Unidentified error when trying to install `rstanarm` package
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Description
Hi rstanarm community,
I am very confused here. Please any help understanding the root of the issue and potentially solve it would be amazing!
All the best Kamau
Summary:
Error when trying to install rstanarm package
Description:
I am simply running the install.packages("rstanarm") and get a lot of errors related to the main challenge is that I try to build from the source a piece of software that is pretty complicated to compile..
How can I solve this issue, or at least understand what is going on here.. I thought it was a matter of updating R and RStudio, but after doing so, I still ran into the same problem.
RStanARM Version:
The version of the rstanarm package you are running (e.g., from packageVersion("rstanarm"))
*Not applicable
R Version:
The version of R you are running (e.g., from getRversion())
> getRversion()
[1] ‘4.0.2’
Operating System:
I am running RStudio in Amazon's AWS EC2 Cloud computing however I experienced exactly the same problem on my personal macOS Big Sur v 11.4 running RStudio 4.1
Reproducible Steps:
install.packages("rstanarm")
Installing package into ‘/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0’
(as ‘lib’ is unspecified)
trying URL 'https://cran.rstudio.com/src/contrib/rstanarm_2.21.1.tar.gz'
Content type 'application/x-gzip' length 3548723 bytes (3.4 MB)
==================================================
downloaded 3.4 MB
* installing *source* package ‘rstanarm’ ...
** package ‘rstanarm’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
"/usr/lib/R/bin/Rscript" -e "source(file.path('..', 'tools', 'make_cc.R')); make_cc(commandArgs(TRUE))" stan_files/jm.stan
Wrote C++ file "stan_files/jm.cc"
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I"../inst/include" -I"/usr/local/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -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'/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include' -I'/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include' -I'/usr/local/lib/R/site-library/RcppParallel/include' `"/usr/lib/R/bin/Rscript" -e "RcppParallel::CxxFlags()"` `"/usr/lib/R/bin/Rscript" -e "StanHeaders:::CxxFlags()"` -fpic -g -O2 -fdebug-prefix-map=/build/r-base-ttHamR/r-base-4.0.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stan_files/jm.cc -o stan_files/jm.o
In file included from /home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/Core:397:0,
from /home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/Dense:1,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13,
from /usr/local/lib/R/site-library/rstan/include/rstan/rstaninc.hpp:3,
from stan_files/jm.hpp:18,
from stan_files/jm.cc:3:
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/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 }; };
^
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/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 }; };
^
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/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 }; };
^
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/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; };
^
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/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; };
^
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/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; };
^
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/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>
^
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/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>
^
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/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>
^
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/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) {
^
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/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) {
^
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/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 /home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/Core:377:0,
from /home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/Dense:1,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13,
from /usr/local/lib/R/site-library/rstan/include/rstan/rstaninc.hpp:3,
from stan_files/jm.hpp:18,
from stan_files/jm.cc:3:
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/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> { \
^
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/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)
^
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/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> { \
^
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/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)
^
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/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> { \
^
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/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)
^
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/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> { \
^
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/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 /home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/Core:370:0,
from /home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/Dense:1,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13,
from /usr/local/lib/R/site-library/rstan/include/rstan/rstaninc.hpp:3,
from stan_files/jm.hpp:18,
from stan_files/jm.cc:3:
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Core/util/XprHelper.h: In instantiation of ‘struct Eigen::internal::find_best_packet<float, 4>’:
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Core/Matrix.h:22:57: required from ‘struct Eigen::internal::traits<Eigen::Matrix<float, 4, 1> >’
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:242:7: required from ‘struct Eigen::internal::traits<Eigen::Quaternion<float> >’
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SSE.h:24:46: required from here
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:187:44: 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>
~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:187:83: 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>
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:187:83: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<float>::type {aka __vector(4) float}’ [-Wignored-attributes]
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:187:83: warning: ignoring attributes on template argument ‘Eigen::internal::unpacket_traits<__vector(4) float>::half {aka __vector(4) float}’ [-Wignored-attributes]
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:205:88: 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 /home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/Core:439:0,
from /home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/Dense:1,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13,
from /usr/local/lib/R/site-library/rstan/include/rstan/rstaninc.hpp:3,
from stan_files/jm.hpp:18,
from stan_files/jm.cc:3:
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<float, 4, 1>, 0>’:
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:300:7: required from ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<float, 4, 1>, 1>’
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:551:7: required from ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<float, 4, 1>, 3>’
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34: required from ‘class Eigen::DenseBase<Eigen::Matrix<float, 4, 1> >’
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34: required from ‘class Eigen::MatrixBase<Eigen::Matrix<float, 4, 1> >’
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:98:7: required from ‘class Eigen::PlainObjectBase<Eigen::Matrix<float, 4, 1> >’
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Core/Matrix.h:178:7: required from ‘class Eigen::Matrix<float, 4, 1>’
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:46:50: required from ‘class Eigen::QuaternionBase<Eigen::Quaternion<float> >’
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:250:7: required from ‘class Eigen::Quaternion<float>’
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SSE.h:27:3: required from here
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/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 /home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/Core:370:0,
from /home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/Dense:1,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13,
from /usr/local/lib/R/site-library/rstan/include/rstan/rstaninc.hpp:3,
from stan_files/jm.hpp:18,
from stan_files/jm.cc:3:
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Core/util/XprHelper.h: In instantiation of ‘struct Eigen::internal::find_best_packet<double, 4>’:
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Core/Matrix.h:22:57: required from ‘struct Eigen::internal::traits<Eigen::Matrix<double, 4, 1> >’
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:242:7: required from ‘struct Eigen::internal::traits<Eigen::Quaternion<double> >’
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SSE.h:88:47: required from here
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:187:44: 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>
~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:187:83: 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>
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:187:83: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<double>::type {aka __vector(2) double}’ [-Wignored-attributes]
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:187:83: warning: ignoring attributes on template argument ‘Eigen::internal::unpacket_traits<__vector(2) double>::half {aka __vector(2) double}’ [-Wignored-attributes]
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:205:88: 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 /home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/Core:439:0,
from /home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/Dense:1,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13,
from /usr/local/lib/R/site-library/rstan/include/rstan/rstaninc.hpp:3,
from stan_files/jm.hpp:18,
from stan_files/jm.cc:3:
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<double, 4, 1>, 0>’:
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:300:7: required from ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<double, 4, 1>, 1>’
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:551:7: required from ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<double, 4, 1>, 3>’
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34: required from ‘class Eigen::DenseBase<Eigen::Matrix<double, 4, 1> >’
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34: required from ‘class Eigen::MatrixBase<Eigen::Matrix<double, 4, 1> >’
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:98:7: required from ‘class Eigen::PlainObjectBase<Eigen::Matrix<double, 4, 1> >’
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Core/Matrix.h:178:7: required from ‘class Eigen::Matrix<double, 4, 1>’
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:46:50: required from ‘class Eigen::QuaternionBase<Eigen::Quaternion<double> >’
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:250:7: required from ‘class Eigen::Quaternion<double>’
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SSE.h:92:3: required from here
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/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/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17,
from /usr/local/lib/R/site-library/BH/include/boost/date_time/time_clock.hpp:17,
from /usr/local/lib/R/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
from /usr/local/lib/R/site-library/rstan/include/rstan/stan_fit.hpp:13,
from /usr/local/lib/R/site-library/rstan/include/rstan/rstaninc.hpp:4,
from stan_files/jm.hpp:18,
from stan_files/jm.cc:3:
/usr/local/lib/R/site-library/BH/include/boost/smart_ptr/detail/shared_count.hpp:356:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include/RcppCommon.h:53,
from /home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include/Rcpp.h:27,
from stan_files/jm.cc:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
from /usr/local/lib/R/site-library/BH/include/boost/date_time/time_clock.hpp:17,
from /usr/local/lib/R/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
from /usr/local/lib/R/site-library/rstan/include/rstan/stan_fit.hpp:13,
from /usr/local/lib/R/site-library/rstan/include/rstan/rstaninc.hpp:4,
from stan_files/jm.hpp:18,
from stan_files/jm.cc:3:
/usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include/RcppCommon.h:53,
from /home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include/Rcpp.h:27,
from stan_files/jm.cc:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
from /usr/local/lib/R/site-library/BH/include/boost/date_time/time_clock.hpp:17,
from /usr/local/lib/R/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
from /usr/local/lib/R/site-library/rstan/include/rstan/stan_fit.hpp:13,
from /usr/local/lib/R/site-library/rstan/include/rstan/rstaninc.hpp:4,
from stan_files/jm.hpp:18,
from stan_files/jm.cc:3:
/usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include/RcppCommon.h:53,
from /home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include/Rcpp.h:27,
from stan_files/jm.cc:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
from /usr/local/lib/R/site-library/BH/include/boost/date_time/time_clock.hpp:17,
from /usr/local/lib/R/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
from /usr/local/lib/R/site-library/rstan/include/rstan/stan_fit.hpp:13,
from /usr/local/lib/R/site-library/rstan/include/rstan/rstaninc.hpp:4,
from stan_files/jm.hpp:18,
from stan_files/jm.cc:3:
/usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include/RcppCommon.h:53,
from /home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include/Rcpp.h:27,
from stan_files/jm.cc:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
from /usr/local/lib/R/site-library/BH/include/boost/date_time/time_clock.hpp:17,
from /usr/local/lib/R/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
from /usr/local/lib/R/site-library/rstan/include/rstan/stan_fit.hpp:13,
from /usr/local/lib/R/site-library/rstan/include/rstan/rstaninc.hpp:4,
from stan_files/jm.hpp:18,
from stan_files/jm.cc:3:
/usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
shared_ptr & operator=( std::auto_ptr<Y> & r )
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include/RcppCommon.h:53,
from /home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include/Rcpp.h:27,
from stan_files/jm.cc:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
from /usr/local/lib/R/site-library/BH/include/boost/date_time/time_clock.hpp:17,
from /usr/local/lib/R/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
from /usr/local/lib/R/site-library/rstan/include/rstan/stan_fit.hpp:13,
from /usr/local/lib/R/site-library/rstan/include/rstan/rstaninc.hpp:4,
from stan_files/jm.hpp:18,
from stan_files/jm.cc:3:
/usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
shared_ptr & operator=( std::auto_ptr<Y> && r )
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include/RcppCommon.h:53,
from /home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include/Rcpp.h:27,
from stan_files/jm.cc:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0,
from /usr/local/lib/R/site-library/BH/include/boost/date_time/time_clock.hpp:17,
from /usr/local/lib/R/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
from /usr/local/lib/R/site-library/rstan/include/rstan/stan_fit.hpp:13,
from /usr/local/lib/R/site-library/rstan/include/rstan/rstaninc.hpp:4,
from stan_files/jm.hpp:18,
from stan_files/jm.cc:3:
/usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
/usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include/RcppCommon.h:53,
from /home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include/Rcpp.h:27,
from stan_files/jm.cc:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from /home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/SparseCore:37:0,
from /home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/Sparse:26,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14,
from /usr/local/lib/R/site-library/rstan/include/rstan/rstaninc.hpp:3,
from stan_files/jm.hpp:18,
from stan_files/jm.cc:3:
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/SparseCore/SparseMatrixBase.h: In instantiation of ‘class Eigen::SparseMatrixBase<Eigen::SparseMatrix<double, 0, int> >’:
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/SparseCore/SparseCompressedBase.h:36:7: required from ‘class Eigen::SparseCompressedBase<Eigen::SparseMatrix<double, 0, int> >’
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:96:7: required from ‘class Eigen::SparseMatrix<double, 0, int>’
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/ConstrainedConjGrad.h:61:25: required from here
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/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 /home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/Core:370:0,
from /home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/Dense:1,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13,
from /usr/local/lib/R/site-library/rstan/include/rstan/rstaninc.hpp:3,
from stan_files/jm.hpp:18,
from stan_files/jm.cc:3:
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Core/util/XprHelper.h: In instantiation of ‘struct Eigen::internal::find_best_packet<int, -1>’:
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Core/Matrix.h:22:57: required from ‘struct Eigen::internal::traits<Eigen::Matrix<int, -1, 1> >’
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:98:7: required from ‘class Eigen::PlainObjectBase<Eigen::Matrix<int, -1, 1> >’
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Core/Matrix.h:178:7: required from ‘class Eigen::Matrix<int, -1, 1>’
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/unsupported/Eigen/src/KroneckerProduct/KroneckerTensorProduct.h:168:29: required from here
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:187:44: 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>
~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:187:83: 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>
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:187:83: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<int>::type {aka __vector(2) long long int}’ [-Wignored-attributes]
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:187:83: warning: ignoring attributes on template argument ‘Eigen::internal::unpacket_traits<__vector(2) long long int>::half {aka __vector(2) long long int}’ [-Wignored-attributes]
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:205:88: 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 /home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/Core:439:0,
from /home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/Dense:1,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13,
from /usr/local/lib/R/site-library/rstan/include/rstan/rstaninc.hpp:3,
from stan_files/jm.hpp:18,
from stan_files/jm.cc:3:
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<int, -1, 1>, 0>’:
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:300:7: required from ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<int, -1, 1>, 1>’
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:551:7: required from ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<int, -1, 1>, 3>’
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34: required from ‘class Eigen::DenseBase<Eigen::Matrix<int, -1, 1> >’
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34: required from ‘class Eigen::MatrixBase<Eigen::Matrix<int, -1, 1> >’
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:98:7: required from ‘class Eigen::PlainObjectBase<Eigen::Matrix<int, -1, 1> >’
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Core/Matrix.h:178:7: required from ‘class Eigen::Matrix<int, -1, 1>’
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/unsupported/Eigen/src/KroneckerProduct/KroneckerTensorProduct.h:168:29: required from here
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/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;
^~~~~~~~~~~~~~~~
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of ‘class Eigen::DenseCoeffsBase<Eigen::Transpose<Eigen::Matrix<int, -1, 1> >, 0>’:
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:300:7: required from ‘class Eigen::DenseCoeffsBase<Eigen::Transpose<Eigen::Matrix<int, -1, 1> >, 1>’
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:551:7: required from ‘class Eigen::DenseCoeffsBase<Eigen::Transpose<Eigen::Matrix<int, -1, 1> >, 3>’
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34: required from ‘class Eigen::DenseBase<Eigen::Transpose<Eigen::Matrix<int, -1, 1> > >’
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34: required from ‘class Eigen::MatrixBase<Eigen::Transpose<Eigen::Matrix<int, -1, 1> > >’
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Core/Transpose.h:115:37: required from ‘class Eigen::TransposeImpl<Eigen::Matrix<int, -1, 1>, Eigen::Dense>’
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Core/Transpose.h:52:37: required from ‘class Eigen::Transpose<Eigen::Matrix<int, -1, 1> >’
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/unsupported/Eigen/src/KroneckerProduct/KroneckerTensorProduct.h:178:72: required from here
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/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]
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<int, -1, -1>, 0>’:
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:300:7: required from ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<int, -1, -1>, 1>’
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:551:7: required from ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<int, -1, -1>, 3>’
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34: required from ‘class Eigen::DenseBase<Eigen::Matrix<int, -1, -1> >’
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34: required from ‘class Eigen::MatrixBase<Eigen::Matrix<int, -1, -1> >’
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:98:7: required from ‘class Eigen::PlainObjectBase<Eigen::Matrix<int, -1, -1> >’
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Core/Matrix.h:178:7: required from ‘class Eigen::Matrix<int, -1, -1>’
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/unsupported/Eigen/src/KroneckerProduct/KroneckerTensorProduct.h:179:36: required from here
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/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 /home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/Core:370:0,
from /home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/Dense:1,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13,
from /usr/local/lib/R/site-library/rstan/include/rstan/rstaninc.hpp:3,
from stan_files/jm.hpp:18,
from stan_files/jm.cc:3:
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Core/util/XprHelper.h: In instantiation of ‘struct Eigen::internal::find_best_packet<double, -1>’:
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Core/Matrix.h:22:57: required from ‘struct Eigen::internal::traits<Eigen::Matrix<double, -1, -1> >’
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:98:7: required from ‘class Eigen::PlainObjectBase<Eigen::Matrix<double, -1, -1> >’
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Core/Matrix.h:178:7: required from ‘class Eigen::Matrix<double, -1, -1>’
/usr/local/lib/R/site-library/StanHeaders/include/stan/math/rev/mat/fun/typedefs.hpp:11:72: required from here
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:187:44: 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>
~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:187:83: 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>
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:187:83: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<double>::type {aka __vector(2) double}’ [-Wignored-attributes]
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:187:83: warning: ignoring attributes on template argument ‘Eigen::internal::unpacket_traits<__vector(2) double>::half {aka __vector(2) double}’ [-Wignored-attributes]
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:205:88: 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 /home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/Core:439:0,
from /home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/Dense:1,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13,
from /usr/local/lib/R/site-library/rstan/include/rstan/rstaninc.hpp:3,
from stan_files/jm.hpp:18,
from stan_files/jm.cc:3:
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<double, -1, -1>, 0>’:
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:300:7: required from ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<double, -1, -1>, 1>’
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:551:7: required from ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<double, -1, -1>, 3>’
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34: required from ‘class Eigen::DenseBase<Eigen::Matrix<double, -1, -1> >’
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34: required from ‘class Eigen::MatrixBase<Eigen::Matrix<double, -1, -1> >’
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:98:7: required from ‘class Eigen::PlainObjectBase<Eigen::Matrix<double, -1, -1> >’
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Core/Matrix.h:178:7: required from ‘class Eigen::Matrix<double, -1, -1>’
/usr/local/lib/R/site-library/StanHeaders/include/stan/math/rev/mat/fun/typedefs.hpp:11:72: required from here
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/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;
^~~~~~~~~~~~~~~~
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<double, -1, 1>, 0>’:
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:300:7: required from ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<double, -1, 1>, 1>’
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:551:7: required from ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<double, -1, 1>, 3>’
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34: required from ‘class Eigen::DenseBase<Eigen::Matrix<double, -1, 1> >’
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34: required from ‘class Eigen::MatrixBase<Eigen::Matrix<double, -1, 1> >’
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:98:7: required from ‘class Eigen::PlainObjectBase<Eigen::Matrix<double, -1, 1> >’
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Core/Matrix.h:178:7: required from ‘class Eigen::Matrix<double, -1, 1>’
/usr/local/lib/R/site-library/StanHeaders/include/stan/math/rev/mat/meta/operands_and_partials.hpp:20:14: required from here
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/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]
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of ‘class Eigen::DenseCoeffsBase<Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, Eigen::Matrix<double, -1, 1> >, 0>’:
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34: required from ‘class Eigen::DenseBase<Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, Eigen::Matrix<double, -1, 1> > >’
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34: required from ‘class Eigen::MatrixBase<Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, Eigen::Matrix<double, -1, 1> > >’
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Core/CwiseNullaryOp.h:60:7: required from ‘class Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, Eigen::Matrix<double, -1, 1> >’
/usr/local/lib/R/site-library/StanHeaders/include/stan/math/rev/mat/meta/operands_and_partials.hpp:23:45: required from here
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/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]
In file included from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/rev/core/matrix_vari.hpp:4:0,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/rev/core.hpp:16,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/rev/mat.hpp:6,
from /usr/local/lib/R/site-library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
from /usr/local/lib/R/site-library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
from /usr/local/lib/R/site-library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10,
from /usr/local/lib/R/site-library/rstan/include/rstan/stan_fit.hpp:35,
from /usr/local/lib/R/site-library/rstan/include/rstan/rstaninc.hpp:4,
from stan_files/jm.hpp:18,
from stan_files/jm.cc:3:
/usr/local/lib/R/site-library/StanHeaders/include/stan/math/rev/mat/fun/Eigen_NumTraits.hpp: At global scope:
/usr/local/lib/R/site-library/StanHeaders/include/stan/math/rev/mat/fun/Eigen_NumTraits.hpp:200:77: error: wrong number of template arguments (8, should be 9)
RhsStorageOrder, ConjugateRhs, ColMajor> {
^
In file included from /home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/Core:454:0,
from /home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/Dense:1,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13,
from /usr/local/lib/R/site-library/rstan/include/rstan/rstaninc.hpp:3,
from stan_files/jm.hpp:18,
from stan_files/jm.cc:3:
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Core/util/BlasUtil.h:35:8: note: provided for ‘template<class Index, class LhsScalar, int LhsStorageOrder, bool ConjugateLhs, class RhsScalar, int RhsStorageOrder, bool ConjugateRhs, int ResStorageOrder, int ResInnerStride> struct Eigen::internal::general_matrix_matrix_product’
struct general_matrix_matrix_product;
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/Core:439:0,
from /home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/Dense:1,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13,
from /usr/local/lib/R/site-library/rstan/include/rstan/rstaninc.hpp:3,
from stan_files/jm.hpp:18,
from stan_files/jm.cc:3:
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of ‘class Eigen::DenseCoeffsBase<Eigen::Diagonal<const Eigen::Matrix<double, -1, -1>, 0>, 0>’:
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:478:7: required from ‘class Eigen::DenseCoeffsBase<Eigen::Diagonal<const Eigen::Matrix<double, -1, -1>, 0>, 2>’
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34: required from ‘class Eigen::DenseBase<Eigen::Diagonal<const Eigen::Matrix<double, -1, -1>, 0> >’
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34: required from ‘class Eigen::MatrixBase<Eigen::Diagonal<const Eigen::Matrix<double, -1, -1>, 0> >’
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Core/Diagonal.h:63:53: required from ‘class Eigen::Diagonal<const Eigen::Matrix<double, -1, -1>, 0>’
/usr/local/lib/R/site-library/StanHeaders/include/stan/math/prim/mat/err/check_pos_definite.hpp:38:29: required from here
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/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;
^~~~~~~~~~~~~~~~
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of ‘class Eigen::DenseCoeffsBase<Eigen::ArrayWrapper<Eigen::Diagonal<const Eigen::Matrix<double, -1, -1>, 0> >, 0>’:
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:478:7: required from ‘class Eigen::DenseCoeffsBase<Eigen::ArrayWrapper<Eigen::Diagonal<const Eigen::Matrix<double, -1, -1>, 0> >, 2>’
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34: required from ‘class Eigen::DenseBase<Eigen::ArrayWrapper<Eigen::Diagonal<const Eigen::Matrix<double, -1, -1>, 0> > >’
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Core/ArrayBase.h:39:34: required from ‘class Eigen::ArrayBase<Eigen::ArrayWrapper<Eigen::Diagonal<const Eigen::Matrix<double, -1, -1>, 0> > >’
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Core/ArrayWrapper.h:42:7: required from ‘class Eigen::ArrayWrapper<Eigen::Diagonal<const Eigen::Matrix<double, -1, -1>, 0> >’
/usr/local/lib/R/site-library/StanHeaders/include/stan/math/prim/mat/err/check_pos_definite.hpp:38:41: required from here
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/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]
/usr/lib/R/etc/Makeconf:174: recipe for target 'stan_files/jm.o' failed
make: *** [stan_files/jm.o] Interrupt
make: *** Deleting intermediate file 'stan_files/jm.cc'
ERROR: compilation failed for package ‘rstanarm’
* removing ‘/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0/rstanarm’
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First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Reproduce install.packages("rstanarm") using the reported R 4.0.2 environment and inspect the build around tools/make_cc.R, stan_files/jm.stan, and the generated stan_files/jm.cc. Identify the actual compiler error beyond the warnings and confirm that the package installs successfully after the relevant build issue is addressed.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- cpp, r
- Domain
- build-system
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100