Ulam() function causes error

Modeling
#1

Hi, I have some troubles running the code below (specifically the ulam() function).

library(rethinking)
data(Wines2012)
d <- Wines2012
dat_list <- list(
  S = standardize(d$score),
  jid = as.integer(d$judge),
  wid = as.integer(d$wine)
)

m1 <- ulam(
  alist(
    S ~ dnorm(mu, sigma),
    mu <- a[jid] + w[wid],
    a[jid] ~ dnorm(0, 0.5),
    w[wid] ~ dnorm(0, 0.5),
    sigma ~ dexp(1)
  ), data = dat_list, chains = 4, cores = 4
)

As soon as I try to run the ulam() function I get the following errors. I’ve tried to run it both in RStudios and VS Code. I have also tried reinstalling R and all the packages. Any help would be much appreciated.

Compiling Stan program…
INFO: Could not find files for the given pattern(s).

In file included from C:/rtools42/ucrt64/include/c++/12.2.0/stdlib.h:36,
from C:/rtools42/ucrt64/lib/gcc/x86_64-w64-mingw32/12.2.0/include/mm_malloc.h:27,
from C:/rtools42/ucrt64/lib/gcc/x86_64-w64-mingw32/12.2.0/include/xmmintrin.h:34,
from C:/rtools42/ucrt64/lib/gcc/x86_64-w64-mingw32/12.2.0/include/immintrin.h:31,
from …/tbb_2020.3/include/tbb/machine/gcc_itsx.h:57,
from …/tbb_2020.3/include/tbb/machine/gcc_ia32_common.h:107,
from …/tbb_2020.3/include/tbb/machine/gcc_generic.h:232,
from …/tbb_2020.3/include/tbb/tbb_machine.h:197,
from …/tbb_2020.3/src/tbbmalloc/Synchronize.h:20,
from …/tbb_2020.3/src/tbbmalloc/Customize.h:29,
from …/tbb_2020.3/src/tbbmalloc/TypeDefinitions.h:54,
from …/tbb_2020.3/src/tbbmalloc/tbbmalloc_internal.h:21,
from …/tbb_2020.3/src/tbbmalloc/backend.cpp:19:
C:/rtools42/ucrt64/include/c++/12.2.0/cstdlib:137:11: error: ‘at_quick_exit’ has not been declared in ‘::’
137 | using ::at_quick_exit;
| ^~~~~~~~~~~~~

C:/rtools42/ucrt64/include/c++/12.2.0/cstdlib:160:11: error: ‘quick_exit’ has not been declared in ‘::’
160 | using ::quick_exit;
| ^~~~~~~~~~
C:/rtools42/ucrt64/include/c++/12.2.0/stdlib.h:43:14: error: ‘at_quick_exit’ has not been declared in ‘std’
43 | using std::at_quick_exit;
| ^~~~~~~~~~~~~
C:/rtools42/ucrt64/include/c++/12.2.0/stdlib.h:46:14: error: ‘quick_exit’ has not been declared in ‘std’
46 | using std::quick_exit;
| ^~~~~~~~~~

cc1plus.exe: note: unrecognized command-line option ‘-Wno-unknown-warning-option’ may have been intended to silence earlier diagnostics

mingw32-make[1]: *** [C:/Users/Michael Dang/Documents/.cmdstan/cmdstan-2.30.1/stan/lib/stan_math/lib/tbb_2020.3/build/Makefile.tbbmalloc:65: backend.o] Error 1

mingw32-make: *** [stan/lib/stan_math/make/libraries:173: stan/lib/stan_math/lib/tbb/tbbmalloc.def] Error 2

Error: An error occured during compilation! See the message above for more information.

#2

You need some additional compiler flags for rtools42, see this post for the fix: Problem with cmdstan unpacking - #5 by andrjohns

#3

I followed the fix and managed to run the code and MCMC however, I still get some of the warnings and got some additional ones. Any suggestions on how to fix them, or should I just ignore it since I can run the ulam() function now?

The output now looks like this:

Compiling Stan program…
Warning in ‘C:/Users/MICHAE~1/AppData/Local/Temp/RtmpAtL0wo/model-2a885fff5a1f.stan’, line 3, column 4: Declaration
of arrays by placing brackets after a variable name is deprecated and
will be removed in Stan 2.32.0. Instead use the array keyword before the
type. This can be changed automatically using the auto-format flag to
stanc
Warning in ‘C:/Users/MICHAE~1/AppData/Local/Temp/RtmpAtL0wo/model-2a885fff5a1f.stan’, line 4, column 4: Declaration
of arrays by placing brackets after a variable name is deprecated and
will be removed in Stan 2.32.0. Instead use the array keyword before the
type. This can be changed automatically using the auto-format flag to
stanc

In file included from stan/lib/stan_math/lib/boost_1.78.0/boost/multi_array/multi_array_ref.hpp:32,
from stan/lib/stan_math/lib/boost_1.78.0/boost/multi_array.hpp:34,
from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint/algebra/multi_array_algebra.hpp:22,
from stan/lib/stan_math/lib/boost_1.78.0/boost/numeric/odeint.hpp:63,
from stan/lib/stan_math/stan/math/prim/functor/ode_rk45.hpp:9,
from stan/lib/stan_math/stan/math/prim/functor/integrate_ode_rk45.hpp:6,
from stan/lib/stan_math/stan/math/prim/functor.hpp:14,
from stan/lib/stan_math/stan/math/rev/fun.hpp:196,
from stan/lib/stan_math/stan/math/rev.hpp:10,
from stan/lib/stan_math/stan/math.hpp:19,
from stan/src/stan/model/model_header.hpp:4,
from C:/Users/MICHAE~1/AppData/Local/Temp/RtmpAtL0wo/model-2a885fff5a1f.hpp:3:
stan/lib/stan_math/lib/boost_1.78.0/boost/functional.hpp:180:45: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
180 | : public boost::functional::detail::unary_function<typename unary_traits::argument_type,bool>
| ^~~~~~~~~~~~~~

In file included from C:/rtools42/ucrt64/include/c++/12.2.0/string:48,
from C:/rtools42/ucrt64/include/c++/12.2.0/bits/locale_classes.h:40,
from C:/rtools42/ucrt64/include/c++/12.2.0/bits/ios_base.h:41,
from C:/rtools42/ucrt64/include/c++/12.2.0/ios:42,
from C:/rtools42/ucrt64/include/c++/12.2.0/istream:38,
from C:/rtools42/ucrt64/include/c++/12.2.0/sstream:38,
from C:/rtools42/ucrt64/include/c++/12.2.0/complex:45,
from stan/lib/stan_math/lib/eigen_3.3.9/Eigen/Core:96,
from stan/lib/stan_math/lib/eigen_3.3.9/Eigen/Dense:1,
from stan/lib/stan_math/stan/math/prim/fun/Eigen.hpp:22,
from stan/lib/stan_math/stan/math/rev.hpp:4:
C:/rtools42/ucrt64/include/c++/12.2.0/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
stan/lib/stan_math/lib/boost_1.78.0/boost/functional.hpp:214:45: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
214 | : public boost::functional::detail::binary_function<
| ^~~~~~~~~~~~~~~
C:/rtools42/ucrt64/include/c++/12.2.0/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
stan/lib/stan_math/lib/boost_1.78.0/boost/functional.hpp:252:45: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
252 | : public boost::functional::detail::unary_function<
| ^~~~~~~~~~~~~~
C:/rtools42/ucrt64/include/c++/12.2.0/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
stan/lib/stan_math/lib/boost_1.78.0/boost/functional.hpp:299:45: warning: ‘template<cl
ass _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
299 | : public boost::functional::detail::unary_function<
| ^~~~~~~~~~~~~~
C:/rtools42/ucrt64/include/c++/12.2.0/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~

stan/lib/stan_math/lib/boost_1.78.0/boost/functional.hpp:345:57: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
345 | class mem_fun_t : public boost::functional::detail::unary_function<T*, S>
| ^~~~~~~~~~~~~~
C:/rtools42/ucrt64/include/c++/12.2.0/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
stan/lib/stan_math/lib/boost_1.78.0/boost/functional.hpp:361:58: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
361 | class mem_fun1_t : public boost::functional::detail::binary_function<T*, A, S>
| ^~~~~~~~~~~~~~~
C:/rtools42/ucrt64/include/c++/12.2.0/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
stan/lib/stan_math/lib/boost_1.78.0/boost/functional.hpp:377:63: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
377 | class const_mem_fun_t : public boost::functional::detail::unary_function<const T*, S>
| ^~~~~~~~~~~~~~
C:/rtools42/ucrt64/include/c++/12.2.0/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
stan/lib/stan_math/lib/boost_1.78.0/boost/functional.hpp:393:64: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
393 | class const_mem_fun1_t : public boost::functional::detail::binary_function<const T*, A, S>
| ^~~~~~~~~~~~~~~
C:/rtools42/ucrt64/include/c++/12.2.0/bits/stl_function.h:131:12: note:
declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
stan/lib/stan_math/lib/boost_1.78.0/boost/functional.hpp:438:61: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
438 | class mem_fun_ref_t : public boost::functional::detail::unary_function<T&, S>
| ^~~~~~~~~~~~~~
C:/rtools42/ucrt64/include/c++/12.2.0/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
stan/lib/stan_math/lib/boost_1.78.0/boost/functional.hpp:454:62: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
454 | class mem_fun1_ref_t : public boost::functional::detail::binary_function<T&, A, S>
| ^~~~~~~~~~~~~~~
C:/rtools42/ucrt64/include/c++/12.2.0/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
stan/lib/stan_math/lib/boost_1.78.0/boost/functional.hpp:470:67: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
470 | class const_mem_fun_ref_t : public boost::functional::detail::unary_function<const T&, S>
| ^~~~~~~~~~~~~~
C:/rtools42/ucrt64/include/c++/12.2.0/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
stan/lib/stan_math/lib/boost_1.78.0/boost/functional.hpp:487:68: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
487 | class const_mem_fun1_ref_t : public boost::functional::detail::binary_function<const T&, A, S>
|
^~~~~~~~~~~~~~~
C:/rtools42/ucrt64/include/c++/12.2.0/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~

stan/lib/stan_math/lib/boost_1.78.0/boost/functional.hpp:533:73: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
533 | class pointer_to_unary_function : public boost::functional::detail::unary_function<Arg,Result>
| ^~~~~~~~~~~~~~
C:/rtools42/ucrt64/include/c++/12.2.0/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
stan/lib/stan_math/lib/boost_1.78.0/boost/functional.hpp:557:74: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
557 | class pointer_to_binary_function : public boost::functional::detail::binary_function<Arg1,Arg2,Result>
| ^~~~~~~~~~~~~~~
C:/rtools42/ucrt64/include/c++/12.2.0/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~

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#4

Yes, those warnings are all safe to ignore

#5

Okay, thanks for the help!