Rstan

mesudell · January 18, 2021, 11:57am

Short summary of the problem:

I’ve been away from my computer and rstan for a period of leave, and on returning coding files that did work now no longer work. I’m finding a few posts that seem similar to my problem (Rstan on Windows - #80 by graham), but the fixes in the posts don’tseem to work (I’m aware i seem to be experiencing this problem a few months later than most?)

I’ve tried re-installing rstan, but it doesnt seem to help. If i run the below example, i get the following error:

example(stan_model, package = "rstan", run.dontrun = TRUE)


Compilation ERROR, function(s)/method(s) not created!
Error in compileCode(f, code, language = language, verbose = verbose) : 
  C:/RBuildTools/4.0/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/8.3.0/../../../../x86_64-w64-mingw32/bin/ld.exe: C:/Users/mesudell/Documents/R/win-library/4.0/rstan/lib/x64/libStanServices.a(stan_fit.o):stan_fit.cpp:(.rdata$_ZZN5boost4math6detail9bessel_j0IeEET_S3_E2P1[_ZZN5boost4math6detail9bessel_j0IeEET_S3_E2P1]+0x0): multiple definition of `boost::math::detail::bessel_j0<long double>(long double)::P1'; file407467ba4bd2.o:file407467ba4bd2.cpp:(.data$_ZZN5boost4math6detail9bessel_j0IeEET_S3_E2P1[_ZZN5boost4math6detail9bessel_j0IeEET_S3_E2P1]+0x0): first defined hereC:/RBuildTools/4.0/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/8.3.0/../../../../x86_64-w64-mingw32/bin/ld.exe: C:/Users/mesudell/Documents/R/win-library/4.0/rstan/lib/x64/libStanServices.a(stan_fit.o):stan_fit.cpp:(.rdata$_ZZN5boost4math6detail9bessel_j0IeEET_S3_E2QC[_ZZN5boost4math6detail9bessel_j0IeEET_S3_E2QC]+0x0): multiple definition of `boost::math::detail::bessel_j0<long double>(long double)::QC'; file407467ba
In addition: Warning message:
In system(paste(CXX, ARGS), ignore.stdout = TRUE, ignore.stderr = TRUE) :
  '-E' not found

Session info:

R version 4.0.2 (2020-06-22)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 17134)

Matrix products: default

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

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

other attached packages:
[1] joineR_1.2.5         survival_3.1-12      rstan_2.21.2         ggplot2_3.3.2        StanHeaders_2.21.0-7

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.5         pillar_1.4.6       compiler_4.0.2     prettyunits_1.1.1  tools_4.0.2        statmod_1.4.34    
 [7] pkgbuild_1.1.0     nlme_3.1-148       lattice_0.20-41    jsonlite_1.7.1     lifecycle_0.2.0    tibble_3.0.3      
[13] gtable_0.3.0       pkgconfig_2.0.3    rlang_0.4.7        Matrix_1.2-18      cli_2.0.2          rstudioapi_0.11   
[19] parallel_4.0.2     curl_4.3           loo_2.3.1          gridExtra_2.3      withr_2.2.0        dplyr_1.0.2       
[25] generics_0.0.2     vctrs_0.3.4        stats4_4.0.2       grid_4.0.2         tidyselect_1.1.0   glue_1.4.2        
[31] inline_0.3.16      R6_2.4.1           processx_3.4.4     fansi_0.4.1        callr_3.4.4        purrr_0.3.4       
[37] magrittr_1.5       splines_4.0.2      codetools_0.2-16   matrixStats_0.56.0 scales_1.1.1       ps_1.3.4          
[43] ellipsis_0.3.1     assertthat_0.2.1   colorspace_1.4-1   V8_3.2.0           RcppParallel_5.0.2 munsell_0.5.0     
[49] crayon_1.3.4

Output of writeLines(readLines(file.path(Sys.getenv("HOME"), ".R/Makevars")))

Error in file(con, "r") : cannot open the connection
In addition: Warning message:
In file(con, "r") :
  cannot open file 'C:\Users\Documents/.R/Makevars': No such file or directory

(I cannot see or create a folder labelled .R - when I try to create it my computer asks for a filename)

Output of 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       Europe/London               
 date     2021-01-18                  

- Packages -----------------------------------------------------------------------------------------------------------
 ! package      * version   date       lib source        
   assertthat     0.2.1     2019-03-21 [1] CRAN (R 4.0.2)
   backports      1.1.9     2020-08-24 [1] CRAN (R 4.0.2)
   BH             1.72.0-3  2020-01-08 [1] CRAN (R 4.0.0)
   callr          3.4.4     2020-09-07 [1] CRAN (R 4.0.2)
   checkmate      2.0.0     2020-02-06 [1] CRAN (R 4.0.2)
   cli            2.0.2     2020-02-28 [1] CRAN (R 4.0.2)
   colorspace     1.4-1     2019-03-18 [1] CRAN (R 4.0.2)
   crayon         1.3.4     2017-09-16 [1] CRAN (R 4.0.2)
   curl           4.3       2019-12-02 [1] CRAN (R 4.0.2)
   desc           1.2.0     2018-05-01 [1] CRAN (R 4.0.2)
   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)
   evaluate       0.14      2019-05-28 [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        3.3.2     2020-06-19 [1] CRAN (R 4.0.2)
   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         0.3.16    2020-09-06 [1] CRAN (R 4.0.2)
   isoband        0.2.2     2020-06-20 [1] CRAN (R 4.0.2)
   jsonlite       1.7.1     2020-09-07 [1] CRAN (R 4.0.2)
   labeling       0.3       2014-08-23 [1] CRAN (R 4.0.0)
   lattice        0.20-41   2020-04-02 [2] CRAN (R 4.0.2)
   lifecycle      0.2.0     2020-03-06 [1] CRAN (R 4.0.2)
   loo            2.3.1     2020-07-14 [1] CRAN (R 4.0.2)
   magrittr       1.5       2014-11-22 [1] CRAN (R 4.0.2)
   MASS           7.3-51.6  2020-04-26 [2] CRAN (R 4.0.2)
   Matrix         1.2-18    2019-11-27 [2] CRAN (R 4.0.2)
   matrixStats    0.56.0    2020-03-13 [1] CRAN (R 4.0.2)
   mgcv           1.8-31    2019-11-09 [2] CRAN (R 4.0.2)
   munsell        0.5.0     2018-06-12 [1] CRAN (R 4.0.2)
   nlme           3.1-148   2020-05-24 [2] CRAN (R 4.0.2)
   pillar         1.4.6     2020-07-10 [1] CRAN (R 4.0.2)
   pkgbuild       1.1.0     2020-07-13 [1] CRAN (R 4.0.2)
   pkgconfig      2.0.3     2019-09-22 [1] CRAN (R 4.0.2)
   pkgload        1.1.0     2020-05-29 [1] CRAN (R 4.0.2)
   praise         1.0.0     2015-08-11 [1] CRAN (R 4.0.2)
   prettyunits    1.1.1     2020-01-24 [1] CRAN (R 4.0.2)
   processx       3.4.4     2020-09-03 [1] CRAN (R 4.0.2)
   ps             1.3.4     2020-08-11 [1] CRAN (R 4.0.2)
   R6             2.4.1     2019-11-12 [1] CRAN (R 4.0.2)
   RColorBrewer   1.1-2     2014-12-07 [1] CRAN (R 4.0.0)
   Rcpp           1.0.5     2020-07-06 [1] CRAN (R 4.0.2)
   RcppEigen      0.3.3.7.0 2019-11-16 [1] CRAN (R 4.0.2)
 D RcppParallel   5.0.2     2020-06-24 [1] CRAN (R 4.0.2)
   rlang          0.4.7     2020-07-09 [1] CRAN (R 4.0.2)
   rprojroot      1.3-2     2018-01-03 [1] CRAN (R 4.0.2)
   rstan          2.21.2    2020-07-27 [1] CRAN (R 4.0.3)
   rstudioapi     0.11      2020-02-07 [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 4.0.3)
   testthat       2.3.2     2020-03-02 [1] CRAN (R 4.0.2)
   tibble         3.0.3     2020-07-10 [1] CRAN (R 4.0.2)
   utf8           1.1.4     2018-05-24 [1] CRAN (R 4.0.2)
   V8             3.2.0     2020-06-19 [1] CRAN (R 4.0.2)
   vctrs          0.3.4     2020-08-29 [1] CRAN (R 4.0.2)
   viridisLite    0.3.0     2018-02-01 [1] CRAN (R 4.0.2)
   withr          2.4.0     2021-01-16 [1] CRAN (R 4.0.2)

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

 D -- DLL MD5 mismatch, broken installation.

I’m aware there have been a lot of posts on this issue, I’ve tried a few fixes (reinstallation, some direct links for StanHeaders…) but can’t seem to get it running. Any help or advice would be gratefully received.

andrjohns · January 18, 2021, 12:28pm

Hi Maria,

Can you restart R, and then reinstall the packages from source:

install.packages(c("StanHeaders","rstan"),type="source")

mesudell · January 18, 2021, 2:46pm

I restarted and set this going about 20 min ago - seems to have got itself into a long loop of errors - too long to paste in but some repeating messages are:

...: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************

                     ^... warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************

warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]

mesudell · January 18, 2021, 3:02pm

Apologies, I spoke too soon - the code finished running. Having loaded the packages using the code above, if I run:

example(stan_model, package = "rstan", run.dontrun = TRUE)

It runs, but I get warning message:


Warning message:
In system(paste(CXX, ARGS), ignore.stdout = TRUE, ignore.stderr = TRUE) :
  '-E' not found

andrjohns · January 18, 2021, 9:51pm

Great that means it’s working. That warning will be fixed in the next release

mesudell · January 18, 2021, 10:40pm

Thanks that’s great!

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Rstan

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