===============================
R CMD BUILD
===============================
* checking for file MetaboDynamics/DESCRIPTION ... OK
* preparing MetaboDynamics:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
-----------------------------------
* installing *source* package MetaboDynamics ...
** using staged installation
** libs
using C++ compiler: g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
using C++17
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"../inst/include" -I"/home/biocbuild/bbs-3.21-bioc/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppEigen/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppParallel/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/rstan/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/StanHeaders/include' -I/usr/local/include -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
In file included from /home/biocbuild/bbs-3.21-bioc/R/site-library/RcppEigen/include/Eigen/Core:205,
from /home/biocbuild/bbs-3.21-bioc/R/site-library/RcppEigen/include/Eigen/Dense:1,
from /home/biocbuild/bbs-3.21-bioc/R/site-library/RcppEigen/include/RcppEigenForward.h:28,
from /home/biocbuild/bbs-3.21-bioc/R/site-library/RcppEigen/include/RcppEigen.h:25,
from RcppExports.cpp:4:
/home/biocbuild/bbs-3.21-bioc/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;
| ^
/home/biocbuild/bbs-3.21-bioc/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;
| ^
/home/biocbuild/bbs-3.21-bioc/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 }; };
| ^
/home/biocbuild/bbs-3.21-bioc/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 }; };
| ^
/home/biocbuild/bbs-3.21-bioc/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 }; };
| ^
/home/biocbuild/bbs-3.21-bioc/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> {
| ^
/home/biocbuild/bbs-3.21-bioc/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> {
| ^
/home/biocbuild/bbs-3.21-bioc/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) {
| ^
/home/biocbuild/bbs-3.21-bioc/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 /home/biocbuild/bbs-3.21-bioc/R/site-library/RcppEigen/include/Eigen/Core:174:
/home/biocbuild/bbs-3.21-bioc/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> { \
| ^
/home/biocbuild/bbs-3.21-bioc/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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.21-bioc/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> { \
| ^
/home/biocbuild/bbs-3.21-bioc/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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.21-bioc/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> { \
| ^
/home/biocbuild/bbs-3.21-bioc/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)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.21-bioc/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> { \
| ^
/home/biocbuild/bbs-3.21-bioc/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 /home/biocbuild/bbs-3.21-bioc/R/site-library/RcppEigen/include/Eigen/Core:165:
/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h: In instantiation of struct Eigen::internal::find_best_packet<float, 4>:
/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/Matrix.h:22:57: required from struct Eigen::internal::traits<Eigen::Matrix<float, 4, 1> >
/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:266:49: required from struct Eigen::internal::traits<Eigen::Quaternion<float> >
/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SIMD.h:24:46: required from here
/home/biocbuild/bbs-3.21-bioc/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>
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.21-bioc/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>
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.21-bioc/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]
/home/biocbuild/bbs-3.21-bioc/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]
/home/biocbuild/bbs-3.21-bioc/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 /home/biocbuild/bbs-3.21-bioc/R/site-library/RcppEigen/include/Eigen/Core:271:
/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of class Eigen::DenseCoeffsBase<Eigen::Matrix<float, 4, 1>, 0>:
/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:302:7: required from class Eigen::DenseCoeffsBase<Eigen::Matrix<float, 4, 1>, 1>
/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:555:7: required from class Eigen::DenseCoeffsBase<Eigen::Matrix<float, 4, 1>, 3>
/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34: required from class Eigen::DenseBase<Eigen::Matrix<float, 4, 1> >
/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34: required from class Eigen::MatrixBase<Eigen::Matrix<float, 4, 1> >
/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:98:7: required from class Eigen::PlainObjectBase<Eigen::Matrix<float, 4, 1> >
/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/Matrix.h:178:7: required from class Eigen::Matrix<float, 4, 1>
/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:46:50: required from class Eigen::QuaternionBase<Eigen::Quaternion<float> >
/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:273:7: required from class Eigen::Quaternion<float>
/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SIMD.h:27:3: required from here
/home/biocbuild/bbs-3.21-bioc/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;
| ^~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h: In instantiation of struct Eigen::internal::find_best_packet<double, 4>:
/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/Matrix.h:22:57: required from struct Eigen::internal::traits<Eigen::Matrix<double, 4, 1> >
/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:266:49: required from struct Eigen::internal::traits<Eigen::Quaternion<double> >
/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SIMD.h:98:47: required from here
/home/biocbuild/bbs-3.21-bioc/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>
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.21-bioc/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>
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.21-bioc/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]
/home/biocbuild/bbs-3.21-bioc/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]
/home/biocbuild/bbs-3.21-bioc/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;
| ^~~~
/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of class Eigen::DenseCoeffsBase<Eigen::Matrix<double, 4, 1>, 0>:
/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:302:7: required from class Eigen::DenseCoeffsBase<Eigen::Matrix<double, 4, 1>, 1>
/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:555:7: required from class Eigen::DenseCoeffsBase<Eigen::Matrix<double, 4, 1>, 3>
/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34: required from class Eigen::DenseBase<Eigen::Matrix<double, 4, 1> >
/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34: required from class Eigen::MatrixBase<Eigen::Matrix<double, 4, 1> >
/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:98:7: required from class Eigen::PlainObjectBase<Eigen::Matrix<double, 4, 1> >
/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/Matrix.h:178:7: required from class Eigen::Matrix<double, 4, 1>
/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:46:50: required from class Eigen::QuaternionBase<Eigen::Quaternion<double> >
/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:273:7: required from class Eigen::Quaternion<double>
/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SIMD.h:102:3: required from here
/home/biocbuild/bbs-3.21-bioc/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 /home/biocbuild/bbs-3.21-bioc/R/site-library/RcppEigen/include/Eigen/SparseCore:37,
from /home/biocbuild/bbs-3.21-bioc/R/site-library/RcppEigen/include/Eigen/Sparse:26,
from /home/biocbuild/bbs-3.21-bioc/R/site-library/RcppEigen/include/RcppEigenForward.h:29:
/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrixBase.h: In instantiation of class Eigen::SparseMatrixBase<Eigen::SparseMatrix<double, 0, int> >:
/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppEigen/include/Eigen/src/SparseCore/SparseCompressedBase.h:36:7: required from class Eigen::SparseCompressedBase<Eigen::SparseMatrix<double, 0, int> >
/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:96:7: required from class Eigen::SparseMatrix<double, 0, int>
/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/ConstrainedConjGrad.h:61:25: required from here
/home/biocbuild/bbs-3.21-bioc/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++17 -shared -L/home/biocbuild/bbs-3.21-bioc/R/lib -L/usr/local/lib -o MetaboDynamics.so RcppExports.o -L/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppParallel/lib/ -Wl,-rpath,/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppParallel/lib/ -ltbb -ltbbmalloc -L/home/biocbuild/bbs-3.21-bioc/R/lib -lR
installing to /tmp/RtmpDLXCcx/Rinstfb3732dc5d1e8/00LOCK-MetaboDynamics/00new/MetaboDynamics/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for MetaboDynamics in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/tmp/RtmpDLXCcx/Rinstfb3732dc5d1e8/00LOCK-MetaboDynamics/00new/MetaboDynamics/libs/MetaboDynamics.so':
/tmp/RtmpDLXCcx/Rinstfb3732dc5d1e8/00LOCK-MetaboDynamics/00new/MetaboDynamics/libs/MetaboDynamics.so: undefined symbol: _rcpp_module_boot_stan_fit4m_ANOVA_partial_pooling_mod
Error: loading failed
Execution halted
ERROR: loading failed
* removing /tmp/RtmpDLXCcx/Rinstfb3732dc5d1e8/MetaboDynamics
-----------------------------------
ERROR: package installation failed