RStan Cannot Open Temporary File

I’m having trouble getting RStan to work - after updating to R 4.0 I ran into a compiler issue very similar to: Compilation Error (Please Help!). After downgrading to R 3.6.3, I am getting a permission error similar to the one documented in: Cannot load dll from temporary directory when using Stan. It was suggested in that thread that antivirus software might be the problem, but temporarily disabling my anti-virus did not fix this issue. RStan was working prior to the installation a few days ago, but I don’t remember what the version was. I currently have R 3.6.3 installed, and the question focuses on the second issue. I am using RStudio 1.3.959 (most recent version).

Running:

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

gives no error, but I get the following:

Warning message:
In file.remove(c(unprocessed, processed)) :
  cannot remove file 'C:\Users\micha\AppData\Local\Temp\RtmpsltHLA\file49901bea335b.stan', reason 'No such file or directory'

However, when I try to sample from my own model (which worked a few days ago), I get the following error:

Error in inDL(x, as.logical(local), as.logical(now), ...) : 
  unable to load shared object 'C:/Users/micha/AppData/Local/Temp/Rtmp8ofFwd/file19bc19fe73c3.dll':
  LoadLibrary failure:  The specified procedure could not be found.

I checked that the dll file in question exists, but for some reason Stan can’t seem to open it.

  • Operating System: Windows 10
  • RStan Version: 2.21.0
  • Output of writeLines(readLines(file.path(Sys.getenv("HOME"), ".R/Makevars"))) (I used a different path to get this: writeLines(readLines("C:\\Users\\micha\\OneDrive\\Documents\\R\\win-library\\3.6\\rstantools\\include\\sys\\Makevars.win"))):
STANHEADERS_SRC = $(shell "$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" -e "message()" -e "cat(system.file('include', 'src', package = 'StanHeaders', mustWork = TRUE))" -e "message()" | grep "StanHeaders")

PKG_CPPFLAGS = -I"../inst/include" -I"$(STANHEADERS_SRC)" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DRCPP_PARALLEL_USE_TBB=1
PKG_CXXFLAGS = $(shell "$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" -e "RcppParallel::CxxFlags()") $(shell "$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" -e "StanHeaders:::CxxFlags()")
PKG_LIBS = $(shell "$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" -e "RcppParallel::RcppParallelLibs()") $(shell "$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" -e "StanHeaders:::LdFlags()")

CXX_STD = CXX14
  • Output of devtools::session_info("rstan"):
- Session info ---------------------------------------------------------------------------------------------------------------
 setting  value                       
 version  R version 3.6.3 (2020-02-29)
 os       Windows 10 x64              
 system   x86_64, mingw32             
 ui       RStudio                     
 language (EN)                        
 collate  English_United States.1252  
 ctype    English_United States.1252  
 tz       America/New_York            
 date     2020-07-12                  

- Packages -------------------------------------------------------------------------------------------------------------------
 ! package      * version   date       lib source        
   assertthat     0.2.1     2019-03-21 [1] CRAN (R 3.6.3)
   backports      1.1.7     2020-05-13 [1] CRAN (R 3.6.3)
   BH             1.72.0-3  2020-01-08 [1] CRAN (R 3.6.2)
   callr          3.4.3     2020-03-28 [1] CRAN (R 3.6.3)
   checkmate      2.0.0     2020-02-06 [1] CRAN (R 3.6.3)
   cli            2.0.2     2020-02-28 [1] CRAN (R 3.6.3)
   colorspace     1.4-1     2019-03-18 [1] CRAN (R 3.6.3)
   crayon         1.3.4     2017-09-16 [1] CRAN (R 3.6.3)
   curl           4.3       2019-12-02 [1] CRAN (R 3.6.3)
   desc           1.2.0     2018-05-01 [1] CRAN (R 3.6.3)
   digest         0.6.25    2020-02-23 [1] CRAN (R 3.6.3)
   ellipsis       0.3.1     2020-05-15 [1] CRAN (R 3.6.3)
   evaluate       0.14      2019-05-28 [1] CRAN (R 3.6.3)
   fansi          0.4.1     2020-01-08 [1] CRAN (R 3.6.3)
   farver         2.0.3     2020-01-16 [1] CRAN (R 3.6.3)
   ggplot2      * 3.3.2     2020-06-19 [1] CRAN (R 3.6.3)
   glue           1.4.1     2020-05-13 [1] CRAN (R 3.6.3)
   gridExtra    * 2.3       2017-09-09 [1] CRAN (R 3.6.3)
   gtable       * 0.3.0     2019-03-25 [1] CRAN (R 3.6.3)
   inline         0.3.15    2018-05-18 [1] CRAN (R 3.6.3)
   isoband        0.2.2     2020-06-20 [1] CRAN (R 3.6.3)
   jsonlite       1.7.0     2020-06-25 [1] CRAN (R 3.6.3)
   labeling       0.3       2014-08-23 [1] CRAN (R 3.6.0)
   lattice        0.20-41   2020-04-02 [1] CRAN (R 3.6.3)
   lifecycle      0.2.0     2020-03-06 [1] CRAN (R 3.6.3)
   loo            2.3.0     2020-07-07 [1] CRAN (R 3.6.3)
   magrittr       1.5       2014-11-22 [1] CRAN (R 3.6.3)
   MASS           7.3-51.6  2020-04-26 [1] CRAN (R 3.6.3)
   Matrix       * 1.2-18    2019-11-27 [2] CRAN (R 3.6.3)
   matrixStats    0.56.0    2020-03-13 [1] CRAN (R 3.6.3)
   mgcv           1.8-31    2019-11-09 [2] CRAN (R 3.6.3)
   munsell        0.5.0     2018-06-12 [1] CRAN (R 3.6.3)
   nlme           3.1-148   2020-05-24 [1] CRAN (R 3.6.3)
   pillar         1.4.6     2020-07-10 [1] CRAN (R 3.6.3)
   pkgbuild       1.0.8     2020-05-07 [1] CRAN (R 3.6.3)
   pkgconfig      2.0.3     2019-09-22 [1] CRAN (R 3.6.3)
   pkgload        1.1.0     2020-05-29 [1] CRAN (R 3.6.3)
   praise         1.0.0     2015-08-11 [1] CRAN (R 3.6.3)
   prettyunits    1.1.1     2020-01-24 [1] CRAN (R 3.6.3)
   processx       3.4.3     2020-07-05 [1] CRAN (R 3.6.3)
   ps             1.3.3     2020-05-08 [1] CRAN (R 3.6.3)
   R6             2.4.1     2019-11-12 [1] CRAN (R 3.6.3)
   RColorBrewer   1.1-2     2014-12-07 [1] CRAN (R 3.6.0)
   Rcpp         * 1.0.5     2020-07-06 [1] CRAN (R 3.6.3)
   RcppEigen      0.3.3.7.0 2019-11-16 [1] CRAN (R 3.6.3)
 D RcppParallel   5.0.2     2020-06-24 [1] CRAN (R 3.6.3)
   rlang        * 0.4.6     2020-05-02 [1] CRAN (R 3.6.3)
   rprojroot      1.3-2     2018-01-03 [1] CRAN (R 3.6.3)
   rstan        * 2.21.1    2020-07-08 [1] CRAN (R 3.6.3)
   rstudioapi     0.11      2020-02-07 [1] CRAN (R 3.6.3)
   scales         1.1.1     2020-05-11 [1] CRAN (R 3.6.3)
   StanHeaders  * 2.21.0-5  2020-06-09 [1] CRAN (R 3.6.3)
   testthat       2.3.2     2020-03-02 [1] CRAN (R 3.6.3)
   tibble       * 3.0.2     2020-07-07 [1] CRAN (R 3.6.3)
   utf8           1.1.4     2018-05-24 [1] CRAN (R 3.6.3)
   V8             3.2.0     2020-06-19 [1] CRAN (R 3.6.3)
   vctrs          0.3.1     2020-06-05 [1] CRAN (R 3.6.3)
   viridisLite    0.3.0     2018-02-01 [1] CRAN (R 3.6.3)
   withr          2.2.0     2020-04-20 [1] CRAN (R 3.6.3)

[1] C:/Users/micha/OneDrive/Documents/R/win-library/3.6
[2] C:/Program Files/R/R-3.6.3/library

 D -- DLL MD5 mismatch, broken installation.

My main questions are: (1) how to fix this issue or alternatively (2) is it better to update R/Rstan and try to solve the original problems. Thank you in advance!

This is ironically good because we had that error come up a few days ago, albeit not in English. Unfortunately, the English version is no more helpful. Does the model that fails have any #include statements?

No, there are no #include statements in my model. I just reran my code (no changes), and the error seems to have fixed itself. I’ll update if it breaks again, but it might have been a temporary issue specific to my computer. Thank you for all your help, and sorry about the confusion.