types.h: At global scope:
./RDGeneral/types.h:49: warning: ‘RDKit::MAX_DOUBLE’ defined but not used
./RDGeneral/types.h:50: warning: ‘RDKit::EPS_DOUBLE’ defined but not used
./RDGeneral/types.h:52: warning: ‘RDKit::MAX_INT’ defined but not used
./RDGeneral/types.h:53: warning: ‘RDKit::MAX_LONGINT’ defined but not used

"g++" -ftemplate-depth-128 -O3 -finline-functions -Wno-inline -Wall 
-fPIC -pthread -Wno-unused-function -DBOOST_THREAD_POSIX 
-DBOOST_THREAD_USE_DLL=1 -DNDEBUG -I"." 
-I"/home/pete/Archive/boost_1_36_0" 
-I"/home/pete/Archive/rdkit/External/Lapack++/include" 
-I"/home/pete/Archive/rdkit/External/vflib-2.0/include" 
-I"/usr/include/python2.5" -c -o 
"Geometry/Wrap/bin/gcc-4.2.3/release/threading-multi/Point.o" 
"Geometry/Wrap/Point.cpp"

...failed gcc.compile.c++ 
Geometry/Wrap/bin/gcc-4.2.3/release/threading-multi/Point.o...
...skipped 
<pGeometry/Wrap/bin/gcc-4.2.3/release/threading-multi>rdGeometry.so for 
lack of <pGeometry/Wrap/bin/gcc-4.2.3/release/threading-multi>Point.o...
...skipped <p/home/pete/Archive/rdkit/Python/Geometry>rdGeometry.so for 
lack of 
<pGeometry/Wrap/bin/gcc-4.2.3/release/threading-multi>rdGeometry.so...
...failed updating 1 target...
...skipped 2 targets...

Hope there's something useful in there!

Peter