R crashing with Rstan/brms

Interfaces RStan
1

Hello!

I have been running brms without issue for months until I recently updated my brms, rstan, and StanHeaders packages. Now some very simple models work but other models that are slightly more complex but that previously ran easily either make R crash or run in an infinite sampling loop that I must eventually stop. Strangely, the same model will produce either the infinite loop or crash R unreliably. In either case, there are no results.

The only errors that appear are “Warning message:
In system(paste(CXX, ARGS), ignore.stdout = TRUE, ignore.stderr = TRUE) :
‘C:/rtools40/usr/mingw_/bin/g++’ not found” which my googling has shown should not matter.

Apparently, this is somewhat common but none of the fixes I have seen have worked. I have unsuccessfully tried:

  1. checking my .R/Makevars file
  2. updating my r version
  3. checking that Rtools is on the PATH
  4. running example(stan_model, package = “rstan”, run.dontrun = TRUE)
    The result is a successful run with just the error above

Thank you for any help you can provide!

Here is an example of a model that did not work:

library(brms)
library(mice)

data(“iris”)

#add NAs
iris2 ← iris
iris2$Sepal.Length[5:10]<-NA
iris2$Petal.Length[15:30]<-NA

#Impute missing at random data
imp ← mice(iris2, m = 5, print = FALSE)

#model in which session aborted/loops

fitbrm8 ← brm_multiple(Sepal.Width ~ Sepal.Length+Petal.Length+(1+Sepal.Length+Petal.Length|Species*Petal.Width),
data = imp,
family = gaussian(),
prior = set_prior(“normal(0,5)”),
control = list(adapt_delta = 0.8),
warmup = 100, iter = 200, chains = 3,
cores = 3)

computer stats:

  • Output of writeLines(readLines(file.path(Sys.getenv("HOME"), ".R/Makevars")))
    CXX14FLAGS += -O3 -mtune=native -arch x86_64 -ftemplate-depth-256

  • Output of devtools::session_info("rstan")

  • Session info -----------------------------------------------------------------------
    setting value
    version R version 4.0.3 (2020-10-10)
    os Windows 10 x64
    system x86_64, mingw32
    ui RStudio
    language (EN)
    collate English_United States.1252
    ctype English_United States.1252
    tz America/Los_Angeles
    date 2020-12-18

  • Packages ---------------------------------------------------------------------------
    package * version date lib source
    assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.0.3)
    backports 1.2.1 2020-12-09 [1] CRAN (R 4.0.3)
    BH 1.72.0-3 2020-01-08 [1] CRAN (R 4.0.3)
    brio 1.1.0 2020-08-31 [1] CRAN (R 4.0.3)
    callr 3.5.1 2020-10-13 [1] CRAN (R 4.0.3)
    checkmate 2.0.0 2020-02-06 [1] CRAN (R 4.0.3)
    cli 2.2.0 2020-11-20 [1] CRAN (R 4.0.3)
    colorspace 2.0-0 2020-11-11 [1] CRAN (R 4.0.3)
    crayon 1.3.4 2017-09-16 [1] CRAN (R 4.0.3)
    curl 4.3 2019-12-02 [1] CRAN (R 4.0.3)
    desc 1.2.0 2018-05-01 [1] CRAN (R 4.0.3)
    diffobj 0.3.2 2020-10-05 [1] CRAN (R 4.0.3)
    digest 0.6.27 2020-10-24 [1] CRAN (R 4.0.3)
    ellipsis 0.3.1 2020-05-15 [1] CRAN (R 4.0.3)
    evaluate 0.14 2019-05-28 [1] CRAN (R 4.0.3)
    fansi 0.4.1 2020-01-08 [1] CRAN (R 4.0.3)
    farver 2.0.3 2020-01-16 [1] CRAN (R 4.0.3)
    ggplot2 3.3.2 2020-06-19 [1] CRAN (R 4.0.3)
    glue 1.4.2 2020-08-27 [1] CRAN (R 4.0.3)
    gridExtra 2.3 2017-09-09 [1] CRAN (R 4.0.3)
    gtable 0.3.0 2019-03-25 [1] CRAN (R 4.0.3)
    inline 0.3.17 2020-12-01 [1] CRAN (R 4.0.3)
    isoband 0.2.3 2020-12-01 [1] CRAN (R 4.0.3)
    jsonlite 1.7.2 2020-12-09 [1] CRAN (R 4.0.3)
    labeling 0.4.2 2020-10-20 [1] CRAN (R 4.0.3)
    lattice 0.20-41 2020-04-02 [2] CRAN (R 4.0.3)
    lifecycle 0.2.0 2020-03-06 [1] CRAN (R 4.0.3)
    loo 2.4.1 2020-12-09 [1] CRAN (R 4.0.3)
    magrittr 2.0.1 2020-11-17 [1] CRAN (R 4.0.3)
    MASS 7.3-53 2020-09-09 [2] CRAN (R 4.0.3)
    Matrix 1.2-18 2019-11-27 [2] CRAN (R 4.0.3)
    matrixStats 0.57.0 2020-09-25 [1] CRAN (R 4.0.3)
    mgcv 1.8-33 2020-08-27 [2] CRAN (R 4.0.3)
    munsell 0.5.0 2018-06-12 [1] CRAN (R 4.0.3)
    nlme 3.1-149 2020-08-23 [2] CRAN (R 4.0.3)
    pillar 1.4.7 2020-11-20 [1] CRAN (R 4.0.3)
    pkgbuild 1.2.0 2020-12-15 [1] CRAN (R 4.0.3)
    pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.0.3)
    pkgload 1.1.0 2020-05-29 [1] CRAN (R 4.0.3)
    praise 1.0.0 2015-08-11 [1] CRAN (R 4.0.3)
    prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.0.3)
    processx 3.4.5 2020-11-30 [1] CRAN (R 4.0.3)
    ps 1.5.0 2020-12-05 [1] CRAN (R 4.0.3)
    R6 2.5.0 2020-10-28 [1] CRAN (R 4.0.3)
    RColorBrewer 1.1-2 2014-12-07 [1] CRAN (R 4.0.3)
    Rcpp 1.0.5 2020-07-06 [1] CRAN (R 4.0.3)
    RcppEigen 0.3.3.9.1 2020-12-17 [1] CRAN (R 4.0.3)
    RcppParallel 5.0.2 2020-06-24 [1] CRAN (R 4.0.3)
    rematch2 2.1.2 2020-05-01 [1] CRAN (R 4.0.3)
    rlang 0.4.9 2020-11-26 [1] CRAN (R 4.0.3)
    rprojroot 2.0.2 2020-11-15 [1] CRAN (R 4.0.3)
    rstan 2.21.2 2020-07-27 [1] CRAN (R 4.0.3)
    rstudioapi 0.13 2020-11-12 [1] CRAN (R 4.0.3)
    scales 1.1.1 2020-05-11 [1] CRAN (R 4.0.3)
    StanHeaders 2.21.0-7 2020-12-17 [1] CRAN (R 4.0.3)
    testthat 3.0.1 2020-12-17 [1] CRAN (R 4.0.3)
    tibble 3.0.4 2020-10-12 [1] CRAN (R 4.0.3)
    utf8 1.1.4 2018-05-24 [1] CRAN (R 4.0.3)
    V8 3.4.0 2020-11-04 [1] CRAN (R 4.0.3)
    vctrs 0.3.6 2020-12-17 [1] CRAN (R 4.0.3)
    viridisLite 0.3.0 2018-02-01 [1] CRAN (R 4.0.3)
    waldo 0.2.3 2020-11-09 [1] CRAN (R 4.0.3)
    withr 2.3.0 2020-09-22 [1] CRAN (R 4.0.3)

[1] C:/Users/karen/OneDrive/Documents/R/win-library/4.0
[2] C:/Program Files/R/R-4.0.3/library

2

When it comes to Windows issues I’ve never seen @andrjohns fail to help!

2 Likes
3

Unfortunately I’m not able to replicate the crashes on a Windows 10 machine. I see that your home directory is a OneDrive folder, do you get the same crashes if you disable/pause syncing before running the model?

Do you get the same crashes if you run brms with backend="cmdstanr"?

1 Like
4

Thank you so much for taking a look at this @andrjohns!

When I tried your first suggestion of pausing OneDrive the infinite loop persisted.

BUT I think we may have found the issue with your second suggestion. When I put backend=“cmdstanr” into the brms equations got the following error.

“Error: Please install the ‘cmdstanr’ package.”

When I tried to install the package, I got the following error:

"Warning in install.packages :

  • package ‘cmdstanr’ is not available for this version of R*

A version of this package for your version of R might be available elsewhere,
see the ideas at
https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages"

I did not find anything on the web page regarding this package.

5

It’s not available from CRAN (yet), but you can use the instructions in this article to install cmdstanr and cmdstan itself:

1 Like
6

Thanks for the instructions. When I followed the instructions above I ran

check_cmdstan_toolchain()
and I got
The CmdStan toolchain is setup properly!

but when I tried to set up the path, I couldn’t set the path because in the cmdstanr folder there was no cmdstan-[version] file.

CmdStan path set to: C:/Users/karen/OneDrive/Documents/R/win-library/4.0/cmdstanr
warning message:
Can’t find CmdStan makefile to detect version number. Path may not point to valid installation.

Thoughts? Thanks!

7

Hmm, were you able to succssfully run install_cmdstan()?

8

When I just reinstalled it the warning message. I was able to get the correct path now though for cmdstanr-[version]:.

tar.exe: could not chdir to ‘C:/Users/karen/OneDrive/Documents/.cmdstanr/cmdstan-2.25.0’
Error: Problem extracting tarball. Exited with return code: 1
In addition: Warning message:
In utils::untar(dest_file, exdir = dir_cmdstan, extras = “–strip-components 1”) :
‘tar.exe -xf “C:\Users\karen\OneDrive\Documents/.cmdstanr/cmdstan-2.25.0.tar.gz” -C “C:/Users/karen/OneDrive/Documents/.cmdstanr/cmdstan-2.25.0” --strip-components 1’ returned error code 1

9

Thanks for sharing the error message. @rok_cesnovar Have you seen this before? Looks like an error extracting the cmdstan tarball on Windows (although I’m not sure if it’s Windows or something else that’s the problem).

10

I have not seen this one before. To me it seems like permission issues. If not, then a wild guess is no space on the disk?

@KAtkin can you try

file.access("C:/Users/karen/OneDrive/Documents/", mode = 2)
file.access("C:/Users/karen/OneDrive/Documents/.cmdstanr", mode = 2)

Thanks.

1 Like
11

Could the original issue (not the installation issues) be related to this issue when compiling the same model a second time?

12

Hello,

Thank you all for your continuing help.

When I tried what @rok_cesnovar suggested I got the following:

  • file.access(“C:/Users/karen/OneDrive/Documents/”, mode = 2)
    C:/Users/karen/OneDrive/Documents/
    0

  • file.access(“C:/Users/karen/OneDrive/Documents/.cmdstanr”, mode = 2)
    C:/Users/karen/OneDrive/Documents/.cmdstanr
    0
    As I understand it “0” means I have access so I moved on.

  • I was correct in that I didn’t have much space on my drive. Thus, I cleared it out and tried to run install_cmdstan() again. I got the new error below:

task.o: duplicate section .rdata$_ZTIN3tbb4taskE[_ZTIN3tbb4taskE]' has different size arena.o: duplicate section .rdata$_ZTIN3tbb4taskE[_ZTIN3tbb4taskE]’ has different size
scheduler.o: duplicate section `.rdata$_ZTIN3tbb4taskE[_ZTIN3tbb4taskE]’ has different size
mingw32-make[1]: Leaving directory ‘C:/Users/karen/OneDrive/Documents/.cmdstanr/cmdstan-2.25.0/stan/lib/stan_math/lib/tbb’

I also tried to replicate the multiple runs situation that @andrewdolman suggested and couldn’t get out = do.call(brm,test_brm) to work even the first time. Perhaps this is something unrelated though. I included the error below.

  • out = do.call(brm,test_brm)
    Error in rbind(deparse.level, …) :
    numbers of columns of arguments do not match

13

You can ignore this. This is just info when builiding cmdstan. Everything should work.

14

Woohoo! I successfully ran the model that originally crashed r.

Thank you so much to @torkar, @andrjohns, @jonah, @rok_cesnovar, and @andrewdolman for all of your help!

Have a happy New Year!

2 Likes