leafcutter
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davidaknowles
Fatal error: tbb/tbb_stddef.h
When installing Leafcutter package in R, I got this error. I have done the installation in Mac, Debian, and Ubuntu, and the error repeats consistently in each Operating System.
> devtools::install_github('davidaknowles/leafcutter/leafcutter')
Downloading GitHub repo davidaknowles/leafcutter@HEAD
Skipping 2 packages not available: Biobase, DirichletMultinomial
-- R CMD build ---------------------------------------------------------------------------------------------------------------------------------------
v checking for file '/tmp/RtmpdLv4qz/remotes4c6ad9b24/davidaknowles-leafcutter-2c9907e/leafcutter/DESCRIPTION' (425ms)
- preparing 'leafcutter':
v checking DESCRIPTION meta-information ...
- cleaning src
- checking for LF line-endings in source and make files and shell scripts (489ms)
- checking for empty or unneeded directories
- building 'leafcutter_0.2.9.tar.gz'
Installing package into '/usr/local/lib/R/site-library'
(as 'lib' is unspecified)
* installing *source* package 'leafcutter' ...
** using staged installation
** libs
using C++ compiler: 'g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0'
using C++14
g++ -std=gnu++14 -I"/usr/local/lib/R/include" -DNDEBUG -I"../inst/include" -I"/usr/local/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -I'/usr/local/lib/R/site-library/StanHeaders/include' -I'/usr/local/lib/R/site-library/rstan/include' -I'/usr/local/lib/R/site-library/BH/include' -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppEigen/include' -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Wformat-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c RcppExports.cpp -o RcppExports.o
In file included from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Core:205,
from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Dense:1,
from /usr/local/lib/R/site-library/RcppEigen/include/RcppEigenForward.h:28,
from /usr/local/lib/R/site-library/RcppEigen/include/RcppEigen.h:25,
from RcppExports.cpp:4:
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:46:40: warning: ignoring attributes on template argument '__m128i' [-Wignored-attributes]
46 | typedef eigen_packet_wrapper<__m128i, 0> Packet4i;
| ^
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:47:40: warning: ignoring attributes on template argument '__m128i' [-Wignored-attributes]
47 | typedef eigen_packet_wrapper<__m128i, 1> Packet16b;
| ^
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:49:39: warning: ignoring attributes on template argument '__m128' [-Wignored-attributes]
49 | template<> struct is_arithmetic<__m128> { enum { value = true }; };
| ^
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:50:40: warning: ignoring attributes on template argument '__m128i' [-Wignored-attributes]
50 | template<> struct is_arithmetic<__m128i> { enum { value = true }; };
| ^
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:51:40: warning: ignoring attributes on template argument '__m128d' [-Wignored-attributes]
51 | template<> struct is_arithmetic<__m128d> { enum { value = true }; };
| ^
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:222:43: warning: ignoring attributes on template argument 'Eigen::internal::Packet4f' {aka '__m128'} [-Wignored-attributes]
222 | template<> struct unpacket_traits<Packet4f> {
| ^
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:228:43: warning: ignoring attributes on template argument 'Eigen::internal::Packet2d' {aka '__m128d'} [-Wignored-attributes]
228 | template<> struct unpacket_traits<Packet2d> {
| ^
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:1124:34: warning: ignoring attributes on template argument 'Eigen::internal::Packet4f' {aka '__m128'} [-Wignored-attributes]
1124 | ptranspose(PacketBlock<Packet4f,4>& kernel) {
| ^
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:1129:34: warning: ignoring attributes on template argument 'Eigen::internal::Packet2d' {aka '__m128d'} [-Wignored-attributes]
1129 | ptranspose(PacketBlock<Packet2d,2>& kernel) {
| ^
In file included from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Core:174,
from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Dense:1,
from /usr/local/lib/R/site-library/RcppEigen/include/RcppEigenForward.h:28,
from /usr/local/lib/R/site-library/RcppEigen/include/RcppEigen.h:25,
from RcppExports.cpp:4:
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/Default/ConjHelper.h:16:60: warning: ignoring attributes on template argument 'Eigen::internal::Packet4f' {aka '__m128'} [-Wignored-attributes]
16 | struct conj_helper<PACKET_REAL, PACKET_CPLX, false, false> { \
| ^
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/Complex.h:173:1: note: in expansion of macro 'EIGEN_MAKE_CONJ_HELPER_CPLX_REAL'
173 | EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet2cf,Packet4f)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/Default/ConjHelper.h:29:60: warning: ignoring attributes on template argument 'Eigen::internal::Packet4f' {aka '__m128'} [-Wignored-attributes]
29 | struct conj_helper<PACKET_CPLX, PACKET_REAL, false, false> { \
| ^
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/Complex.h:173:1: note: in expansion of macro 'EIGEN_MAKE_CONJ_HELPER_CPLX_REAL'
173 | EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet2cf,Packet4f)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/Default/ConjHelper.h:16:60: warning: ignoring attributes on template argument 'Eigen::internal::Packet2d' {aka '__m128d'} [-Wignored-attributes]
16 | struct conj_helper<PACKET_REAL, PACKET_CPLX, false, false> { \
| ^
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/Complex.h:298:1: note: in expansion of macro 'EIGEN_MAKE_CONJ_HELPER_CPLX_REAL'
298 | EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet1cd,Packet2d)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/Default/ConjHelper.h:29:60: warning: ignoring attributes on template argument 'Eigen::internal::Packet2d' {aka '__m128d'} [-Wignored-attributes]
29 | struct conj_helper<PACKET_CPLX, PACKET_REAL, false, false> { \
| ^
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/Complex.h:298:1: note: in expansion of macro 'EIGEN_MAKE_CONJ_HELPER_CPLX_REAL'
298 | EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet1cd,Packet2d)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Core:165,
from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Dense:1,
from /usr/local/lib/R/site-library/RcppEigen/include/RcppEigenForward.h:28,
from /usr/local/lib/R/site-library/RcppEigen/include/RcppEigen.h:25,
from RcppExports.cpp:4:
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h: In instantiation of 'struct Eigen::internal::find_best_packet<float, 4>':
/usr/local/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/local/lib/R/site-library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:266:49: required from 'struct Eigen::internal::traits<Eigen::Quaternion<float> >'
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SIMD.h:24:46: required from here
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:44: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits<float>::type' {aka '__m128'} [-Wignored-attributes]
190 | bool Stop = Size==Dynamic || (Size%unpacket_traits<PacketType>::size)==0 || is_same<PacketType,typename unpacket_traits<PacketType>::half>::value>
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits<float>::type' {aka '__m128'} [-Wignored-attributes]
190 | bool Stop = Size==Dynamic || (Size%unpacket_traits<PacketType>::size)==0 || is_same<PacketType,typename unpacket_traits<PacketType>::half>::value>
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits<float>::type' {aka '__m128'} [-Wignored-attributes]
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument 'Eigen::internal::unpacket_traits<__vector(4) float>::half' {aka '__m128'} [-Wignored-attributes]
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:208:88: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits<float>::type' {aka '__m128'} [-Wignored-attributes]
208 | typedef typename find_best_packet_helper<Size,typename packet_traits<T>::type>::type type;
| ^~~~
In file included from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Core:271,
from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Dense:1,
from /usr/local/lib/R/site-library/RcppEigen/include/RcppEigenForward.h:28,
from /usr/local/lib/R/site-library/RcppEigen/include/RcppEigen.h:25,
from RcppExports.cpp:4:
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of 'class Eigen::DenseCoeffsBase<Eigen::Matrix<float, 4, 1>, 0>':
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:302:7: required from 'class Eigen::DenseCoeffsBase<Eigen::Matrix<float, 4, 1>, 1>'
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:555:7: required from 'class Eigen::DenseCoeffsBase<Eigen::Matrix<float, 4, 1>, 3>'
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34: required from 'class Eigen::DenseBase<Eigen::Matrix<float, 4, 1> >'
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34: required from 'class Eigen::MatrixBase<Eigen::Matrix<float, 4, 1> >'
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:98:7: required from 'class Eigen::PlainObjectBase<Eigen::Matrix<float, 4, 1> >'
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Matrix.h:178:7: required from 'class Eigen::Matrix<float, 4, 1>'
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:46:50: required from 'class Eigen::QuaternionBase<Eigen::Quaternion<float> >'
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:273:7: required from 'class Eigen::Quaternion<float>'
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SIMD.h:27:3: required from here
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits<float>::type' {aka '__m128'} [-Wignored-attributes]
56 | >::type PacketReturnType;
| ^~~~~~~~~~~~~~~~
In file included from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Core:165,
from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Dense:1,
from /usr/local/lib/R/site-library/RcppEigen/include/RcppEigenForward.h:28,
from /usr/local/lib/R/site-library/RcppEigen/include/RcppEigen.h:25,
from RcppExports.cpp:4:
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h: In instantiation of 'struct Eigen::internal::find_best_packet<double, 4>':
/usr/local/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/local/lib/R/site-library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:266:49: required from 'struct Eigen::internal::traits<Eigen::Quaternion<double> >'
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SIMD.h:98:47: required from here
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:44: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits<double>::type' {aka '__m128d'} [-Wignored-attributes]
190 | bool Stop = Size==Dynamic || (Size%unpacket_traits<PacketType>::size)==0 || is_same<PacketType,typename unpacket_traits<PacketType>::half>::value>
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits<double>::type' {aka '__m128d'} [-Wignored-attributes]
190 | bool Stop = Size==Dynamic || (Size%unpacket_traits<PacketType>::size)==0 || is_same<PacketType,typename unpacket_traits<PacketType>::half>::value>
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits<double>::type' {aka '__m128d'} [-Wignored-attributes]
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument 'Eigen::internal::unpacket_traits<__vector(2) double>::half' {aka '__m128d'} [-Wignored-attributes]
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:208:88: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits<double>::type' {aka '__m128d'} [-Wignored-attributes]
208 | typedef typename find_best_packet_helper<Size,typename packet_traits<T>::type>::type type;
| ^~~~
In file included from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Core:271,
from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Dense:1,
from /usr/local/lib/R/site-library/RcppEigen/include/RcppEigenForward.h:28,
from /usr/local/lib/R/site-library/RcppEigen/include/RcppEigen.h:25,
from RcppExports.cpp:4:
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of 'class Eigen::DenseCoeffsBase<Eigen::Matrix<double, 4, 1>, 0>':
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:302:7: required from 'class Eigen::DenseCoeffsBase<Eigen::Matrix<double, 4, 1>, 1>'
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:555:7: required from 'class Eigen::DenseCoeffsBase<Eigen::Matrix<double, 4, 1>, 3>'
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34: required from 'class Eigen::DenseBase<Eigen::Matrix<double, 4, 1> >'
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34: required from 'class Eigen::MatrixBase<Eigen::Matrix<double, 4, 1> >'
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:98:7: required from 'class Eigen::PlainObjectBase<Eigen::Matrix<double, 4, 1> >'
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Matrix.h:178:7: required from 'class Eigen::Matrix<double, 4, 1>'
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:46:50: required from 'class Eigen::QuaternionBase<Eigen::Quaternion<double> >'
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:273:7: required from 'class Eigen::Quaternion<double>'
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SIMD.h:102:3: required from here
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits<double>::type' {aka '__m128d'} [-Wignored-attributes]
56 | >::type PacketReturnType;
| ^~~~~~~~~~~~~~~~
In file included from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/SparseCore:37,
from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Sparse:26,
from /usr/local/lib/R/site-library/RcppEigen/include/RcppEigenForward.h:29,
from /usr/local/lib/R/site-library/RcppEigen/include/RcppEigen.h:25,
from RcppExports.cpp:4:
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrixBase.h: In instantiation of 'class Eigen::SparseMatrixBase<Eigen::SparseMatrix<double, 0, int> >':
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/SparseCore/SparseCompressedBase.h:36:7: required from 'class Eigen::SparseCompressedBase<Eigen::SparseMatrix<double, 0, int> >'
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:96:7: required from 'class Eigen::SparseMatrix<double, 0, int>'
/usr/local/lib/R/site-library/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/ConstrainedConjGrad.h:61:25: required from here
/usr/local/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 '__m128d'} [-Wignored-attributes]
47 | >::type PacketReturnType;
| ^~~~~~~~~~~~~~~~
g++ -std=gnu++14 -I"/usr/local/lib/R/include" -DNDEBUG -I"../inst/include" -I"/usr/local/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -I'/usr/local/lib/R/site-library/StanHeaders/include' -I'/usr/local/lib/R/site-library/rstan/include' -I'/usr/local/lib/R/site-library/BH/include' -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppEigen/include' -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Wformat-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stanExports_bb_glm.cc -o stanExports_bb_glm.o
In file included from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/prim/core.hpp:4,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/prim.hpp:10,
from /usr/local/lib/R/site-library/StanHeaders/include/src/stan/io/dump.hpp:7,
from /usr/local/lib/R/site-library/rstan/include/rstan/stan_fit.hpp:43,
from /usr/local/lib/R/site-library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_bb_glm.h:20,
from stanExports_bb_glm.cc:5:
/usr/local/lib/R/site-library/StanHeaders/include/stan/math/prim/core/init_threadpool_tbb.hpp:9:10: fatal error: tbb/tbb_stddef.h: No such file or directory
9 | #include <tbb/tbb_stddef.h>
| ^~~~~~~~~~~~~~~~~~
compilation terminated.
I have the same issue, it comes from Rstanheaders using old version of TBB library, but I haven't figure out how to make it work.
I have the same issue as well, install R TBB package can be done successfully, and tbb/tbb_stddef.h file is present in the TBB/include/tbb/ folder, but still the package builder could find it.
