Stan programs not compiling on Ubuntu server


#1

Hi all,

We have Rstan running our models on AWS and they’ve been unable to compile models for the last few weeks. The same models compile and run fine on my mac. We had a very similar issue with last month’s release, but loading Rcpp before trying to compile the models seemed to resolve the problem. We’ve also tried downgrading R and rstan.

The error message when I try to compile the models is:

Error in compileCode(f, code, language = language, verbose = verbose) :

  Compilation ERROR, function(s)/method(s) not created! In file included from /usr/local/lib/R/site-library/BH/include/boost/config.hpp:39:0,
from /usr/local/lib/R/site-library/BH/include/boost/math/tools/config.hpp:13,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/rev/core/var.hpp:7,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/rev/core/gevv_vvv_vari.hpp:5,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/rev/core.hpp:12,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math/rev/mat.hpp:4,
from /usr/local/lib/R/site-library/StanHeaders/include/stan/math.hpp:4,
from /usr/local/lib/R/site-library/StanHeaders/include/src/stan/model/model_header.hpp:4,
from file3a4975fc9efc.cpp:8:
/usr/local/lib/R/site-library/BH/include/boost/config/compiler/gcc.hpp:186:0: warning: “BOOST_NO_CXX11_ Calls: backtest … stan_model -> cxxfunctionplus -> cxxfunction -> compileCode

Operating System: Ubuntu 14.04.4
Interface Version: 2.15.1

> 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 '/home/deploy/.R/Makevars': No such file or directory
> devtools::session_info('rstan')
Session info -------------------------------------------------------------------
 setting  value                       
 version  R version 3.3.1 (2016-06-21)
 system   x86_64, linux-gnu           
 ui       X11                         
 language (EN)                        
 collate  en_US.UTF-8                 
 tz       <NA>                        
 date     2017-10-03                  

Packages -----------------------------------------------------------------------
 package      * version   date       source         
 assertthat     0.2.0     2017-04-11 CRAN (R 3.3.1) 
 BH             1.62.0-1  2016-11-19 cran (@1.62.0-)
 colorspace     1.3-2     2016-12-14 CRAN (R 3.3.1) 
 dichromat      2.0-0     2013-01-24 CRAN (R 3.3.1) 
 digest         0.6.12    2017-01-27 CRAN (R 3.3.1) 
 ggplot2        2.2.1     2016-12-30 CRAN (R 3.3.1) 
 gridExtra      2.2.1     2016-02-29 CRAN (R 3.3.1) 
 gtable         0.2.0     2016-02-26 CRAN (R 3.3.1) 
 inline         0.3.14    2015-04-13 CRAN (R 3.3.1) 
 labeling       0.3       2014-08-23 CRAN (R 3.3.1) 
 lattice        0.20-35   2017-03-25 CRAN (R 3.3.1) 
 lazyeval       0.2.0     2016-06-12 CRAN (R 3.3.1) 
 magrittr       1.5       2014-11-22 CRAN (R 3.3.1) 
 MASS           7.3-47    2017-04-21 CRAN (R 3.3.1) 
 Matrix         1.2-10    2017-04-28 CRAN (R 3.3.1) 
 munsell        0.4.3     2016-02-13 CRAN (R 3.3.1) 
 plyr           1.8.4     2016-06-08 CRAN (R 3.3.1) 
 RColorBrewer   1.1-2     2014-12-07 CRAN (R 3.3.1) 
 Rcpp           0.12.12   2017-07-15 cran (@0.12.12)
 RcppEigen      0.3.2.9.0 2016-08-21 CRAN (R 3.3.1) 
 reshape2       1.4.2     2016-10-22 cran (@1.4.2)  
 rlang          0.1.1     2017-05-18 CRAN (R 3.3.1) 
 rstan          2.15.1    2017-04-19 CRAN (R 3.3.1) 
 scales         0.4.1     2016-11-09 CRAN (R 3.3.1) 
 StanHeaders    2.15.0-1  2017-04-19 CRAN (R 3.3.1) 
 stringi        1.1.5     2017-04-07 CRAN (R 3.3.1) 
 stringr        1.2.0     2017-02-18 CRAN (R 3.3.1) 
 tibble         1.3.1     2017-05-17 CRAN (R 3.3.1) 

#2

That cannot help matters, but I think there should be more to the error message than just the warning involving BOOST_NO_CXX11.


#3

Thanks @bgoodri for the help (offline as well as here). The error seemed to be that we did not have the .R/Makevars file. Possibly in the refactor we dropped this part of the rstan install.

In any case, following the instructions here: https://github.com/stan-dev/rstan/wiki/Installing-RStan-on-Mac-or-Linux#configuration helped.