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View Code? Open in Web Editor NEWR package wrapping libnabo: fast K Nearest Neighbor search for low dimensions
Home Page: https://github.com/ethz-asl/libnabo
License: Other
nabor's Issues
Make WKNN a templated class
would avoid divergence between WKNNF/WKNND and should be perfectly feasible
using libnabo as a model
loading of package fails
I cannot load the package:
R> library('nabor')
Error in .doLoadActions(where, attach) :
error in load action .__A__.1 for package nabor: loadModule(module, NULL, env = where, loadNow = TRUE): Unable to load module "class_WKNNF": cannot allocate vector of size 1043074.4 Gb
Error: package or namespace load failed for ‘nabor’
Reinstallation does not help. Any ideas?
Improper handling of NA/NaN values by knn
The knn function outputs seemingly OK results even if the query or data matrices contain NA or NaN values. The results are invalid of course (can't compute distances to missing coordinates), but no warning or error is returned by the function. This is problematic, particularly because the documentation for knn does not seem to include any hints on how missing values are treated.
Cheers, and many thanks for this wonderful package,
Cornel
Example:
packageDescription("nabor")["Version"]
$Version
[1] "0.4.4"
targets <- matrix(c(1,2,3,1,2,3,1,2,3), nrow=3, ncol=3)
query <- matrix(c(NA,2,3,1,2,3,1,NaN,3), nrow=3, ncol=3)
query
[,1] [,2] [,3]
[1,] NA 1 1
[2,] 2 2 NaN
[3,] 3 3 3
targets[knn(targets, query, k=1)$nn.idx,]
[,1] [,2] [,3]
[1,] 1 1 1
[2,] 1 1 1
[3,] 3 3 3
query[knn(query, targets, k=1)$nn.idx,]
[,1] [,2] [,3]
[1,] 3 3 3
[2,] 3 3 3
[3,] 3 3 3
No radius search
"For R users nabor provides a function, knn, that is a drop in replacement for the nn2 function in the RANN R package"
Not quite - RANN::nn2 also has a radius search function that limits the nearest neighbour search up to a radius, and I don't see this in nabor.
It would be useful to have a function that finds all neighbours within a distance radius (rather than a fixed K number of neighbours), returning this in a ragged list rather than matrix data structures...
Trouble installing nabor
I'm trying to install nabor on debian linux 10.
> install.packages('nabor')
Installing package into ‘/home/johan/R/x86_64-pc-linux-gnu-library/3.5’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/nabor_0.5.0.tar.gz'
I get errors during the compilation:
g++ -I"/usr/share/R/include" -DNDEBUG -I. -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/lib/R/site-library/RcppEigen/include" -I"/home/johan/R/x86_64-pc-linux-gnu-library/3.5/BH/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c RcppExports.cpp -o RcppExports.o
In file included from /usr/lib/R/site-library/RcppEigen/include/Eigen/Core:392,
from /usr/lib/R/site-library/RcppEigen/include/Eigen/Dense:1,
from /usr/lib/R/site-library/RcppEigen/include/RcppEigenForward.h:30,
from /usr/lib/R/site-library/RcppEigen/include/RcppEigen.h:25,
from RcppExports.cpp:4:
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:60:39: warning: ignoring attributes on template argument ‘__m128’ {aka ‘__vector(4) float’} [-Wignored-attributes]
template<> struct is_arithmetic<__m128> { enum { value = true }; };
^
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:61:40: warning: ignoring attributes on template argument ‘__m128i’ {aka ‘__vector(2) long long int’} [-Wignored-attributes]
template<> struct is_arithmetic<__m128i> { enum { value = true }; };
^
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:62:40: warning: ignoring attributes on template argument ‘__m128d’ {aka ‘__vector(2) double’} [-Wignored-attributes]
template<> struct is_arithmetic<__m128d> { enum { value = true }; };
^
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:161:43: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4f’ {aka ‘__vector(4) float’} [-Wignored-attributes]
template<> struct unpacket_traits<Packet4f> { typedef float type; enum {size=4, alignment=Aligned16}; typedef Packet4f half; };
^
In file included from /usr/lib/R/site-library/RcppEigen/include/Eigen/Core:392,
from /usr/lib/R/site-library/RcppEigen/include/Eigen/Dense:1,
from /usr/lib/R/site-library/RcppEigen/include/RcppEigenForward.h:30,
from /usr/lib/R/site-library/RcppEigen/include/RcppEigen.h:25,
from RcppExports.cpp:4:
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:162:43: warning: ignoring attributes on template argument ‘Eigen::internal::Packet2d’ {aka ‘__vector(2) double’} [-Wignored-attributes]
template<> struct unpacket_traits<Packet2d> { typedef double type; enum {size=2, alignment=Aligned16}; typedef Packet2d half; };
^
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:163:43: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4i’ {aka ‘__vector(2) long long int’} [-Wignored-attributes]
template<> struct unpacket_traits<Packet4i> { typedef int type; enum {size=4, alignment=Aligned16}; typedef Packet4i half; };
^
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:718:35: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4f’ {aka ‘__vector(4) float’} [-Wignored-attributes]
struct palign_impl<Offset,Packet4f>
^
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:741:35: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4i’ {aka ‘__vector(2) long long int’} [-Wignored-attributes]
struct palign_impl<Offset,Packet4i>
^
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:764:35: warning: ignoring attributes on template argument ‘Eigen::internal::Packet2d’ {aka ‘__vector(2) double’} [-Wignored-attributes]
struct palign_impl<Offset,Packet2d>
^
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:778:34: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4f’ {aka ‘__vector(4) float’} [-Wignored-attributes]
ptranspose(PacketBlock<Packet4f,4>& kernel) {
^
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:783:34: warning: ignoring attributes on template argument ‘Eigen::internal::Packet2d’ {aka ‘__vector(2) double’} [-Wignored-attributes]
ptranspose(PacketBlock<Packet2d,2>& kernel) {
^
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:790:34: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4i’ {aka ‘__vector(2) long long int’} [-Wignored-attributes]
ptranspose(PacketBlock<Packet4i,4>& kernel) {
^
In file included from /usr/lib/R/site-library/RcppEigen/include/Eigen/Core:374,
from /usr/lib/R/site-library/RcppEigen/include/Eigen/Dense:1,
from /usr/lib/R/site-library/RcppEigen/include/RcppEigenForward.h:30,
from /usr/lib/R/site-library/RcppEigen/include/RcppEigen.h:25,
from RcppExports.cpp:4:
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/Default/ConjHelper.h:15:70: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4f’ {aka ‘__vector(4) float’} [-Wignored-attributes]
template<> struct conj_helper<PACKET_REAL, PACKET_CPLX, false,false> { \
^
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/Complex.h:232:1: note: in expansion of macro ‘EIGEN_MAKE_CONJ_HELPER_CPLX_REAL’
EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet2cf,Packet4f)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/Default/ConjHelper.h:22:70: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4f’ {aka ‘__vector(4) float’} [-Wignored-attributes]
template<> struct conj_helper<PACKET_CPLX, PACKET_REAL, false,false> { \
^
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/Complex.h:232:1: note: in expansion of macro ‘EIGEN_MAKE_CONJ_HELPER_CPLX_REAL’
EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet2cf,Packet4f)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/Default/ConjHelper.h:15:70: warning: ignoring attributes on template argument ‘Eigen::internal::Packet2d’ {aka ‘__vector(2) double’} [-Wignored-attributes]
template<> struct conj_helper<PACKET_REAL, PACKET_CPLX, false,false> { \
^
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/Complex.h:417:1: note: in expansion of macro ‘EIGEN_MAKE_CONJ_HELPER_CPLX_REAL’
EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet1cd,Packet2d)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/Default/ConjHelper.h:22:70: warning: ignoring attributes on template argument ‘Eigen::internal::Packet2d’ {aka ‘__vector(2) double’} [-Wignored-attributes]
template<> struct conj_helper<PACKET_CPLX, PACKET_REAL, false,false> { \
^
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/Complex.h:417:1: note: in expansion of macro ‘EIGEN_MAKE_CONJ_HELPER_CPLX_REAL’
EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet1cd,Packet2d)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/lib/R/site-library/RcppEigen/include/Eigen/Core:367,
from /usr/lib/R/site-library/RcppEigen/include/Eigen/Dense:1,
from /usr/lib/R/site-library/RcppEigen/include/RcppEigenForward.h:30,
from /usr/lib/R/site-library/RcppEigen/include/RcppEigen.h:25,
from RcppExports.cpp:4:
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h: In instantiation of ‘struct Eigen::internal::find_best_packet<float, 4>’:
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Matrix.h:22:57: required from ‘struct Eigen::internal::traits<Eigen::Matrix<float, 4, 1> >’
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:224:7: required from ‘struct Eigen::internal::traits<Eigen::Quaternion<float> >’
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SSE.h:24:46: required from here
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:170:44: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<float>::type’ {aka ‘__vector(4) float’} [-Wignored-attributes]
bool Stop = Size==Dynamic || (Size%unpacket_traits<PacketType>::size)==0 || is_same<PacketType,typename unpacket_traits<PacketType>::half>::value>
~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:170:83: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<float>::type’ {aka ‘__vector(4) float’} [-Wignored-attributes]
bool Stop = Size==Dynamic || (Size%unpacket_traits<PacketType>::size)==0 || is_same<PacketType,typename unpacket_traits<PacketType>::half>::value>
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:170:83: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<float>::type’ {aka ‘__vector(4) float’} [-Wignored-attributes]
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:170:83: warning: ignoring attributes on template argument ‘Eigen::internal::unpacket_traits<__vector(4) float>::half’ {aka ‘__vector(4) float’} [-Wignored-attributes]
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:188:88: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<float>::type’ {aka ‘__vector(4) float’} [-Wignored-attributes]
typedef typename find_best_packet_helper<Size,typename packet_traits<T>::type>::type type;
^~~~
In file included from /usr/lib/R/site-library/RcppEigen/include/Eigen/Core:434,
from /usr/lib/R/site-library/RcppEigen/include/Eigen/Dense:1,
from /usr/lib/R/site-library/RcppEigen/include/RcppEigenForward.h:30,
from /usr/lib/R/site-library/RcppEigen/include/RcppEigen.h:25,
from RcppExports.cpp:4:
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<float, 4, 1>, 0>’:
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:300:7: required from ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<float, 4, 1>, 1>’
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:551:7: required from ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<float, 4, 1>, 3>’
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34: required from ‘class Eigen::DenseBase<Eigen::Matrix<float, 4, 1> >’
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34: required from ‘class Eigen::MatrixBase<Eigen::Matrix<float, 4, 1> >’
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:98:7: required from ‘class Eigen::PlainObjectBase<Eigen::Matrix<float, 4, 1> >’
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Matrix.h:178:7: required from ‘class Eigen::Matrix<float, 4, 1>’
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:46:50: required from ‘class Eigen::QuaternionBase<Eigen::Quaternion<float> >’
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:232:7: required from ‘class Eigen::Quaternion<float>’
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SSE.h:27:3: required from here
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:55:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<float>::type’ {aka ‘__vector(4) float’} [-Wignored-attributes]
>::type PacketReturnType;
^~~~~~~~~~~~~~~~
In file included from /usr/lib/R/site-library/RcppEigen/include/Eigen/Core:367,
from /usr/lib/R/site-library/RcppEigen/include/Eigen/Dense:1,
from /usr/lib/R/site-library/RcppEigen/include/RcppEigenForward.h:30,
from /usr/lib/R/site-library/RcppEigen/include/RcppEigen.h:25,
from RcppExports.cpp:4:
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h: In instantiation of ‘struct Eigen::internal::find_best_packet<double, 4>’:
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Matrix.h:22:57: required from ‘struct Eigen::internal::traits<Eigen::Matrix<double, 4, 1> >’
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:224:7: required from ‘struct Eigen::internal::traits<Eigen::Quaternion<double> >’
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SSE.h:88:47: required from here
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:170:44: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<double>::type’ {aka ‘__vector(2) double’} [-Wignored-attributes]
bool Stop = Size==Dynamic || (Size%unpacket_traits<PacketType>::size)==0 || is_same<PacketType,typename unpacket_traits<PacketType>::half>::value>
~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:170:83: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<double>::type’ {aka ‘__vector(2) double’} [-Wignored-attributes]
bool Stop = Size==Dynamic || (Size%unpacket_traits<PacketType>::size)==0 || is_same<PacketType,typename unpacket_traits<PacketType>::half>::value>
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:170:83: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<double>::type’ {aka ‘__vector(2) double’} [-Wignored-attributes]
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:170:83: warning: ignoring attributes on template argument ‘Eigen::internal::unpacket_traits<__vector(2) double>::half’ {aka ‘__vector(2) double’} [-Wignored-attributes]
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:188:88: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<double>::type’ {aka ‘__vector(2) double’} [-Wignored-attributes]
typedef typename find_best_packet_helper<Size,typename packet_traits<T>::type>::type type;
^~~~
In file included from /usr/lib/R/site-library/RcppEigen/include/Eigen/Core:434,
from /usr/lib/R/site-library/RcppEigen/include/Eigen/Dense:1,
from /usr/lib/R/site-library/RcppEigen/include/RcppEigenForward.h:30,
from /usr/lib/R/site-library/RcppEigen/include/RcppEigen.h:25,
from RcppExports.cpp:4:
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<double, 4, 1>, 0>’:
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:300:7: required from ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<double, 4, 1>, 1>’
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:551:7: required from ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<double, 4, 1>, 3>’
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34: required from ‘class Eigen::DenseBase<Eigen::Matrix<double, 4, 1> >’
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34: required from ‘class Eigen::MatrixBase<Eigen::Matrix<double, 4, 1> >’
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:98:7: required from ‘class Eigen::PlainObjectBase<Eigen::Matrix<double, 4, 1> >’
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Matrix.h:178:7: required from ‘class Eigen::Matrix<double, 4, 1>’
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:46:50: required from ‘class Eigen::QuaternionBase<Eigen::Quaternion<double> >’
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:232:7: required from ‘class Eigen::Quaternion<double>’
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SSE.h:92:3: required from here
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:55:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<double>::type’ {aka ‘__vector(2) double’} [-Wignored-attributes]
>::type PacketReturnType;
^~~~~~~~~~~~~~~~
In file included from /usr/lib/R/site-library/RcppEigen/include/Eigen/SparseCore:37,
from /usr/lib/R/site-library/RcppEigen/include/Eigen/Sparse:26,
from /usr/lib/R/site-library/RcppEigen/include/RcppEigenForward.h:31,
from /usr/lib/R/site-library/RcppEigen/include/RcppEigen.h:25,
from RcppExports.cpp:4:
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrixBase.h: In instantiation of ‘class Eigen::SparseMatrixBase<Eigen::SparseMatrix<double, 0, int> >’:
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/SparseCore/SparseCompressedBase.h:36:7: required from ‘class Eigen::SparseCompressedBase<Eigen::SparseMatrix<double, 0, int> >’
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:96:7: required from ‘class Eigen::SparseMatrix<double, 0, int>’
/usr/lib/R/site-library/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/ConstrainedConjGrad.h:61:25: required from here
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrixBase.h:47:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<double>::type’ {aka ‘__vector(2) double’} [-Wignored-attributes]
>::type PacketReturnType;
^~~~~~~~~~~~~~~~
In file included from /usr/lib/R/site-library/RcppEigen/include/Eigen/Core:367,
from /usr/lib/R/site-library/RcppEigen/include/Eigen/Dense:1,
from /usr/lib/R/site-library/RcppEigen/include/RcppEigenForward.h:30,
from /usr/lib/R/site-library/RcppEigen/include/RcppEigen.h:25,
from RcppExports.cpp:4:
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h: In instantiation of ‘struct Eigen::internal::find_best_packet<int, -1>’:
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Matrix.h:22:57: required from ‘struct Eigen::internal::traits<Eigen::Matrix<int, -1, 1> >’
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:98:7: required from ‘class Eigen::PlainObjectBase<Eigen::Matrix<int, -1, 1> >’
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Matrix.h:178:7: required from ‘class Eigen::Matrix<int, -1, 1>’
/usr/lib/R/site-library/RcppEigen/include/unsupported/Eigen/src/KroneckerProduct/KroneckerTensorProduct.h:168:29: required from here
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:170:44: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<int>::type’ {aka ‘__vector(2) long long int’} [-Wignored-attributes]
bool Stop = Size==Dynamic || (Size%unpacket_traits<PacketType>::size)==0 || is_same<PacketType,typename unpacket_traits<PacketType>::half>::value>
~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:170:83: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<int>::type’ {aka ‘__vector(2) long long int’} [-Wignored-attributes]
bool Stop = Size==Dynamic || (Size%unpacket_traits<PacketType>::size)==0 || is_same<PacketType,typename unpacket_traits<PacketType>::half>::value>
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:170:83: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<int>::type’ {aka ‘__vector(2) long long int’} [-Wignored-attributes]
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:170:83: warning: ignoring attributes on template argument ‘Eigen::internal::unpacket_traits<__vector(2) long long int>::half’ {aka ‘__vector(2) long long int’} [-Wignored-attributes]
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:188:88: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<int>::type’ {aka ‘__vector(2) long long int’} [-Wignored-attributes]
typedef typename find_best_packet_helper<Size,typename packet_traits<T>::type>::type type;
^~~~
In file included from /usr/lib/R/site-library/RcppEigen/include/Eigen/Core:434,
from /usr/lib/R/site-library/RcppEigen/include/Eigen/Dense:1,
from /usr/lib/R/site-library/RcppEigen/include/RcppEigenForward.h:30,
from /usr/lib/R/site-library/RcppEigen/include/RcppEigen.h:25,
from RcppExports.cpp:4:
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<int, -1, 1>, 0>’:
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:300:7: required from ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<int, -1, 1>, 1>’
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:551:7: required from ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<int, -1, 1>, 3>’
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34: required from ‘class Eigen::DenseBase<Eigen::Matrix<int, -1, 1> >’
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34: required from ‘class Eigen::MatrixBase<Eigen::Matrix<int, -1, 1> >’
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:98:7: required from ‘class Eigen::PlainObjectBase<Eigen::Matrix<int, -1, 1> >’
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Matrix.h:178:7: required from ‘class Eigen::Matrix<int, -1, 1>’
/usr/lib/R/site-library/RcppEigen/include/unsupported/Eigen/src/KroneckerProduct/KroneckerTensorProduct.h:168:29: required from here
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:55:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<int>::type’ {aka ‘__vector(2) long long int’} [-Wignored-attributes]
>::type PacketReturnType;
^~~~~~~~~~~~~~~~
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of ‘class Eigen::DenseCoeffsBase<Eigen::Transpose<Eigen::Matrix<int, -1, 1> >, 0>’:
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:300:7: required from ‘class Eigen::DenseCoeffsBase<Eigen::Transpose<Eigen::Matrix<int, -1, 1> >, 1>’
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:551:7: required from ‘class Eigen::DenseCoeffsBase<Eigen::Transpose<Eigen::Matrix<int, -1, 1> >, 3>’
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34: required from ‘class Eigen::DenseBase<Eigen::Transpose<Eigen::Matrix<int, -1, 1> > >’
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34: required from ‘class Eigen::MatrixBase<Eigen::Transpose<Eigen::Matrix<int, -1, 1> > >’
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Transpose.h:115:37: required from ‘class Eigen::TransposeImpl<Eigen::Matrix<int, -1, 1>, Eigen::Dense>’
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Transpose.h:52:37: required from ‘class Eigen::Transpose<Eigen::Matrix<int, -1, 1> >’
/usr/lib/R/site-library/RcppEigen/include/unsupported/Eigen/src/KroneckerProduct/KroneckerTensorProduct.h:178:72: required from here
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:55:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<int>::type’ {aka ‘__vector(2) long long int’} [-Wignored-attributes]
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<int, -1, -1>, 0>’:
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:300:7: required from ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<int, -1, -1>, 1>’
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:551:7: required from ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<int, -1, -1>, 3>’
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34: required from ‘class Eigen::DenseBase<Eigen::Matrix<int, -1, -1> >’
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34: required from ‘class Eigen::MatrixBase<Eigen::Matrix<int, -1, -1> >’
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:98:7: required from ‘class Eigen::PlainObjectBase<Eigen::Matrix<int, -1, -1> >’
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Matrix.h:178:7: required from ‘class Eigen::Matrix<int, -1, -1>’
/usr/lib/R/site-library/RcppEigen/include/unsupported/Eigen/src/KroneckerProduct/KroneckerTensorProduct.h:179:36: required from here
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:55:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<int>::type’ {aka ‘__vector(2) long long int’} [-Wignored-attributes]
In file included from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:77,
from /usr/lib/R/site-library/RcppEigen/include/RcppEigen.h:26,
from RcppExports.cpp:4:
/usr/local/lib/R/site-library/Rcpp/include/Rcpp/Rmath.h: In function ‘double R::pythag(double, double)’:
/usr/local/lib/R/site-library/Rcpp/include/Rcpp/Rmath.h:222:57: error: ‘::Rf_pythag’ has not been declared
inline double pythag(double a, double b) { return ::Rf_pythag(a, b); }
^~~~~~~~~
/usr/local/lib/R/site-library/Rcpp/include/Rcpp/Rmath.h:222:57: note: suggested alternative: ‘pythag’
inline double pythag(double a, double b) { return ::Rf_pythag(a, b); }
^~~~~~~~~
pythag
In file included from /usr/lib/R/site-library/RcppEigen/include/Eigen/Core:367,
from /usr/lib/R/site-library/RcppEigen/include/Eigen/Dense:1,
from /usr/lib/R/site-library/RcppEigen/include/RcppEigenForward.h:30,
from /usr/lib/R/site-library/RcppEigen/include/RcppEigen.h:25,
from RcppExports.cpp:4:
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h: In instantiation of ‘struct Eigen::internal::find_best_packet<double, -1>’:
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Matrix.h:22:57: required from ‘struct Eigen::internal::traits<Eigen::Matrix<double, -1, -1> >’
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Map.h:18:8: required from ‘struct Eigen::internal::traits<Eigen::Map<Eigen::Matrix<double, -1, -1> > >’
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/util/ForwardDeclarations.h:32:54: required from ‘struct Eigen::internal::accessors_level<Eigen::Map<Eigen::Matrix<double, -1, -1> > >’
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/util/ForwardDeclarations.h:113:75: required from ‘class Eigen::Map<Eigen::Matrix<double, -1, -1> >’
/usr/local/lib/R/site-library/Rcpp/include/Rcpp/InputParameter.h:64:11: required from ‘class Rcpp::ConstInputParameter<Eigen::Map<Eigen::Matrix<double, -1, -1> > >’
RcppExports.cpp:16:91: required from here
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:170:44: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<double>::type’ {aka ‘__vector(2) double’} [-Wignored-attributes]
bool Stop = Size==Dynamic || (Size%unpacket_traits<PacketType>::size)==0 || is_same<PacketType,typename unpacket_traits<PacketType>::half>::value>
~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:170:83: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<double>::type’ {aka ‘__vector(2) double’} [-Wignored-attributes]
bool Stop = Size==Dynamic || (Size%unpacket_traits<PacketType>::size)==0 || is_same<PacketType,typename unpacket_traits<PacketType>::half>::value>
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:170:83: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<double>::type’ {aka ‘__vector(2) double’} [-Wignored-attributes]
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:170:83: warning: ignoring attributes on template argument ‘Eigen::internal::unpacket_traits<__vector(2) double>::half’ {aka ‘__vector(2) double’} [-Wignored-attributes]
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:188:88: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<double>::type’ {aka ‘__vector(2) double’} [-Wignored-attributes]
typedef typename find_best_packet_helper<Size,typename packet_traits<T>::type>::type type;
^~~~
In file included from /usr/lib/R/site-library/RcppEigen/include/Eigen/Core:434,
from /usr/lib/R/site-library/RcppEigen/include/Eigen/Dense:1,
from /usr/lib/R/site-library/RcppEigen/include/RcppEigenForward.h:30,
from /usr/lib/R/site-library/RcppEigen/include/RcppEigen.h:25,
from RcppExports.cpp:4:
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<double, -1, -1>, 0>’:
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:300:7: required from ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<double, -1, -1>, 1>’
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:551:7: required from ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<double, -1, -1>, 3>’
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34: required from ‘class Eigen::DenseBase<Eigen::Matrix<double, -1, -1> >’
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34: required from ‘class Eigen::MatrixBase<Eigen::Matrix<double, -1, -1> >’
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:98:7: required from ‘class Eigen::PlainObjectBase<Eigen::Matrix<double, -1, -1> >’
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Matrix.h:178:7: required from ‘class Eigen::Matrix<double, -1, -1>’
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Map.h:24:30: required from ‘struct Eigen::internal::traits<Eigen::Map<Eigen::Matrix<double, -1, -1> > >’
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/util/ForwardDeclarations.h:32:54: required from ‘struct Eigen::internal::accessors_level<Eigen::Map<Eigen::Matrix<double, -1, -1> > >’
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/util/ForwardDeclarations.h:113:75: required from ‘class Eigen::Map<Eigen::Matrix<double, -1, -1> >’
/usr/local/lib/R/site-library/Rcpp/include/Rcpp/InputParameter.h:64:11: required from ‘class Rcpp::ConstInputParameter<Eigen::Map<Eigen::Matrix<double, -1, -1> > >’
RcppExports.cpp:16:91: required from here
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:55:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<double>::type’ {aka ‘__vector(2) double’} [-Wignored-attributes]
>::type PacketReturnType;
^~~~~~~~~~~~~~~~
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of ‘class Eigen::DenseCoeffsBase<Eigen::Map<Eigen::Matrix<double, -1, -1> >, 0>’:
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:300:7: required from ‘class Eigen::DenseCoeffsBase<Eigen::Map<Eigen::Matrix<double, -1, -1> >, 1>’
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:551:7: required from ‘class Eigen::DenseCoeffsBase<Eigen::Map<Eigen::Matrix<double, -1, -1> >, 3>’
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34: required from ‘class Eigen::DenseBase<Eigen::Map<Eigen::Matrix<double, -1, -1> > >’
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34: required from ‘class Eigen::MatrixBase<Eigen::Map<Eigen::Matrix<double, -1, -1> > >’
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/MapBase.h:37:34: required from ‘class Eigen::MapBase<Eigen::Map<Eigen::Matrix<double, -1, -1> >, 0>’
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/MapBase.h:215:34: required from ‘class Eigen::MapBase<Eigen::Map<Eigen::Matrix<double, -1, -1> >, 1>’
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Map.h:94:79: required from ‘class Eigen::Map<Eigen::Matrix<double, -1, -1> >’
/usr/local/lib/R/site-library/Rcpp/include/Rcpp/InputParameter.h:64:11: required from ‘class Rcpp::ConstInputParameter<Eigen::Map<Eigen::Matrix<double, -1, -1> > >’
RcppExports.cpp:16:91: required from here
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:55:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<double>::type’ {aka ‘__vector(2) double’} [-Wignored-attributes]
make: *** [/usr/lib/R/etc/Makeconf:171: RcppExports.o] Error 1
ERROR: compilation failed for package ‘nabor’
* removing ‘/home/johan/R/x86_64-pc-linux-gnu-library/3.5/nabor’
UBSAN issue when libnabo calculates maxNodeCount
BDR wrote
But this has a UBSAN error: see http://www.stats.ox.ac.uk/pub/bdr/memtests/UBSAN/nabor/ and http://cran.r-project.org/doc/manuals/r-patched/R-exts.html#Using-Undefined-Behaviour-Sanitizer for the background (-2147483648 - 1 is NA_integer_ - 1).
ask for your help about your "nabor" package
Hi. your r package nabor is really helpful. But recently I encountered a problem. After I construct the big kd-tree for the whole dataset, how to extract a small kd-tree (for a sub-dataset of the whole dataset) from the original big kd-tree? in other words, how to deletes some nodes from the big kd-tree? (this could accelerate the searching process, since the deleted nodes are the ones that I am 100% sure to be not the k nearest samples,) Many Thank for your help! Best wishes.
remove register keyword from libnabo
BDR quoth
The C keyword 'register' was deprecated in C++11. Now it has been removed in C++17, clang trunk (to be released as clang 6.0.0 in a couple of months) has started warning on its use by default.
Packages
BayesXsrc DatABEL FCNN4R FNN FRESA.CAD KODAMA Matching NPBayesImpute OjaNP RANN RSNNS RSSL SnakeCharmR TAQMNGR TransferEntropy bipartite cems distances divest dpmixsim logconPH ltsk mixcat mombf msr mvPot nabor nonlinearTseries phreeqc reticulate rstpm2 smoothSurv
invoke this warning. Please remove C++ uses of 'register' at the next update.
Several months have now gone by and R-devel now defaults to C++11 if available. Packages
FCNN4R FNN KODAMA NPBayesImpute OjaNP RANN RSNNS RSSL SnakeCharmR TransferEntropy bipartite distances dpmixsim ltsk mixcat msr nabor nonlinearTseries phreeqc smoothSurv
have not yet been updated to remove 'register'. Please do so before Aug 10 to safely retain the package on CRAN.
(If for some reason you wish to retain 'register' you could declare your code to be C++98: see 'Writing R Extensions'.)
Fix warning related to registration of native routines
Latest r-devel (as of 20 Feb 2017) has a problem.
Result: NOTE
File ‘nabor/libs/nabor.so’:
Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’
It is good practice to register native routines and to disable symbol
search.
See:
https://cran.r-project.org/web/checks/check_results_jefferis_at_gmail.com.html#nabor
CRAN version Install fails on Ubuntu 16.04
Not sure why - error message pasted below.
Dev version works though 👍 great work.
> install.packages("nabor")
Installing package into ‘/home/robin/R/x86_64-pc-linux-gnu-library/3.3’
(as ‘lib’ is unspecified)
trying URL 'https://cran.rstudio.com/src/contrib/nabor_0.4.6.tar.gz'
Content type 'application/x-gzip' length 38592 bytes (37 KB)
==================================================
downloaded 37 KB
* installing *source* package ‘nabor’ ...
** package ‘nabor’ successfully unpacked and MD5 sums checked
** libs
g++ -I/usr/share/R/include -DNDEBUG -I. -I"/home/robin/R/x86_64-pc-linux-gnu-library/3.3/Rcpp/include" -I"/home/robin/R/x86_64-pc-linux-gnu-library/3.3/RcppEigen/include" -I"/home/robin/R/x86_64-pc-linux-gnu-library/3.3/BH/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c RcppExports.cpp -o RcppExports.o
g++ -I/usr/share/R/include -DNDEBUG -I. -I"/home/robin/R/x86_64-pc-linux-gnu-library/3.3/Rcpp/include" -I"/home/robin/R/x86_64-pc-linux-gnu-library/3.3/RcppEigen/include" -I"/home/robin/R/x86_64-pc-linux-gnu-library/3.3/BH/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c WKNN.cpp -o WKNN.o
g++ -I/usr/share/R/include -DNDEBUG -I. -I"/home/robin/R/x86_64-pc-linux-gnu-library/3.3/Rcpp/include" -I"/home/robin/R/x86_64-pc-linux-gnu-library/3.3/RcppEigen/include" -I"/home/robin/R/x86_64-pc-linux-gnu-library/3.3/BH/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c brute_force_cpu.cpp -o brute_force_cpu.o
g++ -I/usr/share/R/include -DNDEBUG -I. -I"/home/robin/R/x86_64-pc-linux-gnu-library/3.3/Rcpp/include" -I"/home/robin/R/x86_64-pc-linux-gnu-library/3.3/RcppEigen/include" -I"/home/robin/R/x86_64-pc-linux-gnu-library/3.3/BH/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c kdtree_cpu.cpp -o kdtree_cpu.o
g++ -I/usr/share/R/include -DNDEBUG -I. -I"/home/robin/R/x86_64-pc-linux-gnu-library/3.3/Rcpp/include" -I"/home/robin/R/x86_64-pc-linux-gnu-library/3.3/RcppEigen/include" -I"/home/robin/R/x86_64-pc-linux-gnu-library/3.3/BH/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c nabo.cpp -o nabo.o
g++ -I/usr/share/R/include -DNDEBUG -I. -I"/home/robin/R/x86_64-pc-linux-gnu-library/3.3/Rcpp/include" -I"/home/robin/R/x86_64-pc-linux-gnu-library/3.3/RcppEigen/include" -I"/home/robin/R/x86_64-pc-linux-gnu-library/3.3/BH/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c nabor.cpp -o nabor.o
g++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o nabor.so RcppExports.o WKNN.o brute_force_cpu.o kdtree_cpu.o nabo.o nabor.o -L/usr/lib/R/lib -lR
installing to /home/robin/R/x86_64-pc-linux-gnu-library/3.3/nabor/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
*** caught segfault ***
address 0x20, cause 'memory not mapped'
Traceback:
1: .Call(Module__classes_info, xp)
2: Module(module, mustStart = TRUE, where = env)
3: doTryCatch(return(expr), name, parentenv, handler)
4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
5: tryCatchList(expr, classes, parentenv, handlers)
6: tryCatch(Module(module, mustStart = TRUE, where = env), error = function(e) e)
7: loadModule(module, NULL, env = where, loadNow = TRUE)
8: Rcpp::loadRcppClass(Class = "WKNNF", where = NS)
9: (function (NS) Rcpp::loadRcppClass(Class = "WKNNF", where = NS))(<environment>)
10: doTryCatch(return(expr), name, parentenv, handler)
11: tryCatchOne(expr, names, parentenv, handlers[[1L]])
12: tryCatchList(expr, classes, parentenv, handlers)
13: tryCatch((function (NS) Rcpp::loadRcppClass(Class = "WKNNF", where = NS))(<environment>), error = function(e) e)
14: eval(expr, envir, enclos)
15: eval(substitute(tryCatch(FUN(WHERE), error = function(e) e), list(FUN = f, WHERE = where)), where)
16: .doLoadActions(where, attach)
17: methods::cacheMetaData(ns, TRUE, ns)
18: loadNamespace(package, lib.loc)
19: doTryCatch(return(expr), name, parentenv, handler)
20: tryCatchOne(expr, names, parentenv, handlers[[1L]])
21: tryCatchList(expr, classes, parentenv, handlers)
22: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call)[1L] prefix <- paste("Error in", dcall, ": ") LONG <- 75L msg <- conditionMessage(e) sm <- strsplit(msg, "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && identical(getOption("show.error.messages"), TRUE)) { cat(msg, file = stderr()) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
23: try({ attr(package, "LibPath") <- which.lib.loc ns <- loadNamespace(package, lib.loc) env <- attachNamespace(ns, pos = pos, deps)})
24: library(pkg_name, lib.loc = lib, character.only = TRUE, logical.return = TRUE)
25: withCallingHandlers(expr, packageStartupMessage = function(c) invokeRestart("muffleMessage"))
26: suppressPackageStartupMessages(library(pkg_name, lib.loc = lib, character.only = TRUE, logical.return = TRUE))
27: doTryCatch(return(expr), name, parentenv, handler)
28: tryCatchOne(expr, names, parentenv, handlers[[1L]])
29: tryCatchList(expr, classes, parentenv, handlers)
30: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call)[1L] prefix <- paste("Error in", dcall, ": ") LONG <- 75L msg <- conditionMessage(e) sm <- strsplit(msg, "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && identical(getOption("show.error.messages"), TRUE)) { cat(msg, file = stderr()) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
31: try(suppressPackageStartupMessages(library(pkg_name, lib.loc = lib, character.only = TRUE, logical.return = TRUE)))
32: tools:::.test_load_package("nabor", "/home/robin/R/x86_64-pc-linux-gnu-library/3.3")
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault (core dumped)
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