Error in compileCode()

[avdminne]

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

[jonah]

Hey Alex, sorry for the hassle.

@avdminne

(Like re-installing stan and StanHeaders from the source, etc.)

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

Error in file(con, "r") : invalid 'description' argument

@Chiraz_BenAbdelkader Can you try installing from these updated links install.packages( "https://artifacts.r-hub.io/StanHeaders_2.21.0-6.tar.gz-5af2069f840e9b971ee5b0e175da5ea6/StanHeaders_2.21.0-6.zip", repos = NULL, type = "win.binary") install.packages( "https://artifacts.r-hub.io/rstan_2.21.2.tar.gz-3145e4a7fcd4016d378efd0e537d8b91/rstan_2.21.2.zip", repos = NULL, type = "win.binary") and let us know if you still get errors? Thanks! Edit: these are the same links as the updated links in t…

[avdminne]

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

[avdminne]

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;

Error in compileCode(f, code, language = language, verbose = verbose) & 'No such file or directory' error

Hi, I am pretty new to Stan. I have been trying to run the schools.stan model example, but I am always getting a list of Errors. Similar issues in the forums have not been helpful for me yet. These are my software versions: Windows 10 RStan version: 2.21.1 StanHeaders: 2.21.0-5 RStudio version: 4.0.2 RTools version: 4.0.0.28 When I run: example(stan_model, run.dontrun = TRUE) I get this output: Fehler in compileCode(f, code, language = language, verbose = verbose) : Compilation ERROR,…

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

[jonah]

@avdminne

I would be interested in getting to know the Makevars procedure a bit better. Could you recommend some further reading for example?

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

Writing R Extensions

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?

[avdminne]

@jonah

had

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;

8schools error Boost not found

Greetings, I am getting started with RStan and I get the following error while running the basic example 8schools.stan: Error in stan_model(file, model_name = model_name, model_code = model_code, : Boost not found; call install.packages(‘BH’) BH (1.65) is installed and loaded. However I came across this other post and wonder if it could be related. rstan compilation error under Boost 1.64 #441 Any help will be greatly appreciated, Cheers! Here is my session info: sessionInfo() R vers…

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

[avdminne]

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

[jonah]

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