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stan-dev / rstanarm

rstanarm R package for Bayesian applied regression modeling
https://mc-stan.org/rstanarm
GNU General Public License v3.0
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Unidentified error when trying to install `rstanarm` package #548

Open kamaulindhardt opened 3 years ago

kamaulindhardt commented 3 years ago

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’
kamaulindhardt commented 3 years ago

Dear authors and collaborators.

Did you have time to look into this issue?

bgoodri commented 2 years ago

Are you using StanHeaders from CRAN?