Error in compileCode

[IndrajeetPatil]

What am I doing wrong here?

# 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

``` r 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 -------------------------------------------------------------- #> package * version date lib #> abind 1.4-5 2016-07-21 [1] #> assertthat 0.2.0 2017-04-11 [1] #> 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] #> callr 3.1.1 2018-12-21 [1] #> cli 1.0.1.9000 2018-10-30 [1] #> coda 0.19-2 2018-10-08 [1] #> colorspace 1.3-2 2016-12-14 [1] #> colourpicker 1.0 2017-09-27 [1] #> crayon 1.3.4 2017-09-16 [1] #> crosstalk 1.0.0 2016-12-21 [1] #> desc 1.2.0 2018-10-30 [1] #> devtools 2.0.1 2018-10-26 [1] #> digest 0.6.18 2018-10-10 [1] #> dplyr 0.8.0 2019-01-06 [1] #> DT 0.5 2018-11-05 [1] #> dygraphs 1.1.1.6 2018-07-11 [1] #> evaluate 0.12 2018-10-09 [1] #> fs 1.2.6 2018-08-23 [1] #> ggplot2 * 3.1.0.9000 2018-12-15 [1] #> ggridges 0.5.1 2018-09-27 [1] #> glue 1.3.0 2018-07-17 [1] #> gridExtra 2.3 2017-09-09 [1] #> gtable 0.2.0 2016-02-26 [1] #> gtools 3.8.1 2018-06-26 [1] #> highr 0.7 2018-06-09 [1] #> htmltools 0.3.6 2017-04-28 [1] #> htmlwidgets 1.3 2018-09-30 [1] #> httpuv 1.4.5.1 2018-12-18 [1] #> igraph 1.2.2 2018-07-27 [1] #> inline 0.3.15 2018-05-18 [1] #> knitr 1.21 2018-12-10 [1] #> later 0.7.5 2018-09-18 [1] #> lattice 0.20-38 2018-11-04 [2] #> lazyeval 0.2.1 2017-10-29 [1] #> loo 2.0.0 2018-04-11 [1] #> magrittr 1.5 2014-11-22 [1] #> markdown 0.9 2018-12-07 [1] #> Matrix 1.2-15 2018-11-01 [1] #> matrixStats 0.54.0 2018-07-23 [1] #> memoise 1.1.0 2017-04-21 [1] #> mime 0.6 2018-10-05 [1] #> miniUI 0.1.1.1 2018-05-18 [1] #> munsell 0.5.0 2018-06-12 [1] #> mvtnorm 1.0-8 2018-05-31 [1] #> nlme 3.1-137 2018-04-07 [2] #> pillar 1.3.1 2018-12-15 [1] #> pkgbuild 1.0.2 2018-10-16 [1] #> pkgconfig 2.0.2 2018-08-16 [1] #> pkgload 1.0.2 2018-10-29 [1] #> plyr 1.8.4 2016-06-08 [1] #> prettyunits 1.0.2 2015-07-13 [1] #> processx 3.2.1 2018-12-05 [1] #> promises 1.0.1 2018-04-13 [1] #> ps 1.3.0 2018-12-21 [1] #> purrr 0.2.99.9000 2019-01-04 [1] #> R6 2.3.0 2018-10-04 [1] #> Rcpp * 1.0.0 2018-11-07 [1] #> remotes 2.0.2 2018-10-30 [1] #> reshape2 1.4.3 2017-12-11 [1] #> rlang 0.3.0.9002 2019-01-04 [1] #> rmarkdown 1.11 2018-12-08 [1] #> rprojroot 1.3-2 2018-01-03 [1] #> rsconnect 0.8.12 2018-12-05 [1] #> rstan * 2.18.2 2018-11-07 [1] #> rstantools 1.5.1 2018-08-22 [1] #> scales 1.0.0 2018-08-09 [1] #> sessioninfo 1.1.1 2018-11-05 [1] #> shiny 1.2.0 2018-11-02 [1] #> shinyjs 1.0 2018-01-08 [1] #> shinystan 2.5.0 2018-05-01 [1] #> shinythemes 1.1.2 2018-11-06 [1] #> StanHeaders * 2.18.0-1 2018-12-13 [1] #> stringi 1.2.4 2018-07-20 [1] #> stringr 1.3.1 2018-05-10 [1] #> testthat 2.0.1 2018-10-13 [1] #> threejs 0.3.1 2017-08-13 [1] #> tibble 2.0.0 2019-01-04 [1] #> tidyselect 0.2.5 2018-10-11 [1] #> usethis 1.4.0.9000 2018-12-12 [1] #> withr 2.1.2 2018-03-15 [1] #> xfun 0.4 2018-10-23 [1] #> xtable 1.8-3 2018-08-29 [1] #> xts 0.11-2 2018-11-05 [1] #> yaml 2.2.0 2018-07-25 [1] #> zoo 1.8-4 2018-09-19 [1] #> source #> CRAN (R 3.5.0) #> CRAN (R 3.5.1) #> CRAN (R 3.6.0) #> CRAN (R 3.5.0) #> CRAN (R 3.5.1) #> CRAN (R 3.5.1) #> CRAN (R 3.5.1) #> CRAN (R 3.5.1) #> CRAN (R 3.6.0) #> Github (r-lib/cli@56538e3) #> CRAN (R 3.5.1) #> CRAN (R 3.5.1) #> CRAN (R 3.5.1) #> CRAN (R 3.5.1) #> CRAN (R 3.5.1) #> Github (r-lib/desc@7c12d36) #> CRAN (R 3.5.1) #> CRAN (R 3.5.1) #> Github (tidyverse/dplyr@59d4600) #> CRAN (R 3.6.0) #> CRAN (R 3.5.1) #> CRAN (R 3.5.1) #> CRAN (R 3.5.1) #> Github (tidyverse/ggplot2@9292832) #> CRAN (R 3.5.1) #> CRAN (R 3.5.1) #> CRAN (R 3.5.1) #> CRAN (R 3.5.1) #> CRAN (R 3.5.0) #> CRAN (R 3.5.1) #> CRAN (R 3.5.1) #> CRAN (R 3.5.1) #> CRAN (R 3.6.0) #> CRAN (R 3.5.1) #> CRAN (R 3.5.1) #> CRAN (R 3.6.0) #> CRAN (R 3.5.1) #> CRAN (R 3.6.0) #> CRAN (R 3.5.1) #> CRAN (R 3.5.1) #> CRAN (R 3.5.1) #> CRAN (R 3.6.0) #> CRAN (R 3.5.1) #> CRAN (R 3.5.1) #> CRAN (R 3.5.1) #> CRAN (R 3.5.1) #> CRAN (R 3.5.1) #> CRAN (R 3.5.1) #> CRAN (R 3.5.0) #> CRAN (R 3.6.0) #> CRAN (R 3.6.0) #> CRAN (R 3.5.1) #> CRAN (R 3.5.1) #> CRAN (R 3.6.0) #> CRAN (R 3.5.1) #> CRAN (R 3.5.1) #> CRAN (R 3.6.0) #> CRAN (R 3.5.1) #> CRAN (R 3.6.0) #> Github (tidyverse/purrr@3b4a013) #> CRAN (R 3.5.1) #> CRAN (R 3.6.0) #> CRAN (R 3.6.0) #> CRAN (R 3.5.1) #> Github (r-lib/rlang@67ff440) #> CRAN (R 3.6.0) #> CRAN (R 3.5.1) #> CRAN (R 3.6.0) #> CRAN (R 3.5.1) #> CRAN (R 3.5.1) #> CRAN (R 3.5.1) #> CRAN (R 3.6.0) #> CRAN (R 3.5.1) #> CRAN (R 3.5.1) #> CRAN (R 3.5.1) #> CRAN (R 3.6.0) #> CRAN (R 3.6.0) #> CRAN (R 3.6.0) #> CRAN (R 3.5.1) #> CRAN (R 3.5.1) #> CRAN (R 3.5.1) #> Github (tidyverse/tibble@d06dd5c) #> CRAN (R 3.5.1) #> Github (r-lib/usethis@923dd75) #> CRAN (R 3.5.1) #> CRAN (R 3.6.0) #> CRAN (R 3.5.1) #> CRAN (R 3.6.0) #> CRAN (R 3.5.1) #> CRAN (R 3.5.2) #> #> [1] C:/Users/inp099/Documents/R/win-library/3.6 #> [2] C:/Program Files/R/R-devel/library ```

[IndrajeetPatil]

Shoot! Sorry, I was supposed to post this to brms repo, but posted it here accidently because I had multiple windows open.