Hi all,
I have a model that compiles and runs perfectly fine in R on my local MacBook (MacOS 10.15.2 ), but does not compile on a remote running Ubuntu 16.04.6 LTS (which I do not have sudo on). I would be very thankful if anyone is able to point me in the right direction! See below for details.
R command
nig <- stan_model("code/nig.stan", auto_write=TRUE, verbose=TRUE)
nig.stan file
functions {
// inverse Gaussian log probability density function
real igauss_lpdf(real x, real phi, real lambda) {
return -log(2*pi())/2 + log(lambda)/2 - 3*log(x)/2
- lambda*square(x - phi)/(2*square(phi)*x);
}
// Jeffrey's log probability density (up to constant)
real jeffreys_lpdf(real x) {
return -3*log(x)/2;
}
}
data {
int<lower=1> p;
int<lower=1> n;
matrix[n, p] x;
vector[n] y;
vector<lower=0>[p] phi;
real<lower=0> lambdaf;
real<lower=0> chi;
real<lower=0> lambdad;
}
parameters {
vector[p] beta;
vector<lower=0>[p] gammasq;
real<lower=0> tausq;
real<lower=0> sigmasq;
}
transformed parameters {
vector<lower=0>[p] gamma = sqrt(gammasq);
real<lower=0> tau = sqrt(tausq);
real<lower=0> sigma = sqrt(sigmasq);
vector<lower=0>[p] betasd = sigma*gamma*tau;
// vector[n] mu;
// mu = x*beta;
}
model {
// priors
target += jeffreys_lpdf(sigmasq);
target += igauss_lpdf(tausq | chi, lambdad);
for(j in 1:p) {
target += igauss_lpdf(gammasq[j] | phi[j], lambdaf);
}
beta ~ normal(0., betasd);
// likelihood
y ~ normal(x*beta, sigma);
}
Console output
TRANSLATING MODEL 'nig' FROM Stan CODE TO C++ CODE NOW.
successful in parsing the Stan model 'nig'.
COMPILING THE C++ CODE FOR MODEL 'nig' NOW.
OS: x86_64, linux-gnu; rstan: 2.19.2; Rcpp: 1.0.3; inline: 0.3.15
>> setting environment variables:
PKG_LIBS = -L'/home/munchmm/Library/R/3.4.2/library/StanHeaders/lib/' -lStanHeaders
PKG_CPPFLAGS = -I"/home/munchmm/Library/R/3.4.2/library/Rcpp/include/" -I"/home/munchmm/Library/R/3.4.2/library/RcppEigen/include/" -I"/home/munchmm/Library/R/3.4.2/library/RcppEigen/include/unsupported" -I"/home/munchmm/Library/R/3.4.2/library/BH/include" -I"/home/munchmm/Library/R/3.4.2/library/StanHeaders/include/src/" -I"/home/munchmm/Library/R/3.4.2/library/StanHeaders/include/" -I"/home/munchmm/Library/R/3.4.2/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS
>> Program source :
*Omitted this because it was too long*
Compilation argument:
/usr/lib/R/bin/R CMD SHLIB file113954a1fa63a.cpp 2> file113954a1fa63a.cpp.err.txt
In file included from /home/munchmm/Library/R/3.4.2/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
from /home/munchmm/Library/R/3.4.2/library/BH/include/boost/shared_ptr.hpp:17,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/stan/math/prim/mat/fun/LDLT_factor.hpp:7,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/stan/math/prim/mat/err/check_ldlt_factor.hpp:6,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/stan/math/prim/mat.hpp:34,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/stan/math/rev/mat.hpp:12,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/stan/math.hpp:4,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/src/stan/model/model_header.hpp:4,
from file113954a1fa63a.cpp:8:
/home/munchmm/Library/R/3.4.2/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: 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++/5/bits/locale_conv.h:41:0,
from /usr/include/c++/5/locale:43,
from /home/munchmm/Library/R/3.4.2/library/BH/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
from /home/munchmm/Library/R/3.4.2/library/BH/include/boost/lexical_cast/detail/converter_lexical.hpp:54,
from /home/munchmm/Library/R/3.4.2/library/BH/include/boost/lexical_cast/try_lexical_convert.hpp:44,
from /home/munchmm/Library/R/3.4.2/library/BH/include/boost/lexical_cast.hpp:32,
from /home/munchmm/Library/R/3.4.2/library/BH/include/boost/math/tools/convert_from_string.hpp:15,
from /home/munchmm/Library/R/3.4.2/library/BH/include/boost/math/constants/constants.hpp:13,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/stan/math/prim/scal/fun/constants.hpp:4,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/stan/math/rev/core/operator_unary_plus.hpp:7,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/stan/math/rev/core.hpp:37,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/stan/math/rev/mat.hpp:4,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/stan/math.hpp:4,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/src/stan/model/model_header.hpp:4,
from file113954a1fa63a.cpp:8:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^
In file included from /home/munchmm/Library/R/3.4.2/library/BH/include/boost/shared_ptr.hpp:17:0,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/stan/math/prim/mat/fun/LDLT_factor.hpp:7,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/stan/math/prim/mat/err/check_ldlt_factor.hpp:6,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/stan/math/prim/mat.hpp:34,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/stan/math/rev/mat.hpp:12,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/stan/math.hpp:4,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/src/stan/model/model_header.hpp:4,
from file113954a1fa63a.cpp:8:
/home/munchmm/Library/R/3.4.2/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++/5/bits/locale_conv.h:41:0,
from /usr/include/c++/5/locale:43,
from /home/munchmm/Library/R/3.4.2/library/BH/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
from /home/munchmm/Library/R/3.4.2/library/BH/include/boost/lexical_cast/detail/converter_lexical.hpp:54,
from /home/munchmm/Library/R/3.4.2/library/BH/include/boost/lexical_cast/try_lexical_convert.hpp:44,
from /home/munchmm/Library/R/3.4.2/library/BH/include/boost/lexical_cast.hpp:32,
from /home/munchmm/Library/R/3.4.2/library/BH/include/boost/math/tools/convert_from_string.hpp:15,
from /home/munchmm/Library/R/3.4.2/library/BH/include/boost/math/constants/constants.hpp:13,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/stan/math/prim/scal/fun/constants.hpp:4,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/stan/math/rev/core/operator_unary_plus.hpp:7,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/stan/math/rev/core.hpp:37,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/stan/math/rev/mat.hpp:4,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/stan/math.hpp:4,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/src/stan/model/model_header.hpp:4,
from file113954a1fa63a.cpp:8:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^
In file included from /home/munchmm/Library/R/3.4.2/library/BH/include/boost/shared_ptr.hpp:17:0,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/stan/math/prim/mat/fun/LDLT_factor.hpp:7,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/stan/math/prim/mat/err/check_ldlt_factor.hpp:6,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/stan/math/prim/mat.hpp:34,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/stan/math/rev/mat.hpp:12,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/stan/math.hpp:4,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/src/stan/model/model_header.hpp:4,
from file113954a1fa63a.cpp:8:
/home/munchmm/Library/R/3.4.2/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++/5/bits/locale_conv.h:41:0,
from /usr/include/c++/5/locale:43,
from /home/munchmm/Library/R/3.4.2/library/BH/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
from /home/munchmm/Library/R/3.4.2/library/BH/include/boost/lexical_cast/detail/converter_lexical.hpp:54,
from /home/munchmm/Library/R/3.4.2/library/BH/include/boost/lexical_cast/try_lexical_convert.hpp:44,
from /home/munchmm/Library/R/3.4.2/library/BH/include/boost/lexical_cast.hpp:32,
from /home/munchmm/Library/R/3.4.2/library/BH/include/boost/math/tools/convert_from_string.hpp:15,
from /home/munchmm/Library/R/3.4.2/library/BH/include/boost/math/constants/constants.hpp:13,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/stan/math/prim/scal/fun/constants.hpp:4,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/stan/math/rev/core/operator_unary_plus.hpp:7,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/stan/math/rev/core.hpp:37,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/stan/math/rev/mat.hpp:4,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/stan/math.hpp:4,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/src/stan/model/model_header.hpp:4,
from file113954a1fa63a.cpp:8:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^
In file included from /home/munchmm/Library/R/3.4.2/library/BH/include/boost/shared_ptr.hpp:17:0,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/stan/math/prim/mat/fun/LDLT_factor.hpp:7,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/stan/math/prim/mat/err/check_ldlt_factor.hpp:6,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/stan/math/prim/mat.hpp:34,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/stan/math/rev/mat.hpp:12,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/stan/math.hpp:4,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/src/stan/model/model_header.hpp:4,
from file113954a1fa63a.cpp:8:
/home/munchmm/Library/R/3.4.2/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++/5/bits/locale_conv.h:41:0,
from /usr/include/c++/5/locale:43,
from /home/munchmm/Library/R/3.4.2/library/BH/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
from /home/munchmm/Library/R/3.4.2/library/BH/include/boost/lexical_cast/detail/converter_lexical.hpp:54,
from /home/munchmm/Library/R/3.4.2/library/BH/include/boost/lexical_cast/try_lexical_convert.hpp:44,
from /home/munchmm/Library/R/3.4.2/library/BH/include/boost/lexical_cast.hpp:32,
from /home/munchmm/Library/R/3.4.2/library/BH/include/boost/math/tools/convert_from_string.hpp:15,
from /home/munchmm/Library/R/3.4.2/library/BH/include/boost/math/constants/constants.hpp:13,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/stan/math/prim/scal/fun/constants.hpp:4,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/stan/math/rev/core/operator_unary_plus.hpp:7,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/stan/math/rev/core.hpp:37,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/stan/math/rev/mat.hpp:4,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/stan/math.hpp:4,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/src/stan/model/model_header.hpp:4,
from file113954a1fa63a.cpp:8:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^
In file included from /home/munchmm/Library/R/3.4.2/library/BH/include/boost/shared_ptr.hpp:17:0,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/stan/math/prim/mat/fun/LDLT_factor.hpp:7,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/stan/math/prim/mat/err/check_ldlt_factor.hpp:6,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/stan/math/prim/mat.hpp:34,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/stan/math/rev/mat.hpp:12,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/stan/math.hpp:4,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/src/stan/model/model_header.hpp:4,
from file113954a1fa63a.cpp:8:
/home/munchmm/Library/R/3.4.2/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++/5/bits/locale_conv.h:41:0,
from /usr/include/c++/5/locale:43,
from /home/munchmm/Library/R/3.4.2/library/BH/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
from /home/munchmm/Library/R/3.4.2/library/BH/include/boost/lexical_cast/detail/converter_lexical.hpp:54,
from /home/munchmm/Library/R/3.4.2/library/BH/include/boost/lexical_cast/try_lexical_convert.hpp:44,
from /home/munchmm/Library/R/3.4.2/library/BH/include/boost/lexical_cast.hpp:32,
from /home/munchmm/Library/R/3.4.2/library/BH/include/boost/math/tools/convert_from_string.hpp:15,
from /home/munchmm/Library/R/3.4.2/library/BH/include/boost/math/constants/constants.hpp:13,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/stan/math/prim/scal/fun/constants.hpp:4,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/stan/math/rev/core/operator_unary_plus.hpp:7,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/stan/math/rev/core.hpp:37,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/stan/math/rev/mat.hpp:4,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/stan/math.hpp:4,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/src/stan/model/model_header.hpp:4,
from file113954a1fa63a.cpp:8:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^
In file included from /home/munchmm/Library/R/3.4.2/library/BH/include/boost/shared_ptr.hpp:17:0,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/stan/math/prim/mat/fun/LDLT_factor.hpp:7,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/stan/math/prim/mat/err/check_ldlt_factor.hpp:6,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/stan/math/prim/mat.hpp:34,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/stan/math/rev/mat.hpp:12,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/stan/math.hpp:4,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/src/stan/model/model_header.hpp:4,
from file113954a1fa63a.cpp:8:
/home/munchmm/Library/R/3.4.2/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++/5/bits/locale_conv.h:41:0,
from /usr/include/c++/5/locale:43,
from /home/munchmm/Library/R/3.4.2/library/BH/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
from /home/munchmm/Library/R/3.4.2/library/BH/include/boost/lexical_cast/detail/converter_lexical.hpp:54,
from /home/munchmm/Library/R/3.4.2/library/BH/include/boost/lexical_cast/try_lexical_convert.hpp:44,
from /home/munchmm/Library/R/3.4.2/library/BH/include/boost/lexical_cast.hpp:32,
from /home/munchmm/Library/R/3.4.2/library/BH/include/boost/math/tools/convert_from_string.hpp:15,
from /home/munchmm/Library/R/3.4.2/library/BH/include/boost/math/constants/constants.hpp:13,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/stan/math/prim/scal/fun/constants.hpp:4,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/stan/math/rev/core/operator_unary_plus.hpp:7,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/stan/math/rev/core.hpp:37,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/stan/math/rev/mat.hpp:4,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/stan/math.hpp:4,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/src/stan/model/model_header.hpp:4,
from file113954a1fa63a.cpp:8:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^
In file included from /home/munchmm/Library/R/3.4.2/library/BH/include/boost/shared_ptr.hpp:17:0,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/stan/math/prim/mat/fun/LDLT_factor.hpp:7,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/stan/math/prim/mat/err/check_ldlt_factor.hpp:6,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/stan/math/prim/mat.hpp:34,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/stan/math/rev/mat.hpp:12,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/stan/math.hpp:4,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/src/stan/model/model_header.hpp:4,
from file113954a1fa63a.cpp:8:
/home/munchmm/Library/R/3.4.2/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>&&)’:
/home/munchmm/Library/R/3.4.2/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++/5/bits/locale_conv.h:41:0,
from /usr/include/c++/5/locale:43,
from /home/munchmm/Library/R/3.4.2/library/BH/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
from /home/munchmm/Library/R/3.4.2/library/BH/include/boost/lexical_cast/detail/converter_lexical.hpp:54,
from /home/munchmm/Library/R/3.4.2/library/BH/include/boost/lexical_cast/try_lexical_convert.hpp:44,
from /home/munchmm/Library/R/3.4.2/library/BH/include/boost/lexical_cast.hpp:32,
from /home/munchmm/Library/R/3.4.2/library/BH/include/boost/math/tools/convert_from_string.hpp:15,
from /home/munchmm/Library/R/3.4.2/library/BH/include/boost/math/constants/constants.hpp:13,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/stan/math/prim/scal/fun/constants.hpp:4,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/stan/math/rev/core/operator_unary_plus.hpp:7,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/stan/math/rev/core.hpp:37,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/stan/math/rev/mat.hpp:4,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/stan/math.hpp:4,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/src/stan/model/model_header.hpp:4,
from file113954a1fa63a.cpp:8:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^
In file included from /home/munchmm/Library/R/3.4.2/library/BH/include/boost/random/detail/integer_log2.hpp:19:0,
from /home/munchmm/Library/R/3.4.2/library/BH/include/boost/random/detail/int_float_pair.hpp:26,
from /home/munchmm/Library/R/3.4.2/library/BH/include/boost/random/exponential_distribution.hpp:27,
from /home/munchmm/Library/R/3.4.2/library/BH/include/boost/random/gamma_distribution.hpp:25,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/stan/math/prim/mat/prob/dirichlet_rng.hpp:5,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/stan/math/prim/mat.hpp:292,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/stan/math/rev/mat.hpp:12,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/stan/math.hpp:4,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/src/stan/model/model_header.hpp:4,
from file113954a1fa63a.cpp:8:
/home/munchmm/Library/R/3.4.2/library/BH/include/boost/pending/integer_log2.hpp: At global scope:
/home/munchmm/Library/R/3.4.2/library/BH/include/boost/pending/integer_log2.hpp:7:89: note: #pragma message: This header is deprecated. Use <boost/integer/integer_log2.hpp> instead.
In file included from /home/munchmm/Library/R/3.4.2/library/BH/include/boost/fusion/functional/invocation/detail/that_ptr.hpp:13:0,
from /home/munchmm/Library/R/3.4.2/library/BH/include/boost/fusion/functional/invocation/invoke.hpp:52,
from /home/munchmm/Library/R/3.4.2/library/BH/include/boost/fusion/functional/adapter/fused.hpp:17,
from /home/munchmm/Library/R/3.4.2/library/BH/include/boost/fusion/functional/generation/make_fused.hpp:13,
from /home/munchmm/Library/R/3.4.2/library/BH/include/boost/fusion/include/make_fused.hpp:11,
from /home/munchmm/Library/R/3.4.2/library/BH/include/boost/numeric/odeint/util/resize.hpp:28,
from /home/munchmm/Library/R/3.4.2/library/BH/include/boost/numeric/odeint/util/state_wrapper.hpp:26,
from /home/munchmm/Library/R/3.4.2/library/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:33,
from /home/munchmm/Library/R/3.4.2/library/BH/include/boost/numeric/odeint.hpp:25,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/stan/math/prim/arr/functor/integrate_ode_rk45.hpp:17,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/stan/math/prim/arr.hpp:46,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/stan/math/prim/mat.hpp:344,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/stan/math/rev/mat.hpp:12,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/stan/math.hpp:4,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/src/stan/model/model_header.hpp:4,
from file113954a1fa63a.cpp:8:
/home/munchmm/Library/R/3.4.2/library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
template<class T> T * get_pointer(std::auto_ptr<T> const& p)
^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
from /usr/include/c++/5/locale:43,
from /home/munchmm/Library/R/3.4.2/library/BH/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
from /home/munchmm/Library/R/3.4.2/library/BH/include/boost/lexical_cast/detail/converter_lexical.hpp:54,
from /home/munchmm/Library/R/3.4.2/library/BH/include/boost/lexical_cast/try_lexical_convert.hpp:44,
from /home/munchmm/Library/R/3.4.2/library/BH/include/boost/lexical_cast.hpp:32,
from /home/munchmm/Library/R/3.4.2/library/BH/include/boost/math/tools/convert_from_string.hpp:15,
from /home/munchmm/Library/R/3.4.2/library/BH/include/boost/math/constants/constants.hpp:13,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/stan/math/prim/scal/fun/constants.hpp:4,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/stan/math/rev/core/operator_unary_plus.hpp:7,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/stan/math/rev/core.hpp:37,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/stan/math/rev/mat.hpp:4,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/stan/math.hpp:4,
from /home/munchmm/Library/R/3.4.2/library/StanHeaders/include/src/stan/model/model_header.hpp:4,
from file113954a1fa63a.cpp:8:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^
Error in dyn.load(libLFile) :
unable to load shared object '/tmp/Rtmpg84wPg/file113957a2e6b6b.so':
/tmp/Rtmpg84wPg/file113957a2e6b6b.so: failed to map segment from shared object
R session info
R version 3.4.4 (2018-03-15)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.6 LTS
Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.6.0
LAPACK: /usr/lib/lapack/liblapack.so.3.6.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8
[4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] pkgbuild_1.0.3 Rcpp_1.0.3 inline_0.3.15 pInc_0.0.0.9000
[5] glmnet_2.0-16 Matrix_1.2-15 cambridge_0.0.0.9000 doParallel_1.0.14
[9] iterators_1.0.9 foreach_1.4.4 rstan_2.19.2 ggplot2_2.2.1
[13] StanHeaders_2.19.0
loaded via a namespace (and not attached):
[1] pillar_1.0.1 compiler_3.4.4 plyr_1.8.4 bitops_1.0-6
[5] prettyunits_1.0.2 tools_3.4.4 digest_0.6.18 memoise_1.1.0
[9] lattice_0.20-38 tibble_1.4.1 gtable_0.2.0 rlang_0.1.6
[13] cli_1.0.1 rstudioapi_0.7 yaml_2.1.13 mvtnorm_1.0-8
[17] loo_2.1.0 gridExtra_2.3 withr_2.1.2 caTools_1.17.1
[21] gtools_3.8.1 devtools_1.13.4 stats4_3.4.4 grid_3.4.4
[25] R6_2.4.0 processx_3.3.1 gdata_2.18.0 ROCR_1.0-7
[29] corpcor_1.6.9 callr_3.2.0 magrittr_1.5 gplots_3.0.1.1
[33] scales_1.0.0 ps_1.3.0 codetools_0.2-15 matrixStats_0.54.0
[37] assertthat_0.2.0 colorspace_1.4-0 KernSmooth_2.23-15 gsl_2.1-6
[41] lazyeval_0.2.1 munsell_0.5.0 crayon_1.3.4