Error in compileCode(f, code, language = language, verbose = verbose) : Compilation ERROR, function(s)/method(s) not created!

Petros · January 13, 2020, 10:58am

Hi,
I am new to rstan. The installation was successfully done within Windows10, in C:
However, when I try to run the first model after the installation instructions, I get the following error message:

Error in compileCode(f, code, language = language, verbose = verbose) :
Compilation ERROR, function(s)/method(s) not created! file27b46fc111f7.cpp:8:39: fatal error: stan/model/model_header.hpp: No such file or directory
#include <stan/model/model_header.hpp>
^
compilation terminated.
make: *** [C:/PROGRA~1/R/R-36~1.2/etc/x64/Makeconf:215: file27b46fc111f7.o] Error 1
In addition: Warning message:
In system(cmd, intern = !verbose) :
running command ‘C:/PROGRA~1/R/R-36~1.2/bin/x64/R CMD SHLIB file27b46fc111f7.cpp 2> file27b46fc111f7.cpp.err.txt’ had status 1
Error in sink(type = “output”) : invalid connection

I had a look at the other similar posts, (re-installation, installing in C:) but they have not worked for me. Any advise would be most appreciated.

Thank you.

bgoodri · January 13, 2020, 1:46pm

It probably installed StanHeaders to some directory that it cannot find. What is

system.file("include", "src", "stan", "model", "model_header.hpp",
            package = "StanHeaders")

?

Petros · January 13, 2020, 1:47pm

Thank you for your response.

system.file(“include”, “src”, “stan”, “model”, “model_header.hpp”, package = “StanHeaders”)
[1] “\\Jericho/home/petros.boutselis/Documents/R/win-library/3.6/StanHeaders/include/src/stan/model/model_header.hpp”

bgoodri · January 13, 2020, 2:00pm

Yeah, having it in a networked drive is tricky. When you do

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

what is the compilation argument, i.e. the line in the middle of the output that starts with g++?

Petros · January 13, 2020, 2:05pm

The output is:
Compilation argument:
C:/PROGRA~1/R/R-36~1.2/bin/x64/R CMD SHLIB file27b442af3432.cpp 2> file27b442af3432.cpp.err.txt
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/PROGRA~1/R/R-36~1.2/include" -DNDEBUG -I"\Jericho/home/petros.boutselis/Documents/R/win-library/3.6/Rcpp/include/" -I"\Jericho/home/petros.boutselis/Documents/R/win-library/3.6/RcppEigen/include/" -I"\Jericho/home/petros.boutselis/Documents/R/win-library/3.6/RcppEigen/include/unsupported" -I"\Jericho/home/petros.boutselis/Documents/R/win-library/3.6/BH/include" -I"\Jericho/home/petros.boutselis/Documents/R/win-library/3.6/StanHeaders/include/src/" -I"\Jericho/home/petros.boutselis/Documents/R/win-library/3.6/StanHeaders/include/" -I"\Jericho/home/petros.boutselis/Documents/R/win-library/3.6/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -std=c++1y -march=core2 -O2 -Wall -mtune=generic -c file27b442af3432.cpp -o file27b442af3432.o
file27b442af3432.cpp:8:39: fatal error: stan/model/model_header.hpp: No such file or directory
#include <stan/model/model_header.hpp>
^
compilation terminated.
make: *** [C:/PROGRA~1/R/R-36~1.2/etc/x64/Makeconf:215: file27b442af3432.o] Error 1

ERROR(s) during compilation: source code errors or compiler configuration errors!

Petros · January 15, 2020, 12:56pm

Hi,
Sorry for coming back, but I wanted to make sure that I have provide you with the right output?
Thank you again for your time.

bgoodri · January 15, 2020, 3:52pm

That is the right output, but I think it does not know what to do with paths that start with \Jericho. Does

example(cxxfunction, package = "inline", run.dontrun = TRUE)
work?

Petros · January 15, 2020, 4:10pm

Unfortunately not:

example(cxxfunction, package = “inline”, run.dontrun = TRUE)

cxxfnc> # default plugin
cxxfnc> fx ← cxxfunction( signature(x = “integer”, y = “numeric” ) , ’
cxxfnc+ return ScalarReal( INTEGER(x)[0] * REAL(y)[0] ) ;
cxxfnc+ ’ )

cxxfnc> fx( 2L, 5 )
[1] 10

cxxfnc> # Rcpp plugin
cxxfnc> if( require( Rcpp ) ){
cxxfnc+
cxxfnc+ fx ← cxxfunction( signature(x = “integer”, y = “numeric” ) , ’
cxxfnc+ return wrap( as(x) * as(y) ) ;
cxxfnc+ ', plugin = “Rcpp” )
cxxfnc+ fx( 2L, 5 )
cxxfnc+
cxxfnc+ ## equivalent shorter form using rcpp()
cxxfnc+ fx ← rcpp(signature(x = “integer”, y = “numeric”),
cxxfnc+ ’ return wrap( as(x) * as(y) ) ; ')
cxxfnc+
cxxfnc+ }
Loading required package: Rcpp

Attaching package: ‘Rcpp’

The following object is masked from ‘package:inline’:

registerPlugin

file26cc77defd9.cpp:4:18: fatal error: Rcpp.h: No such file or directory
#include <Rcpp.h>
^
compilation terminated.
make: *** [C:/PROGRA~1/R/R-36~1.2/etc/x64/Makeconf:215: file26cc77defd9.o] Error 1

ERROR(s) during compilation: source code errors or compiler configuration errors!

Program source:
1:
2: // includes from the plugin
3:
4: #include <Rcpp.h>
5:
6:
7: #ifndef BEGIN_RCPP
8: #define BEGIN_RCPP
9: #endif
10:
11: #ifndef END_RCPP
12: #define END_RCPP
13: #endif
14:
15: using namespace Rcpp;
16:
17: // user includes
18:
19:
20: // declarations
21: extern “C” {
22: SEXP file26cc77defd9( SEXP x, SEXP y) ;
23: }
24:
25: // definition
26:
27: SEXP file26cc77defd9( SEXP x, SEXP y ){
28: BEGIN_RCPP
29:
30: return wrap( as(x) * as(y) ) ;
31:
32: END_RCPP
33: }
34:
35:
Error in compileCode(f, code, language = language, verbose = verbose) :
Compilation ERROR, function(s)/method(s) not created! file26cc77defd9.cpp:4:18: fatal error: Rcpp.h: No such file or directory
#include <Rcpp.h>
^
compilation terminated.
make: *** [C:/PROGRA~1/R/R-36~1.2/etc/x64/Makeconf:215: file26cc77defd9.o] Error 1
In addition: Warning message:
In system(cmd, intern = !verbose) :
running command ‘C:/PROGRA~1/R/R-36~1.2/bin/x64/R CMD SHLIB file26cc77defd9.cpp 2> file26cc77defd9.cpp.err.txt’ had status 1

bgoodri · January 15, 2020, 4:39pm

Both of these error messages are saying it cannot find files that are in packages that are installed in your home directory. I think you need to figure out a way to install packages somewhere in C:/. Or maybe map the network drive your home directory is on to some place in C:/ or at least that has the same conventions for specifying paths.

Petros · January 15, 2020, 8:43pm

Thank you very much for the advice.

MauritsM · January 31, 2020, 4:08pm

Hi! Sorry to hijack this thread, but I’m running into a similar problem. If you prefer I open a new thread, please let me know.

When trying to compile a Stan model I get the following error:

Error in compileCode(f, code, language = language, verbose = verbose) : 
Compilation ERROR, function(s)/method(s) not created! file339c2b2f763d.cpp:31:40: error: 
expected template-name before '<' token
   : public stan::model::model_base_crtp<model339c3e6c6dd_8b930d0c26abd40c299b4f2a09342bab> {
                                        ^
file339c2b2f763d.cpp:31:40: error: expected '{' before '<' token
file339c2b2f763d.cpp:31:40: error: expected unqualified-id before '<' token
In file included from J:/Documents/R/win-library/3.6/BH/include/boost/winapi/time.hpp:13:0,
                 from J:/Documents/R/win 
library/3.6/BH/include/boost/date_time/microsec_time_clock.hpp:24,
                 from J:/Documents/R/win- 
library/3.6/BH/include/boost/date_time/posix_time/posix_time_types.hpp:11,
                 from J:/Documents/R/win-library/3.6/rstan/include/rstan/stan_fit.hpp:13,
                 from J:/Documents/R/win-library/3.6/rstan/include/rstan/rstaninc.hpp:3,
                 from file339c2b2f763d.cpp:520:
J:/Documents/R/win-library/3.6/BH/include
In addition: Warning message:
In system(cmd, intern = !verbose) :
  running command 'C:/PROGRA~1/R/R-36~1.2/bin/x64/R CMD SHLIB file339c2b2f763d.cpp 2> 
file339c2b2f763d.cpp.err.txt' had status 1
Error in sink(type = "output") : invalid connection

I’m not quite sure what’s going wrong, although it seems similar to the problem described here. I’m able to run

 example(cxxfunction, package = "inline", run.dontrun = TRUE)

without errors.

Do you have any advice on what I could try to get Stan working?

bgoodri · January 31, 2020, 6:11pm

I think the easiest thing to do would be to install the rstan that goes with that version of StanHeaders. But things with CRAN are a bit in flux at the moment, so you have to do

install.packages("https://win-builder.r-project.org/l26BR4T0nUlo/rstan_2.21.1.zip",
                 repos = NULL)

MauritsM · January 31, 2020, 7:15pm

Thanks! I tried but unfortunately run into a new problem:

Error: package or namespace load failed for ‘rstan’ in inDL(x, as.logical(local), as.logical(now), ...):
unable to load shared object 'J:/Documents/R/win-library/3.6/rstan/libs/x64/rstan.dll':
LoadLibrary failure:  The specified procedure could not be found.
In addition: Warning message:
package ‘rstan’ was built under R version 4.0.0

bgoodri · January 31, 2020, 7:39pm

Hmm. Maybe try installing from GitHub

remotes::install_github("stan-dev/rstan", ref = "develop",
                        subdir = "rstan/rstan")

?

MauritsM · January 31, 2020, 10:20pm

Sadly I’m having some trouble getting that to compile from source. Variations of the errors and warnings I see all the time are:

J:/Documents/R/win-library/3.6/StanHeaders/include/stan/math/prim/scal/meta/require_generics.hpp:736:53: warning: variadic 
templates only available with -std=c++11 or -std=gnu++11
template <template <class...> class TypeCheck, class... Check>
                                                    ^
J:/Documents/R/win-library/3.6/StanHeaders/include/stan/math/prim/scal/meta/require_generics.hpp:737:1: error: expected 
unqualified-id before 'using'
using require_all_not_std_vector_st
^

And it ends with

make: *** [C:/PROGRA~1/R/R-36~1.2/etc/i386/Makeconf:215: sparse_extractors.o] Error 1
ERROR: compilation failed for package 'rstan'
* removing 'J:/Documents/R/win-library/3.6/rstan'
* restoring previous 'J:/Documents/R/win-library/3.6/rstan'
Error: Failed to install 'rstan' from GitHub:
(converted from warning) installation of package 
‘C:/Users/maum/AppData/Local/Temp/RtmpIXM05M/file3e88678f6169/rstan_2.21.1.tar.gz’ had non-zero exit status
In addition: Warning message:
In utils::untar(tarfile, ...) :
‘tar.exe -xf "C:\Users\maum\AppData\Local\Temp\RtmpIXM05M\file3e886f114dd6.tar.gz" -C 
"C:/Users/maum/AppData/Local/Temp/RtmpIXM05M/remotes3e88eac4bec"’ returned error code 1

Unfortunately I have no idea what these errors mean - any advice is greatly appreciated.

P.S. the installation errors and warnings go on for multiple screens - let me know if you want me to capture them entirely.

MauritsM · January 31, 2020, 10:43pm

Hold on, for whatever reason, using rstan 2.19.2 with StanHeaders 2.21.0-1 is now working (mostly) as expected. I’ll do some more testing, but if you don’t hear from me, please don’t spend any time on this anymore! :-)

bgoodri · January 31, 2020, 11:24pm

I have spent the last 3 months on it, so another little bit won’t hurt much.

MauritsM · January 31, 2020, 11:50pm

Haha, thanks for your help so far!

Unfortunately I seem to have celebrated a bit too early. Some of the simpler Stan models (i.e. 8 schools) compile and sample just fine, but a slightly more complex model gives this error:

Error in compileCode(f, code, language = language, verbose = verbose) : 
  Compilation ERROR, function(s)/method(s) not created! 
C:\Users\maum\AppData\Local\Temp\cc553bQO.s: Assembler messages:
C:\Users\maum\AppData\Local\Temp\cc553bQO.s:8510: Error: invalid register for .seh_savexmm
C:\Users\maum\AppData\Local\Temp\cc553bQO.s:8512: Error: invalid register for .seh_savexmm
C:\Users\maum\AppData\Local\Temp\cc553bQO.s:17711: Error: invalid register for .seh_savexmm
C:\Users\maum\AppData\Local\Temp\cc553bQO.s:88036: Error: invalid register for .seh_savexmm
C:\Users\maum\AppData\Local\Temp\cc553bQO.s:88038: Error: invalid register for .seh_savexmm
C:\Users\maum\AppData\Local\Temp\cc553bQO.s:88040: Error: invalid register for .seh_savexmm
C:\Users\maum\AppData\Local\Temp\cc553bQO.s:121760: Error: invalid register for .seh_savexmm
C:\Users\maum\AppData\Local\Temp\cc553bQO.s:186054: Error: invalid register for .seh_savexmm
C:\Users\maum\AppData\Local\Temp\cc553bQO.s:188560: Error: invalid register for .seh_savexmm
C:\Users\maum\AppData\Local\Temp\cc553bQO.
In addition: Warning message:
In system(cmd, intern = !verbose) :
  running command 'C:/PROGRA~1/R/R-36~1.2/bin/x64/R CMD SHLIB file2828102563db.cpp 2>     file2828102563db.cpp.err.txt' had status 1
Error in sink(type = "output") : invalid connection

Does this seem related?

To be precise this shows up when trying to compile the model with stan_model().

bgoodri · February 1, 2020, 12:13am

Things like that are usually due to having -mtune=native -march=native and the compiler misdiagnosing the processor. If you have that in CXX11FLAGS or something, try removing it.

jhaeberl · February 1, 2020, 7:09pm

Hi. Not sure whether it is acceptable to use this thread but I am experiencing issues compiling Stan models. I installed RStan without any issues.
Win 10, 64 bit, R 3.6.2, Rtools 3.5.0.4
However, when I try to run the following command:
example(stan_model, run.dontrun = TRUE)
I get the following errors:

g++.exe: error: Files/R/R-3.6.2/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp: No such file or directory
g++.exe: error: Files/R/R-3.6.2/library/StanHeaders/include: No such file or directory
g++.exe: error: Files/R/R-3.6.2/library/RcppEigen/include: No such file or directory

The “compilation argument” is as follows:

C:/PROGRA~1/R/R-36~1.2/bin/x64/R CMD SHLIB file355079371150.cpp 2> file355079371150.cpp.err.txt
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/PROGRA~1/R/R-36~1.2/include" -DNDEBUG -I"C:/Program Files/R/R-3.6.2/library/Rcpp/include/" -I"C:/Program Files/R/R-3.6.2/library/RcppEigen/include/" -I"C:/Program Files/R/R-3.6.2/library/RcppEigen/include/unsupported" -I"C:/Program Files/R/R-3.6.2/library/BH/include" -I"C:/Program Files/R/R-3.6.2/library/StanHeaders/include/src/" -I"C:/Program Files/R/R-3.6.2/library/StanHeaders/include/" -I"C:/Program Files/R/R-3.6.2/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -std=c++1y -march=core2 -include C:/Program Files/R/R-3.6.2/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp -I C:/Program Files/R/R-3.6.2/library/StanHeaders/include -I C:/Program Files/R/R-3.6.2/library/RcppEigen/include -O3 -march=corei7 -mtune=corei7 -c file355079371150.cpp -o file355079371150.o

I noticed that the files or directories that cannot be found happen to be those that are not in quotes in the compilation argument, namely

-include C:/Program Files/R/R-3.6.2/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp -I C:/Program Files/R/R-3.6.2/library/StanHeaders/include -I C:/Program Files/R/R-3.6.2/library/RcppEigen/include

and the errors complain that
Files/R/R-3.6.2/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp
doesn’t exist, etc. The paths have been mangled.

Needless to say, these files and directories all exist on my machine.

Is there a way to force the paths to be properly quoted? And would that solve the problem?

Thank you for any help you may be to provide.

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