StanHeaders eigen.hpp not found on new RStan install

Interfaces RStan
,
1

I have a computationally expensive series of models I need to run and have been given access to a remote workstation on my campus (using LogMeIn), since it’s impractical to run them from my laptop at home. I have admin privileges on the workstation, but I cannot seem to get RStan working (nor can I seem to install it from source). I run the following code:

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

I get most of the usual compilation stuff (omitted for space but can include parts if necessary) and it runs through line 372 twice. The second time, the error I get is

Compilation ERROR, function(s)/method(s) not created!

Error in compileCode(f, code, language = language, verbose = verbose) : 
  cc1plus.exe: fatal error: \ds.fordham.edu/DFS/Users/mhimmelstein/My Documents/R/win-library/4.0/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp: No such file or directorycompilation terminated.make: *** [C:/PROGRA~1/R/R-40~1.2/etc/x64/Makeconf:229: file3e387256459a.o] Error 1

I’ve also tried installing RStan from source and that also fails, but I’m not sure if it would help (it goes for a few minutes then has an issue creating a DLL, I already lost the error in my console but can reproduce it if that would help as well, it would just take a few minutes), and saving the packages to the local drive rather than my network drive (I get the same error).

  • Operating System : Windows 10
  • RStan Version: 2.21.1 (StanHeaders version 2.21.0-6 I believe)
  • Output of writeLines(readLines(file.path(Sys.getenv("HOME"), ".R/Makevars"))) 
CXX14FLAGS += -O3 -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2
  • Output of devtools::session_info("rstan") 
> 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 States.1252  
 ctype    English_United States.1252  
 tz       America/New_York            
 date     2020-10-05                  

- Packages -------------------------------------------------------------------------------------------------------------
 ! package      * version   date       lib source        
   assertthat     0.2.1     2019-03-21 [1] CRAN (R 4.0.2)
   backports      1.1.10    2020-09-15 [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    0.57.0    2020-09-25 [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 4.0.2)
   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  * 2.21.0-6  2020-08-16 [1] CRAN (R 4.0.2)
   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          2.2.0     2020-04-20 [1] CRAN (R 4.0.2)

[1] \\ds.fordham.edu/DFS/Users/mhimmelstein/My Documents/R/win-library/4.0
[2] C:/Program Files/R/R-4.0.2/library

 D -- DLL MD5 mismatch, broken installation.

I’ve seen a few topics on this and I know there have been others with similar issues, but it seemed like there was hope this would be corrected with the latest version of StanHeaders, so I figured it made more sense to open a new topic than build on ones that are possibly out of date/a bit different.

Thanks for any help you’re able to provide.

2

These network mounted drives are difficult to deal with (on Windows). What is

dir(system.file("include", package = "StanHeaders"),
    pattern = "Eigen.hpp$", recursive = TRUE, full.names = TRUE)

?

1 Like
3 
"\\\\ds.fordham.edu/DFS/Users/mhimmelstein/My Documents/R/win-library/4.0/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp"

For whatever its worth, this is the workstation in my office and I have admin access to the C:\ drive as well, though installing to the C:\ library path

"C:/Program Files/R/R-4.0.2/library"

Causes the same error with the local path (taken from your suggestion in this thread: Compilation error stan/math/prim/mat/fun/Eigen.hpp: No such file or directory)

4

SOLVED! Though no idea how generalizable this would be.

I migrated all of my packages from the remote drive to the local drive and I can get the example model to run.

If there’s any troubleshooting I can do to help you figure out which packages it was I’m happy to do it, but it didn’t work when I just moved StanHeaders, BH, Rcpp, and RcppEigen. I also tried it with rstan itself in addition to those four and that didn’t do it, so presumably its another package or packages that needs to be local?

5

I would have guessed StanHeaders, BH, Rcpp, RcppEigen, RcppParallel, and rstan would have been sufficient but it is probably easier to just set .libPaths() to prioritize some directory with a canonical Windows path and put all of the non-standard R packages there.

1 Like
6

Yeah that’s the plan, but if I have a chance I’ll test if moving RcppParallel too would have worked.