Error in compileCode()

Dear all,

I get the following error - while running a stan model - after I updated R to 4.02. (Which I regret now…)

Error in compileCode(f, code, language = language, verbose = verbose) : 
  Compilation ERROR, function(s)/method(s) not created! C:/rtools40/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/8.3.0/../../../../x86_64-w64-mingw32/bin/ld.exe: filec6c78d428af.o:filec6c78d428af.cpp:(.text+0x132c): undefined reference to `rstan::stan_fit::stan_fit(SEXPREC*, int)'
C:/rtools40/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/8.3.0/../../../../x86_64-w64-mingw32/bin/ld.exe: filec6c78d428af.o:filec6c78d428af.cpp:(.text$_ZN3tbb8internal26task_scheduler_observer_v3D1Ev[_ZN3tbb8internal26task_scheduler_observer_v3D1Ev]+0x14): undefined reference to `tbb::internal::task_scheduler_observer_v3::observe(bool)'
C:/rtools40/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/8.3.0/../../../../x86_64-w64-mingw32/bin/ld.exe: filec6c78d428af.o:filec6c78d428af.cpp:(.text$_ZN3tbb8internal26task_scheduler_observer_v3D0Ev[_ZN3tbb8internal26task_scheduler_observer_v3D0Ev]+0x1c): undefined reference to `tbb::internal::task_scheduler_observer_v3::observe(bool)'
C:/rtools40/mingw64/bin/../lib/gcc/x86_64
In addition: Warning message:
In file.remove(c(unprocessed, processed)) :
  cannot remove file 'C:\Users\avdminne\AppData\Local\Temp\Rtmp2RBKKS\filec6c6f41831.stan', reason 'No such file or directory'
Error in sink(type = "output") : invalid connection

It ran fine before the update. I did re-install Rtools to the latest version as well.

pkgbuild::has_build_tools(debug = TRUE)
[1] TRUE

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     2020-07-23                  

- Packages --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
 ! package      * version   date       lib source        
   assertthat     0.2.1     2019-03-21 [1] CRAN (R 4.0.2)
   backports      1.1.7     2020-05-13 [1] CRAN (R 4.0.0)
   BH             1.72.0-3  2020-01-08 [1] CRAN (R 4.0.0)
   callr          3.4.3     2020-03-28 [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           1.4.1     2020-05-13 [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         0.3.15    2018-05-18 [1] CRAN (R 4.0.2)
   isoband        0.2.2     2020-06-20 [1] CRAN (R 4.0.2)
   jsonlite       1.7.0     2020-06-25 [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       3.4.3     2020-07-05 [1] CRAN (R 4.0.2)
   ps             1.3.3     2020-05-08 [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        * 2.21.1    2020-07-08 [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  * 2.21.0-5  2020-06-09 [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          0.3.2     2020-07-15 [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] C:/Users/avdminne/Documents/ListPrice/Packages
[2] C:/Program Files/R/R-4.0.2/library

 D -- DLL MD5 mismatch, broken installation.

I have seen some similar topics on this forum, but non of the suggestions there seem to solve it for me. (Like re-installing stan and StanHeaders from the source, etc.)
Does anyone have a clue as to why stan refuses to run all of a sudden? Running stan with VERBOSE = TRUE doesn’t really help me that much, but let me know if you need that.

Many thanks,
Alex

Hey Alex, sorry for the hassle.

What about installing from binary and not source using the links from this post:

I Jonah,

many thanks for the quick response! I got it to work on my laptop, but not so much on my desktop yet. I think it has to do with the Makevars “thing”. In all honesty, I have seen that “thing”’ come up multiple times on this forum, but I have no idea what it does or how it exactly works. Do you know what the exact steps are?

file.edit("~/.R/Makevars.win")

CXX14FLAGS=-O3 -march=native -mtune=native
CXX11FLAGS=-O3 -march=corei7 -mtune=corei7

CXX14FLAGS=-O3 -march=native -mtune=native
CXX11FLAGS=-O3 -march=corei7 -mtune=corei7

CXX14FLAGS=-O3 -march=native -mtune=native
CXX11FLAGS=-O3 -march=corei7 -mtune=corei7

CXX14FLAGS=-O3 -march=native -mtune=native
CXX11FLAGS=-O3 -march=corei7 -mtune=corei7

CXX14FLAGS=-O3 -march=native -mtune=native
CXX11FLAGS=-O3 -march=corei7 -mtune=corei7

CXX14FLAGS=-O3 -march=native -mtune=native
CXX11FLAGS=-O3 -march=corei7 -mtune=corei7

CXX14FLAGS=-O3 -march=native -mtune=native
CXX11FLAGS=-O3 -march=corei7 -mtune=corei7

CXX14FLAGS=-O3 -march=native -mtune=native
CXX11FLAGS=-O3 -march=corei7 -mtune=corei7

CXX14FLAGS=-O3 -march=native -mtune=native
CXX11FLAGS=-O3 -march=corei7 -mtune=corei7

CXX14FLAGS=-O3 -march=native -mtune=native
CXX11FLAGS=-O3 -march=corei7 -mtune=corei7

CXX14FLAGS=-O3 -march=native -mtune=native
CXX11FLAGS=-O3 -march=corei7 -mtune=corei7

CXX14FLAGS=-O3 -march=native -mtune=native
CXX11FLAGS=-O3 -march=corei7 -mtune=corei7

CXX14FLAGS=-O3 -march=native -mtune=native
CXX11FLAGS=-O3 -march=corei7 -mtune=corei7

CXX14FLAGS=-O3 -march=native -mtune=native
CXX11FLAGS=-O3 -march=corei7 -mtune=corei7

CXX14FLAGS=-O3 -march=native -mtune=native
CXX11FLAGS=-O3 -march=corei7 -mtune=corei7

CXX14FLAGS=-O3 -march=native -mtune=native
CXX11FLAGS=-O3 -march=corei7 -mtune=corei7

My understanding is that I delete every line that has the -march=native -mtune=native in it? And subsequently save the new file? Is that it?

Again, thank you very much.
Alex

Wait, upon closer inspection, the link to rstan is probably updated in the meantime.
Was in time with my laptop, but apparently not with my desktop. I noticed someone else had the same issue;

I keep an eye out for that post. Still, I would be interested in getting to know the Makevars procedure a bit better. Could you recommend some further reading for example?
Alex

I think it’s confusing for everyone ;) I wish I had a good resource to point to but I’m not sure. Basically Makevars is a file where you can specify options for compilers. The official resource from CRAN is

https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Using-Makevars

but I don’t find that to be particularly educational unfortunately!

Did you end up getting it running on your desktop? I think with the version of rstan available at the links in my previous post, you can get away with deleting everything from the Makevars file. @bgoodri @stevebronder is that right?

I am able to download rstan now via the link. Unfortunately, I get the following error message now;

Error in stan_model(file, model_name = model_name, model_code = model_code,  : 
  Boost not found; call install.packages('BH')

To state the obvious, BH is installed. I did notice one other earlier message mentioning the same issue;

However, the solution in that post was to simply restart R. That doesn’t work for me…
Sorry for the many questions. I have been using Stan for years now, and only recently has it started to give me issues that I have never had before.
Alex

Ignore my previous message. After restarting my entire PC, it did work!
Many thanks, finally back to Stan.

Sorry for the hassle, but glad it’s working now!