Compilation error

Interfaces RStan
1

Hello everyone.

I’m trying to set up rstan, for use with brms. Despite following instructions, and reinstalling several times, I can’t even get the example() to run.

I’m on Windows 10
I have Microsoft R Open 4.0.2, in RStudio 2021.09.2 Build 382
RTools 4.0 is working
I installed rstan, StanHeaders, Rcpp, RcppEigen, RcppParallel, BH using install.packages(“package name”, source = TRUE, dependencies = TRUE)

writeLines(readLines(file.path(Sys.getenv(“HOME”), “.R/Makevars”))) results in
Error in file(con, “r”) : cannot open the connection
In addition: Warning message:
In file(con, “r”) :
cannot open file ‘C:/Users/lewis/Documents/.R/Makevars’: No such file or directory

I had created a Makevars.win file in ~/.R as instructed, which is still there, containing a blank new line then
CXX14FLAGS += -mtune=native -O3 -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2

There’s no difference after renaming it to Makevars (no extension)

devtools::session_info(“rstan”)

  • Session info ------------------------------------------------------------------------------------
    setting value
    version R version 4.0.2 (2020-06-22)
    os Windows 10 x64
    system x86_64, mingw32
    ui RStudio
    language (EN)
    collate English_United Kingdom.1252
    ctype English_United Kingdom.1252
    tz Australia/Darwin
    date 2022-02-06

  • Packages ----------------------------------------------------------------------------------------
    package * version date lib source
    backports 1.1.10 2020-09-15 [1] CRAN (R 4.0.2)
    BH 1.78.0-0 2021-12-15 [1] CRAN (R 4.0.2)
    callr 3.6.0 2021-03-28 [1] CRAN (R 4.0.4)
    checkmate 2.0.0 2020-02-06 [1] CRAN (R 4.0.2)
    cli 2.4.0 2021-04-05 [1] CRAN (R 4.0.5)
    colorspace 1.4-1 2019-03-18 [1] CRAN (R 4.0.2)
    crayon 1.4.1 2021-02-08 [1] CRAN (R 4.0.5)
    desc 1.3.0 2021-03-05 [1] CRAN (R 4.0.5)
    digest 0.6.25 2020-02-23 [1] CRAN (R 4.0.2)
    ellipsis 0.3.1 2020-05-15 [1] CRAN (R 4.0.2)
    fansi 0.4.1 2020-01-08 [1] CRAN (R 4.0.2)
    farver 2.0.3 2020-01-16 [1] CRAN (R 4.0.2)
    ggplot2 * 3.3.3 2020-12-30 [1] CRAN (R 4.0.5)
    glue 1.4.2 2020-08-27 [1] CRAN (R 4.0.2)
    gridExtra 2.3 2017-09-09 [1] CRAN (R 4.0.2)
    gtable 0.3.0 2019-03-25 [1] CRAN (R 4.0.2)
    inline 0.3.17 2020-12-01 [1] CRAN (R 4.0.5)
    isoband 0.2.4 2021-03-03 [1] CRAN (R 4.0.5)
    labeling 0.4.2 2020-10-20 [1] CRAN (R 4.0.3)
    lattice 0.20-41 2020-04-02 [2] CRAN (R 4.0.2)
    lifecycle 1.0.0 2021-02-15 [1] CRAN (R 4.0.5)
    loo 2.4.1 2020-12-09 [1] CRAN (R 4.0.5)
    magrittr 2.0.1 2020-11-17 [1] CRAN (R 4.0.5)
    MASS 7.3-53.1 2021-02-12 [1] CRAN (R 4.0.5)
    Matrix 1.2-18 2019-11-27 [1] CRAN (R 4.0.3)
    matrixStats 0.58.0 2021-01-29 [1] CRAN (R 4.0.5)
    mgcv 1.8-34 2021-02-16 [1] CRAN (R 4.0.5)
    munsell 0.5.0 2018-06-12 [1] CRAN (R 4.0.2)
    nlme 3.1-152 2021-02-04 [1] CRAN (R 4.0.5)
    pillar 1.4.6 2020-07-10 [1] CRAN (R 4.0.2)
    pkgbuild 1.2.0 2020-12-15 [1] CRAN (R 4.0.5)
    pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.0.2)
    prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.0.2)
    processx 3.5.1 2021-04-04 [1] CRAN (R 4.0.5)
    ps 1.6.0 2021-02-28 [1] CRAN (R 4.0.5)
    R6 2.5.0 2020-10-28 [1] CRAN (R 4.0.5)
    RColorBrewer 1.1-2 2014-12-07 [1] CRAN (R 4.0.0)
    Rcpp 1.0.8 2022-01-13 [1] CRAN (R 4.0.5)
    RcppEigen 0.3.3.9.1 2020-12-17 [1] CRAN (R 4.0.5)
    RcppParallel 5.0.2 2020-06-24 [1] CRAN (R 4.0.2)
    rlang 0.4.10 2020-12-30 [1] CRAN (R 4.0.5)
    rprojroot 2.0.2 2020-11-15 [1] CRAN (R 4.0.5)
    rstan * 2.21.3 2021-12-19 [1] CRAN (R 4.0.2)
    scales 1.1.1 2020-05-11 [1] CRAN (R 4.0.2)
    StanHeaders * 2.21.0-7 2020-12-17 [1] CRAN (R 4.0.5)
    tibble 3.0.4 2020-10-12 [1] CRAN (R 4.0.2)
    utf8 1.1.4 2018-05-24 [1] CRAN (R 4.0.2)
    vctrs 0.3.7 2021-03-29 [1] CRAN (R 4.0.5)
    viridisLite 0.4.0 2021-04-13 [1] CRAN (R 4.0.2)
    withr 2.4.1 2021-01-26 [1] CRAN (R 4.0.5)

[1] C:/Users/lewis/Documents/R/win-library/4.0
[2] C:/Program Files/Microsoft/R Open/R-4.0.2/library

Compilation ERROR, function(s)/method(s) not created!
Error in compileCode(f, code, language = language, verbose = verbose) : 
  C:/rtools40/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/8.3.0/../../../../x86_64-w64-mingw32/bin/ld.exe: file890d2891.o:file890d2891.cpp:(.text$_ZN3tbb8internal26task_scheduler_observer_v3D0Ev[_ZN3tbb8internal26task_scheduler_observer_v3D0Ev]+0x1c): undefined reference to `tbb::internal::task_scheduler_observer_v3::observe(bool)'C:/rtools40/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/8.3.0/../../../../x86_64-w64-mingw32/bin/ld.exe: file890d2891.o:file890d2891.cpp:(.text$_ZN3tbb10interface623task_scheduler_observerD0Ev[_ZN3tbb10interface623task_scheduler_observerD0Ev]+0x1c): undefined reference to `tbb::internal::task_scheduler_observer_v3::observe(bool)'C:/rtools40/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/8.3.0/../../../../x86_64-w64-mingw32/bin/ld.exe: file890d2891.o:file890d2891.cpp:(.text$_ZN3tbb10interface623task_scheduler_observerD0Ev[_ZN3tbb10interface623task_scheduler_observerD0Ev]+0x37): undefined reference to `tbb::internal::task_scheduler_observer_v3::observe(bool)'C:/

traceback() gives:
13: stop(tail(errmsg))
12: compileCode(f, code, language = language, verbose = verbose)
11: cxxfunction(sig = sig, body = body, plugin = plugin, includes = includes,
settings = settings, …, verbose = verbose)
10: force(code)
9: withr::with_path(rtools_path(), code)
8: 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”),
“”))
7: 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)
6: stan_model(model_code = stancode, verbose = TRUE) at Rex8903be3557f#9
5: eval(ei, envir)
4: eval(ei, envir)
3: withVisible(eval(ei, envir))
2: source(tf, local, echo = echo, prompt.echo = paste0(prompt.prefix,
getOption(“prompt”)), continue.echo = paste0(prompt.prefix,
getOption(“continue”)), verbose = verbose, max.deparse.length = Inf,
encoding = “UTF-8”, skip.echo = skips, keep.source = TRUE)
1: example(stan_model, package = “rstan”, run.dontrun = TRUE)

I’m stumped.

2

The error here is not with your Makevars. Unfortunately R Open has some compatibility issues with the current rstan.

If you’re aiming to use brms, I’d recommend installing cmdstanr: Getting started with CmdStanR • cmdstanr

and using the brms option backend="cmdstanr"

3

Thanks, much more promising:

All 4 chains finished successfully.
Mean chain execution time: 5.9 seconds.
Total execution time: 24.4 seconds.

Just one error that’s hard to resolve:

Error in loadNamespace(name) : there is no package called ‘posterior’

Difficult to install posterior for some reason:
Error: object ‘format_glimpse’ is not exported by ‘namespace:pillar’
Execution halted
ERROR: lazy loading failed for package ‘posterior’

  • removing ‘C:/Users/lewis/Documents/R/win-library/4.0/posterior’
    Warning in install.packages :
    installation of package ‘C:/Users/lewis/Desktop/posterior_1.2.0.tar.gz’ had non-zero exit status

Am I going about the lack of posterior wrong?

4

Try reinstalling the pillar package and then installing the posterior package again, that might fix it

5

Aaaahhh. That’s better. Success. Thanks very much, the first brms vignette is working.

1 Like