Error in compileCode(), Compilation ERROR, Warning message: In system(cmd, intern = !verbose) , Error in sink(type = "output")

Interfaces RStan
1

Hello people. I have a giant problem in Rstan that I believe is compiled. Before, the RStan program worked very well, but I don’t know if it was because of an update to the R packages (through Rstudio) that it started to give the problem.

First I will inform the configuration of my system.

sessionInfo()

R version 3.6.2 (2019-12-12)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 8.1 x64 (build 9600)

Matrix products: default

locale:
[1] LC_COLLATE=Portuguese_Brazil.1252 LC_CTYPE=Portuguese_Brazil.1252
[3] LC_MONETARY=Portuguese_Brazil.1252 LC_NUMERIC=C
[5] LC_TIME=Portuguese_Brazil.1252

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

other attached packages:
[1] rstan_2.19.3 ggplot2_3.3.0 StanHeaders_2.21.0-1

loaded via a namespace (and not attached):
[1] Rcpp_1.0.2 pillar_1.4.3 compiler_3.6.2 prettyunits_1.1.1 tools_3.6.2
[6] packrat_0.5.0 pkgbuild_1.0.6 lifecycle_0.2.0 tibble_2.1.3 gtable_0.3.0
[11] pkgconfig_2.0.3 rlang_0.4.5 cli_2.0.2 rstudioapi_0.11 parallel_3.6.2
[16] loo_2.2.0 gridExtra_2.3 withr_2.1.2 dplyr_0.8.5 stats4_3.6.2
[21] grid_3.6.2 tidyselect_0.2.5 glue_1.3.1 inline_0.3.15 R6_2.4.1
[26] processx_3.4.2 fansi_0.4.1 callr_3.4.2 purrr_0.3.2 magrittr_1.5
[31] scales_1.1.0 ps_1.3.2 matrixStats_0.55.0 assertthat_0.2.1 colorspace_1.4-1
[36] munsell_0.5.0 crayon_1.3.4

Now, I will explain how the error occurs. I simply run a model (indicated in RStan Getting Started https://github.com/stan-dev/rstan/wiki/RStan-Getting-Started) and it returns that error. I have already uninstalled R and Rstudio. reinstalled and searched the internet for similar errors but I can’t find a solution. I thank you for your attention.

Error in compileCode(f, code, language = language, verbose = verbose) :
Compilation ERROR, function(s)/method(s) not created! g++.exe: error: Zarzar/Documents/R/win-library/3.6/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp: No such file or directory
g++.exe: error: Zarzar/Documents/R/win-library/3.6/StanHeaders/include: No such file or directory
g++.exe: error: Zarzar/Documents/R/win-library/3.6/RcppEigen/include: No such file or directory
make: *** [C:/PROGRA~1/R/R-36~1.2/etc/x64/Makeconf:215: file223c26296dc5.o] Error 1
Além disso: Warning message:
In system(cmd, intern = !verbose) :
execução do comando ‘C:/PROGRA~1/R/R-36~1.2/bin/x64/R CMD SHLIB file223c26296dc5.cpp 2> file223c26296dc5.cpp.err.txt’ teve status 1
Error in sink(type = “output”) : conexão inválida

Please I need a very detailed guidance on what to do and how to do it on windows if it is something complicated.

Sincerely Carlos A. Zarzar

2

If you are going to use R 3.6 on Windows, then you need to install StanHeaders from source via

install.packages("StanHeaders", type = "source")
3

Yes @bgoodri, I have guaranteed that the package “StanHeaders” was installed. But the same error keeps showing up.

Error in compileCode(f, code, language = language, verbose = verbose) :
Compilation ERROR, function(s)/method(s) not created! g++.exe: error: Zarzar/Documents/R/win-library/3.6/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp: No such file or directory
g++.exe: error: Zarzar/Documents/R/win-library/3.6/StanHeaders/include: No such file or directory
g++.exe: error: Zarzar/Documents/R/win-library/3.6/RcppEigen/include: No such file or directory
make: *** [C:/PROGRA~1/R/R-36~1.2/etc/x64/Makeconf:215: file216c2f6ab0e.o] Error 1
Além disso: Warning message:
In system(cmd, intern = !verbose) :
execução do comando ‘C:/PROGRA~1/R/R-36~1.2/bin/x64/R CMD SHLIB file216c2f6ab0e.cpp 2> file216c2f6ab0e.cpp.err.txt’ teve status 1
Error in sink(type = “output”) : conexão inválida

sessionInfo()

R version 3.6.2 (2019-12-12)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 8.1 x64 (build 9600)

Matrix products: default

locale:
[1] LC_COLLATE=Portuguese_Brazil.1252 LC_CTYPE=Portuguese_Brazil.1252
[3] LC_MONETARY=Portuguese_Brazil.1252 LC_NUMERIC=C
[5] LC_TIME=Portuguese_Brazil.1252

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

other attached packages:
[1] rstan_2.19.3 ggplot2_3.3.0 StanHeaders_2.21.0-1

loaded via a namespace (and not attached):
[1] Rcpp_1.0.2 rstudioapi_0.11 magrittr_1.5 tidyselect_0.2.5 munsell_0.5.0
[6] colorspace_1.4-1 R6_2.4.1 rlang_0.4.5 fansi_0.4.1 dplyr_0.8.5
[11] tools_3.6.2 pkgbuild_1.0.6 parallel_3.6.2 grid_3.6.2 packrat_0.5.0
[16] gtable_0.3.0 loo_2.2.0 cli_2.0.2 withr_2.1.2 matrixStats_0.55.0
[21] assertthat_0.2.1 tibble_2.1.3 lifecycle_0.2.0 crayon_1.3.4 processx_3.4.2
[26] gridExtra_2.3 purrr_0.3.2 callr_3.4.2 ps_1.3.2 inline_0.3.15
[31] glue_1.3.1 compiler_3.6.2 pillar_1.4.3 scales_1.1.0 prettyunits_1.1.1
[36] stats4_3.6.2 pkgconfig_2.0.3

What else do you suggest? have you any idea what it might be?

Thank you very much for your attention.

4

Ah, you need the StanHeaders that goes with rstan 2.19

install.packages(
"https://cran.r-project.org/src/contrib/StanHeaders_2.19.2.tar.gz",
repos = NULL, type = "source")
5

Great @bgoodri. Thank you very much for your attention. Solved problem!