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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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Cannot Install RStanARM in Ubuntu 20.04.3 #560

Closed hbunyamin closed 2 years ago

hbunyamin commented 2 years ago

Summary:

Unable to Install rstanarm

Description:

I have installed Ubuntu 20.04.3 LTS and cannot install rstanarm from the []()

Reproducible Steps:

Install from the official site

R Version:

4.1.2

Operating System:

Ubuntu 20.04.3

The Console Message

g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG   -I"/usr/lib/R/site-library/Rcpp/include/"  -I"/usr/lib/R/site-library/RcppEigen/include/"  -I"/usr/lib/R/site-library/RcppEigen/include/unsupported"  -I"/usr/lib/R/site-library/BH/include" -I"/usr/lib/R/site-library/StanHeaders/include/src/"  -I"/usr/lib/R/site-library/StanHeaders/include/"  -I"/usr/lib/R/site-library/RcppParallel/include/"  -I"/home/hbunyamin/R/x86_64-pc-linux-gnu-library/4.1/rstan/include" -DEIGEN_NO_DEBUG  -DBOOST_DISABLE_ASSERTS  -DBOOST_PENDING_INTEGER_LOG2_HPP  -DSTAN_THREADS  -DBOOST_NO_AUTO_PTR  -include '/usr/lib/R/site-library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp'  -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-i2PIHO/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c dummy.cpp -o dummy.o
In file included from /usr/lib/R/site-library/RcppEigen/include/Eigen/Core:397,
                 from /usr/lib/R/site-library/RcppEigen/include/Eigen/Dense:1,
                 from /usr/lib/R/site-library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13,
                 from <command-line>:
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:60:39: warning: ignoring attributes on template argument ‘__m128’ {aka ‘__vector(4) float’} [-Wignored-attributes]
   60 | template<> struct is_arithmetic<__m128>  { enum { value = true }; };
      |                                       ^
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:61:40: warning: ignoring attributes on template argument ‘__m128i’ {aka ‘__vector(2) long long int’} [-Wignored-attributes]
   61 | template<> struct is_arithmetic<__m128i> { enum { value = true }; };
      |                                        ^
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:62:40: warning: ignoring attributes on template argument ‘__m128d’ {aka ‘__vector(2) double’} [-Wignored-attributes]
   62 | template<> struct is_arithmetic<__m128d> { enum { value = true }; };
      |                                        ^
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:161:43: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4f’ {aka ‘__vector(4) float’} [-Wignored-attributes]
  161 | template<> struct unpacket_traits<Packet4f> { typedef float  type; enum {size=4, alignment=Aligned16}; typedef Packet4f half; };
      |                                           ^
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:162:43: warning: ignoring attributes on template argument ‘Eigen::internal::Packet2d’ {aka ‘__vector(2) double’} [-Wignored-attributes]
  162 | template<> struct unpacket_traits<Packet2d> { typedef double type; enum {size=2, alignment=Aligned16}; typedef Packet2d half; };
      |                                           ^
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:163:43: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4i’ {aka ‘__vector(2) long long int’} [-Wignored-attributes]
  163 | template<> struct unpacket_traits<Packet4i> { typedef int    type; enum {size=4, alignment=Aligned16}; typedef Packet4i half; };
      |                                           ^
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:718:35: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4f’ {aka ‘__vector(4) float’} [-Wignored-attributes]
  718 | struct palign_impl<Offset,Packet4f>
      |                                   ^
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:741:35: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4i’ {aka ‘__vector(2) long long int’} [-Wignored-attributes]
  741 | struct palign_impl<Offset,Packet4i>
      |                                   ^
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:764:35: warning: ignoring attributes on template argument ‘Eigen::internal::Packet2d’ {aka ‘__vector(2) double’} [-Wignored-attributes]
  764 | struct palign_impl<Offset,Packet2d>
      |                                   ^
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:778:34: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4f’ {aka ‘__vector(4) float’} [-Wignored-attributes]
  778 | ptranspose(PacketBlock<Packet4f,4>& kernel) {
      |                                  ^
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:783:34: warning: ignoring attributes on template argument ‘Eigen::internal::Packet2d’ {aka ‘__vector(2) double’} [-Wignored-attributes]
  783 | ptranspose(PacketBlock<Packet2d,2>& kernel) {
      |                                  ^
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:790:34: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4i’ {aka ‘__vector(2) long long int’} [-Wignored-attributes]
  790 | ptranspose(PacketBlock<Packet4i,4>& kernel) {
      |                                  ^
In file included from /usr/lib/R/site-library/RcppEigen/include/Eigen/Core:377,
                 from /usr/lib/R/site-library/RcppEigen/include/Eigen/Dense:1,
                 from /usr/lib/R/site-library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13,
                 from <command-line>:
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/Default/ConjHelper.h:15:70: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4f’ {aka ‘__vector(4) float’} [-Wignored-attributes]
   15 |   template<> struct conj_helper<PACKET_REAL, PACKET_CPLX, false,false> {                                          \
      |                                                                      ^
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/Complex.h:232:1: note: in expansion of macro ‘EIGEN_MAKE_CONJ_HELPER_CPLX_REAL’
  232 | EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet2cf,Packet4f)
      | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/Default/ConjHelper.h:22:70: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4f’ {aka ‘__vector(4) float’} [-Wignored-attributes]
   22 |   template<> struct conj_helper<PACKET_CPLX, PACKET_REAL, false,false> {                                          \
      |                                                                      ^
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/Complex.h:232:1: note: in expansion of macro ‘EIGEN_MAKE_CONJ_HELPER_CPLX_REAL’
  232 | EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet2cf,Packet4f)
      | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/Default/ConjHelper.h:15:70: warning: ignoring attributes on template argument ‘Eigen::internal::Packet2d’ {aka ‘__vector(2) double’} [-Wignored-attributes]
   15 |   template<> struct conj_helper<PACKET_REAL, PACKET_CPLX, false,false> {                                          \
      |                                                                      ^
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/Complex.h:417:1: note: in expansion of macro ‘EIGEN_MAKE_CONJ_HELPER_CPLX_REAL’
  417 | EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet1cd,Packet2d)
      | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/Default/ConjHelper.h:22:70: warning: ignoring attributes on template argument ‘Eigen::internal::Packet2d’ {aka ‘__vector(2) double’} [-Wignored-attributes]
   22 |   template<> struct conj_helper<PACKET_CPLX, PACKET_REAL, false,false> {                                          \
      |                                                                      ^
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/Complex.h:417:1: note: in expansion of macro ‘EIGEN_MAKE_CONJ_HELPER_CPLX_REAL’
  417 | EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet1cd,Packet2d)
      | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/lib/R/site-library/RcppEigen/include/Eigen/Core:370,
                 from /usr/lib/R/site-library/RcppEigen/include/Eigen/Dense:1,
                 from /usr/lib/R/site-library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13,
                 from <command-line>:
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h: In instantiation of ‘struct Eigen::internal::find_best_packet<float, 4>’:
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Matrix.h:22:57:   required from ‘struct Eigen::internal::traits<Eigen::Matrix<float, 4, 1> >’
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:242:7:   required from ‘struct Eigen::internal::traits<Eigen::Quaternion<float> >’
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SSE.h:24:46:   required from here
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:187:44: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<float>::type’ {aka ‘__vector(4) float’} [-Wignored-attributes]
  187 |          bool Stop = Size==Dynamic || (Size%unpacket_traits<PacketType>::size)==0 || is_same<PacketType,typename unpacket_traits<PacketType>::half>::value>
      |                                       ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:187:83: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<float>::type’ {aka ‘__vector(4) float’} [-Wignored-attributes]
  187 |          bool Stop = Size==Dynamic || (Size%unpacket_traits<PacketType>::size)==0 || is_same<PacketType,typename unpacket_traits<PacketType>::half>::value>
      |                      ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:187:83: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<float>::type’ {aka ‘__vector(4) float’} [-Wignored-attributes]
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:187:83: warning: ignoring attributes on template argument ‘Eigen::internal::unpacket_traits<__vector(4) float>::half’ {aka ‘__vector(4) float’} [-Wignored-attributes]
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:205:88: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<float>::type’ {aka ‘__vector(4) float’} [-Wignored-attributes]
  205 |   typedef typename find_best_packet_helper<Size,typename packet_traits<T>::type>::type type;
      |                                                                                        ^~~~
In file included from /usr/lib/R/site-library/RcppEigen/include/Eigen/Core:439,
                 from /usr/lib/R/site-library/RcppEigen/include/Eigen/Dense:1,
                 from /usr/lib/R/site-library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13,
                 from <command-line>:
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<float, 4, 1>, 0>’:
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:300:7:   required from ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<float, 4, 1>, 1>’
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:551:7:   required from ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<float, 4, 1>, 3>’
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34:   required from ‘class Eigen::DenseBase<Eigen::Matrix<float, 4, 1> >’
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34:   required from ‘class Eigen::MatrixBase<Eigen::Matrix<float, 4, 1> >’
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:98:7:   required from ‘class Eigen::PlainObjectBase<Eigen::Matrix<float, 4, 1> >’
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Matrix.h:178:7:   required from ‘class Eigen::Matrix<float, 4, 1>’
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:46:50:   required from ‘class Eigen::QuaternionBase<Eigen::Quaternion<float> >’
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:250:7:   required from ‘class Eigen::Quaternion<float>’
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SSE.h:27:3:   required from here
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:55:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<float>::type’ {aka ‘__vector(4) float’} [-Wignored-attributes]
   55 |                      >::type PacketReturnType;
      |                              ^~~~~~~~~~~~~~~~
In file included from /usr/lib/R/site-library/RcppEigen/include/Eigen/Core:370,
                 from /usr/lib/R/site-library/RcppEigen/include/Eigen/Dense:1,
                 from /usr/lib/R/site-library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13,
                 from <command-line>:
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h: In instantiation of ‘struct Eigen::internal::find_best_packet<double, 4>’:
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Matrix.h:22:57:   required from ‘struct Eigen::internal::traits<Eigen::Matrix<double, 4, 1> >’
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:242:7:   required from ‘struct Eigen::internal::traits<Eigen::Quaternion<double> >’
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SSE.h:88:47:   required from here
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:187:44: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<double>::type’ {aka ‘__vector(2) double’} [-Wignored-attributes]
  187 |          bool Stop = Size==Dynamic || (Size%unpacket_traits<PacketType>::size)==0 || is_same<PacketType,typename unpacket_traits<PacketType>::half>::value>
      |                                       ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:187:83: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<double>::type’ {aka ‘__vector(2) double’} [-Wignored-attributes]
  187 |          bool Stop = Size==Dynamic || (Size%unpacket_traits<PacketType>::size)==0 || is_same<PacketType,typename unpacket_traits<PacketType>::half>::value>
      |                      ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:187:83: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<double>::type’ {aka ‘__vector(2) double’} [-Wignored-attributes]
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:187:83: warning: ignoring attributes on template argument ‘Eigen::internal::unpacket_traits<__vector(2) double>::half’ {aka ‘__vector(2) double’} [-Wignored-attributes]
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:205:88: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<double>::type’ {aka ‘__vector(2) double’} [-Wignored-attributes]
  205 |   typedef typename find_best_packet_helper<Size,typename packet_traits<T>::type>::type type;
      |                                                                                        ^~~~
In file included from /usr/lib/R/site-library/RcppEigen/include/Eigen/Core:439,
                 from /usr/lib/R/site-library/RcppEigen/include/Eigen/Dense:1,
                 from /usr/lib/R/site-library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13,
                 from <command-line>:
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<double, 4, 1>, 0>’:
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:300:7:   required from ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<double, 4, 1>, 1>’
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:551:7:   required from ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<double, 4, 1>, 3>’
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34:   required from ‘class Eigen::DenseBase<Eigen::Matrix<double, 4, 1> >’
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34:   required from ‘class Eigen::MatrixBase<Eigen::Matrix<double, 4, 1> >’
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:98:7:   required from ‘class Eigen::PlainObjectBase<Eigen::Matrix<double, 4, 1> >’
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Matrix.h:178:7:   required from ‘class Eigen::Matrix<double, 4, 1>’
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:46:50:   required from ‘class Eigen::QuaternionBase<Eigen::Quaternion<double> >’
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:250:7:   required from ‘class Eigen::Quaternion<double>’
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SSE.h:92:3:   required from here
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:55:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<double>::type’ {aka ‘__vector(2) double’} [-Wignored-attributes]
   55 |                      >::type PacketReturnType;
      |                              ^~~~~~~~~~~~~~~~
gcc -std=gnu99 -std=gnu11 -I"/usr/share/R/include" -DNDEBUG   -I"/usr/lib/R/site-library/Rcpp/include/"  -I"/usr/lib/R/site-library/RcppEigen/include/"  -I"/usr/lib/R/site-library/RcppEigen/include/unsupported"  -I"/usr/lib/R/site-library/BH/include" -I"/usr/lib/R/site-library/StanHeaders/include/src/"  -I"/usr/lib/R/site-library/StanHeaders/include/"  -I"/usr/lib/R/site-library/RcppParallel/include/"  -I"/home/hbunyamin/R/x86_64-pc-linux-gnu-library/4.1/rstan/include" -DEIGEN_NO_DEBUG  -DBOOST_DISABLE_ASSERTS  -DBOOST_PENDING_INTEGER_LOG2_HPP  -DSTAN_THREADS  -DBOOST_NO_AUTO_PTR  -include '/usr/lib/R/site-library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp'  -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1     -g -O2 -fdebug-prefix-map=/build/r-base-i2PIHO/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -I/tmp/RtmpwKJjXk/R.INSTALL8054666eee35/nloptr/src/nlopt_src/include -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-i2PIHO/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c init_nloptr.c -o init_nloptr.o
In file included from /usr/lib/R/site-library/RcppEigen/include/Eigen/Core:88,
                 from /usr/lib/R/site-library/RcppEigen/include/Eigen/Dense:1,
                 from /usr/lib/R/site-library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13,
                 from <command-line>:
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:1: error: unknown type name ‘namespace’
  628 | namespace Eigen {
      | ^~~~~~~~~
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:17: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘{’ token
  628 | namespace Eigen {
      |                 ^
In file included from /usr/lib/R/site-library/RcppEigen/include/Eigen/Dense:1,
                 from /usr/lib/R/site-library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13,
                 from <command-line>:
/usr/lib/R/site-library/RcppEigen/include/Eigen/Core:96:10: fatal error: complex: No such file or directory
   96 | #include <complex>
      |          ^~~~~~~~~
compilation terminated.
make: *** [/usr/lib/R/etc/Makeconf:168: init_nloptr.o] Error 1
ERROR: compilation failed for package ‘nloptr’
* removing ‘/home/hbunyamin/R/x86_64-pc-linux-gnu-library/4.1/nloptr’
Warning in install.packages :
  installation of package ‘nloptr’ had non-zero exit status
ERROR: dependency ‘httpuv’ is not available for package ‘shiny’
* removing ‘/home/hbunyamin/R/x86_64-pc-linux-gnu-library/4.1/shiny’
Warning in install.packages :
  installation of package ‘shiny’ had non-zero exit status
ERROR: dependencies ‘curl’, ‘openssl’ are not available for package ‘rsconnect’
* removing ‘/home/hbunyamin/R/x86_64-pc-linux-gnu-library/4.1/rsconnect’
Warning in install.packages :
  installation of package ‘rsconnect’ had non-zero exit status
ERROR: dependency ‘igraph’ is not available for package ‘threejs’
* removing ‘/home/hbunyamin/R/x86_64-pc-linux-gnu-library/4.1/threejs’
Warning in install.packages :
  installation of package ‘threejs’ had non-zero exit status
ERROR: dependencies ‘minqa’, ‘nloptr’ are not available for package ‘lme4’
* removing ‘/home/hbunyamin/R/x86_64-pc-linux-gnu-library/4.1/lme4’
Warning in install.packages :
  installation of package ‘lme4’ had non-zero exit status
ERROR: dependency ‘shiny’ is not available for package ‘miniUI’
* removing ‘/home/hbunyamin/R/x86_64-pc-linux-gnu-library/4.1/miniUI’
Warning in install.packages :
  installation of package ‘miniUI’ had non-zero exit status
ERROR: dependency ‘shiny’ is not available for package ‘shinyjs’
* removing ‘/home/hbunyamin/R/x86_64-pc-linux-gnu-library/4.1/shinyjs’
Warning in install.packages :
  installation of package ‘shinyjs’ had non-zero exit status
ERROR: dependency ‘shiny’ is not available for package ‘shinythemes’
* removing ‘/home/hbunyamin/R/x86_64-pc-linux-gnu-library/4.1/shinythemes’
Warning in install.packages :
  installation of package ‘shinythemes’ had non-zero exit status
ERROR: dependencies ‘miniUI’, ‘shiny’, ‘shinyjs’ are not available for package ‘colourpicker’
* removing ‘/home/hbunyamin/R/x86_64-pc-linux-gnu-library/4.1/colourpicker’
Warning in install.packages :
  installation of package ‘colourpicker’ had non-zero exit status
ERROR: dependencies ‘shiny’, ‘colourpicker’, ‘rsconnect’, ‘shinyjs’, ‘shinythemes’, ‘threejs’ are not available for package ‘shinystan’
* removing ‘/home/hbunyamin/R/x86_64-pc-linux-gnu-library/4.1/shinystan’
Warning in install.packages :
  installation of package ‘shinystan’ had non-zero exit status
ERROR: dependencies ‘lme4’, ‘shinystan’ are not available for package ‘rstanarm’
* removing ‘/home/hbunyamin/R/x86_64-pc-linux-gnu-library/4.1/rstanarm’
Warning in install.packages :
  installation of package ‘rstanarm’ had non-zero exit status
andrjohns commented 2 years ago

That error appears to indicate a failure to install the nloptr package, rather than rstanarm.

Can you make sure you have the necessary build dependencies installed on your system:

sudo apt install build-essential r-base-dev

Then restart R and try installing nloptr again:

install.packages("nloptr")

If that succeeds can you then try the rstanarm install again?

hbunyamin commented 2 years ago

Apparently, before I install rstanarm, I need to install as follows:

sudo apt install build-essential r-base-dev sudo apt-get install -y libcurl4-openssl-dev

Thank you so much @andrjohns !