Compile error

General
1

Hi stan users,

I installed the rstan 2.18.2 following the instructions. However, there are always errors when compiling.

Error in compileCode(f, code, language = language, verbose = verbose) :
Compilation ERROR, function(s)/method(s) not created! In file included from C:/Program Files/R/R-3.5.3/library/BH/include/boost/random/detail/integer_log2.hpp:19:0,
from C:/Program Files/R/R-3.5.3/library/BH/include/boost/random/detail/int_float_pair.hpp:26,
from C:/Program Files/R/R-3.5.3/library/BH/include/boost/random/exponential_distribution.hpp:27,
from C:/Program Files/R/R-3.5.3/library/BH/include/boost/random/gamma_distribution.hpp:25,
from C:/Program Files/R/R-3.5.3/library/StanHeaders/include/stan/math/prim/mat/prob/dirichlet_rng.hpp:5,
from C:/Program Files/R/R-3.5.3/library/StanHeaders/include/stan/math/prim/mat.hpp:276,
from C:/Program Files/R/R-3.5.3/library/StanHeaders/include/stan/math/rev/mat.hpp:12,
from C:/Program Files/R/R-3.5.3/library/StanHeaders/include/stan/math.hpp:4,
from C:/Program Files/R/R-3.5.3/library/StanHeaders
In addition: Warning message:
In system(cmd, intern = !verbose) :
running command ‘C:/PROGRA~1/R/R-35~1.3/bin/x64/R CMD SHLIB file15cc6e2f1671.cpp 2> file15cc6e2f1671.cpp.err.txt’ had status 1
Error in sink(type = “output”) : invalid connection

How can I fix this problem?

Thanks.

2

If you do something like

stancode <- 'data {real y_mean;} parameters {real y;} model {y ~ normal(y_mean,1);}'
mod <- stan_model(model_code = stancode, verbose = TRUE)

what is the string surrounding the word error: (with the colon) in the output?

3

Thanks for your reply. I removed the following steps and it can run successfully.
Sys.setenv(LOCAL_CPPFLAGS = ‘-march=native’)
options(mc.cores = parallel::detectCores())

4

I have the exact same error under Red Hat 7. The error message when running the suggested code is:

Error in compileCode(f, code, language = language, verbose = verbose) :
Compilation ERROR, function(s)/method(s) not created! In file included from /ext/home/ericiulescua/R/x86_64-redhat-linux-gnu-library/3.5/BH/include/boost/random/detail/integer_log2.hpp:19:0,
from /ext/home/ericiulescua/R/x86_64-redhat-linux-gnu-library/3.5/BH/include/boost/random/detail/int_float_pair.hpp:26,
from /ext/home/ericiulescua/R/x86_64-redhat-linux-gnu-library/3.5/BH/include/boost/random/exponential_distribution.hpp:27,
from /ext/home/ericiulescua/R/x86_64-redhat-linux-gnu-library/3.5/BH/include/boost/random/gamma_distribution.hpp:25,
from /ext/home/ericiulescua/R/x86_64-redhat-linux-gnu-library/3.5/StanHeaders/include/stan/math/prim/mat/prob/dirichlet_rng.hpp:5,
from /ext/home/ericiulescua/R/x86_64-redhat-linux-gnu-library/3.5/StanHeaders/include/stan/math/prim/mat.hpp:292,
from /ext/home/ericiulescua/R/x86_64-redhat-linux-gnu-library/3.5/StanHeaders/include/stan/m

It can’t find the headers. I have the following session info:

R version 3.5.2 (2018-12-20)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: OpenShift Enterprise

Matrix products: default
BLAS/LAPACK: /usr/lib64/R/lib/libRblas.so

locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8
[4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] rstan_2.18.2 StanHeaders_2.18.1-10 ggplot2_3.2.0

loaded via a namespace (and not attached):
[1] Rcpp_1.0.1 rstudioapi_0.10 magrittr_1.5 tidyselect_0.2.5
[5] munsell_0.5.0 colorspace_1.4-1 R6_2.4.0 rlang_0.4.0
[9] dplyr_0.8.1 tools_3.5.2 parallel_3.5.2 pkgbuild_1.0.3
[13] grid_3.5.2 gtable_0.3.0 loo_2.1.0 cli_1.1.0
[17] withr_2.1.2 matrixStats_0.54.0 yaml_2.2.0 lazyeval_0.2.2
[21] assertthat_0.2.1 tibble_2.1.3 crayon_1.3.4 processx_3.4.0
[25] gridExtra_2.3 callr_3.3.0 purrr_0.3.2 ps_1.3.0
[29] inline_0.3.15 glue_1.3.1 compiler_3.5.2 pillar_1.4.2
[33] prettyunits_1.0.2 scales_1.0.0 stats4_3.5.2 pkgconfig_2.0.2

5

Any new on this topic? I have the same problem in RH7

6

I think this has been made into a GitHub issue here: https://github.com/stan-dev/rstan/issues/666

7

We need a verbose = TRUE when you call stan or sampling to see what it tries to compile and why it fails to find the libraries correctly.

8

Here in early 2021, the solution for me was to update to the most recent version of R. Details on that can be found here Install/Update R & RStudio