What am I doing wrong here?
I have spent a lot of time going through old GitHub issues but haven’t really managed to get around this issue.
# setup
set.seed(123)
library(brms)
#> Loading required package: Rcpp
#> Loading required package: ggplot2
#> Registered S3 method overwritten by 'xts':
#> method from
#> as.zoo.xts zoo
#> Loading 'brms' package (version 2.7.0). Useful instructions
#> can be found by typing help('brms'). A more detailed introduction
#> to the package is available through vignette('brms_overview').
#> Run theme_set(theme_default()) to use the default bayesplot theme.
library(rstan)
#> Loading required package: StanHeaders
#> rstan (Version 2.18.2, GitRev: 2e1f913d3ca3)
#> For execution on a local, multicore CPU with excess RAM we recommend calling
#> options(mc.cores = parallel::detectCores()).
#> To avoid recompilation of unchanged Stan programs, we recommend calling
#> rstan_options(auto_write = TRUE)
#> For improved execution time, we recommend calling
#> Sys.setenv(LOCAL_CPPFLAGS = '-march=native')
#> although this causes Stan to throw an error on a few processors.
# check compilers
pkgbuild::has_rtools()
#> [1] TRUE
system('where make')
#> C:\Rtools\bin\make.exe
system('g++ -v')
#> Using built-in specs.
#> COLLECT_GCC=C:\Rtools\mingw_32\bin\G__~1.EXE
#> COLLECT_LTO_WRAPPER=C:/Rtools/mingw_32/bin/../libexec/gcc/i686-w64-mingw32/4.9.3/lto-wrapper.exe
#> Target: i686-w64-mingw32
#> Configured with: ../../../src/gcc-4.9.3/configure --host=i686-w64-mingw32 --build=i686-w64-mingw32 --target=i686-w64-mingw32 --prefix=/mingw32 --with-sysroot=/home/Jeroen/mingw-gcc-4.9.3/i686-493-posix-dwarf-rt_v3-s/mingw32 --with-gxx-include-dir=/mingw32/i686-w64-mingw32/include/c++ --enable-static --disable-shared --disable-multilib --enable-languages=c,c++,fortran,lto --enable-libstdcxx-time=yes --enable-threads=posix --enable-libgomp --enable-libatomic --enable-lto --enable-graphite --enable-checking=release --enable-fully-dynamic-string --enable-version-specific-runtime-libs --disable-sjlj-exceptions --with-dwarf2 --disable-isl-version-check --disable-cloog-version-check --disable-libstdcxx-pch --disable-libstdcxx-debug --enable-bootstrap --disable-rpath --disable-win32-registry --disable-nls --disable-werror --disable-symvers --with-gnu-as --with-gnu-ld --with-arch=i686 --with-tune=generic --with-libiconv --with-system-zlib --with-gmp=/home/Jeroen/mingw-gcc-4.9.3/prerequisites/i686-w64-mingw32-static --with-mpfr=/home/Jeroen/mingw-gcc-4.9.3/prerequisites/i686-w64-mingw32-static --with-mpc=/home/Jeroen/mingw-gcc-4.9.3/prerequisites/i686-w64-mingw32-static --with-isl=/home/Jeroen/mingw-gcc-4.9.3/prerequisites/i686-w64-mingw32-static --with-cloog=/home/Jeroen/mingw-gcc-4.9.3/prerequisites/i686-w64-mingw32-static --enable-cloog-backend=isl --with-pkgversion='i686-posix-dwarf, Built by MinGW-W64 project' --with-bugurl=http://sourceforge.net/projects/mingw-w64 CFLAGS='-O2 -pipe -I/home/Jeroen/mingw-gcc-4.9.3/i686-493-posix-dwarf-rt_v3-s/mingw32/opt/include -I/home/Jeroen/mingw-gcc-4.9.3/prerequisites/i686-zlib-static/include -I/home/Jeroen/mingw-gcc-4.9.3/prerequisites/i686-w64-mingw32-static/include' CXXFLAGS='-O2 -pipe -I/home/Jeroen/mingw-gcc-4.9.3/i686-493-posix-dwarf-rt_v3-s/mingw32/opt/include -I/home/Jeroen/mingw-gcc-4.9.3/prerequisites/i686-zlib-static/include -I/home/Jeroen/mingw-gcc-4.9.3/prerequisites/i686-w64-mingw32-static/include' CPPFLAGS= LDFLAGS='-pipe -L/home/Jeroen/mingw-gcc-4.9.3/i686-493-posix-dwarf-rt_v3-s/mingw32/opt/lib -L/home/Jeroen/mingw-gcc-4.9.3/prerequisites/i686-zlib-static/lib -L/home/Jeroen/mingw-gcc-4.9.3/prerequisites/i686-w64-mingw32-static/lib -Wl,--large-address-aware'
#> Thread model: posix
#> gcc version 4.9.3 (i686-posix-dwarf, Built by MinGW-W64 project)
# check toolchain
fx <-
inline::cxxfunction(
signature(x = "integer", y = "numeric") ,
'
return ScalarReal( INTEGER(x)[0] * REAL(y)[0] ) ;'
)
fx(2L, 5) # should be 10
#> [1] 10
# running model brms model
brms_crossedRE <-
brms::brm(
formula = mpg ~ wt + (1 | cyl) + (1 + wt | gear),
data = mtcars,
iter = 100,
chains = 2
)
#> Compiling the C++ model
#> Error in compileCode(f, code, language = language, verbose = verbose): Compilation ERROR, function(s)/method(s) not created! In file included from C:/Users/inp099/Documents/R/win-library/3.6/BH/include/boost/random/detail/integer_log2.hpp:19:0,
#> from C:/Users/inp099/Documents/R/win-library/3.6/BH/include/boost/random/detail/int_float_pair.hpp:26,
#> from C:/Users/inp099/Documents/R/win-library/3.6/BH/include/boost/random/exponential_distribution.hpp:27,
#> from C:/Users/inp099/Documents/R/win-library/3.6/BH/include/boost/random/gamma_distribution.hpp:25,
#> from C:/Users/inp099/Documents/R/win-library/3.6/StanHeaders/include/stan/math/prim/mat/prob/dirichlet_rng.hpp:5,
#> from C:/Users/inp099/Documents/R/win-library/3.6/StanHeaders/include/stan/math/prim/mat.hpp:276,
#> from C:/Users/inp099/Documents/R/win-library/3.6/StanHeaders/include/stan/math/rev/mat.hpp:12,
#> from C:/Users/inp099/Documents/R/win-library/3.6/StanHeaders/include/stan/math.hpp:4,
#> from C:/Users/inp099/Documents/R/win-library/3.6/StanHeaders/include/src/stan/model/model_header.hpp:4,
#> from file29b4531a2e9b.cpp:8:
#> C:/Users/inp099/Documents/R/win-library/3.6/BH/include/boost/pending/integer_log2.hpp:7:89: note: #pragma message: This header is deprecated. Use <boost/integer/integer_log2.hpp> instead.
#> BOOST_HEADER_DEPRECATED("<boost/integer/integer_log2.hpp>");
#> ^
#> C:/Users/inp099/Documents/R/win-library/3.6/StanHeaders/libs/x64/StanHeaders.dll: file not recognized: File format not recognized
#> collect2.exe: error: ld returned 1 exit status
#> Error in sink(type = "output"): invalid connection
Here is the traceback-
traceback()
21.
stop(paste("Compilation ERROR, function(s)/method(s) not created!",
paste(errmsg, collapse = "\n")))
20.
compileCode(f, code, language = language, verbose = verbose)
19.
cxxfunction(sig = sig, body = body, plugin = plugin, includes = includes,
settings = settings, ..., verbose = verbose)
18.
force(code)
17.
withr::with_path(rtools_path(), code)
16.
pkgbuild::with_build_tools(cxxfunction(sig = sig, body = body,
plugin = plugin, includes = includes, settings = settings,
..., verbose = verbose), required = rstan_options("required") &&
!identical(Sys.getenv("WINDOWS"), "TRUE") && !identical(Sys.getenv("R_PACKAGE_SOURCE"), ...
15.
cxxfunctionplus(signature(), body = paste(" return Rcpp::wrap(\"",
model_name, "\");", sep = ""), includes = inc, plugin = "rstan",
save_dso = save_dso | auto_write, module_name = paste("stan_fit4",
model_cppname, "_mod", sep = ""), verbose = verbose)
14.
.fun(model_code = .x1) at <text>#1
13.
eval(expr, envir, ...)
12.
eval(expr, envir, ...)
11.
eval2(call, envir = args, enclos = parent.frame())
10.
run(rstan::stan_model, stan_model_args)
9.
eval(expr, envir)
8.
eval(expr, envir)
7.
eval(expr, pf)
6.
eval(expr, pf)
5.
withVisible(eval(expr, pf))
4.
evalVis(expr)
3.
utils::capture.output(out <- eval(expr, envir), type = type,
...)
2.
eval_silent(run(rstan::stan_model, stan_model_args), silent = silence_stan_model,
type = "message")
1.
brms::brm(formula = mpg ~ wt + (1 | cyl) + (1 + wt | gear), data = mtcars,
iter = 500, chains = 2)
Created on 2019-01-08 by the reprex package (v0.2.1)
Session info
devtools::session_info()
#> - Session info ----------------------------------------------------------
#> setting value
#> version R Under development (unstable) (2018-11-30 r75724)
#> os Windows 10 x64
#> system x86_64, mingw32
#> ui RTerm
#> language (EN)
#> collate English_United States.1252
#> ctype English_United States.1252
#> tz Asia/Calcutta
#> date 2019-01-08
#>
#> - Packages --------------------------------------------------------------
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#> backports 1.1.3 2018-12-14 [1]
#> base64enc 0.1-3 2015-07-28 [1]
#> bayesplot 1.6.0 2018-08-02 [1]
#> bridgesampling 0.6-0 2018-10-21 [1]
#> brms * 2.7.0 2018-12-17 [1]
#> Brobdingnag 1.2-6 2018-08-13 [1]
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#> [1] C:/Users/inp099/Documents/R/win-library/3.6
#> [2] C:/Program Files/R/R-devel/library