Stan Compilation Error

[Ding Zhou]

Dear experts,

I just successfully installed rstan 2.12.1 on my laptop, but when I tried to run this test function:

fx <- inline::cxxfunction( signature(x = "integer", y = "numeric" ) , '
    return ScalarReal( INTEGER(x)[0] * REAL(y)[0] ) ;
' )
fx( 2L, 5 ) # should be 10

It showed the following error "Error in compileCode(f, code, language = language, verbose = verbose) : Compilation ERROR, function(s)/method(s) not created!"  Even if I ignored this error and proceeded to 8schools function, it still had the same error.  I've double checked the installation of Rtools and gcc, and both of them worked well.  Also I've reinstalled R, but it still didn't work.  My installation info is as follows.  Could you please help me solve this problem?  Thanks a lot!

OS: Windows 8 (64 bit)

R version: 3.3.1

RStudio version: 0.99.903

C++ compilar version: Rtools 33 

gcc version: 4.6.3

> sessionInfo()

R version 3.3.1 (2016-06-21)

Platform: x86_64-w64-mingw32/x64 (64-bit)

Running under: Windows >= 8 x64 (build 9200)

locale:

[1] LC_COLLATE=Chinese (Simplified)_China.936 

[2] LC_CTYPE=Chinese (Simplified)_China.936   

[3] LC_MONETARY=Chinese (Simplified)_China.936

[4] LC_NUMERIC=C                              

[5] LC_TIME=Chinese (Simplified)_China.936    

attached base packages:

[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):

[1] rsconnect_0.4.3 tools_3.3.1     inline_0.3.14  

> Sys.getenv("PATH")

[1] "C:\\Program Files\\R\\R-3.3.1\\bin\\x64;c:\\Rtools\\bin;c:\\Rtools\\gcc-4.6.3\\bin;C:\\Program Files (x86)\\Common Files\\Intel\\Shared Libraries\\redist\\intel64\\mpirt;C:\\Program Files (x86)\\Common Files\\Intel\\Shared Libraries\\redist\\intel64\\compiler;C:\\Program Files (x86)\\Common Files\\Intel\\Shared Libraries\\redist\\ia32\\mpirt;C:\\Program Files (x86)\\Common Files\\Intel\\Shared Libraries\\redist\\ia32\\compiler;C:\\Program Files (x86)\\Python3.4.3\\;C:\\Program Files (x86)\\Python3.4.3\\Scripts;C:\\ProgramData\\Oracle\\Java\\javapath;C:\\Program Files (x86)\\Calibre2\\;D:\\CTEX\\UserData\\miktex\\bin;D:\\CTEX\\MiKTeX\\miktex\\bin;D:\\CTEX\\CTeX\\ctex\\bin;D:\\CTEX\\CTeX\\cct\\bin;D:\\CTEX\\CTeX\\ty\\bin;D:\\CTEX\\Ghostscript\\gs9.05\\bin;D:\\CTEX\\GSview\\gsview;D:\\CTEX\\WinEdt;C:\\Program Files (x86)\\Skype\\Phone\\;D:\\gbk2uni;C:\\Program Files (x86)\\SAS\\SharedFiles\\Formats;D:\\ggobi;D:\\TeXLive\\2014\\bin\\win32;C:\\Rtools\\bin;C:\\Rtools\\gcc-4.6.3\\bin;D:\\Rtools\\bin;D:\\Rtools\\gcc-4.6.3\\bin;C:\\Program Files (x86)\\Common Files\\Intel\\Shared Libraries\\redist\\intel64\\mpirt;C:\\Program Files (x86)\\Common Files\\Intel\\Shared Libraries\\redist\\intel64\\compiler;C:\\Program Files (x86)\\Common Files\\Intel\\Shared Libraries\\redist\\ia32\\mpirt;C:\\Program Files (x86)\\Common Files\\Intel\\Shared Libraries\\redist\\ia32\\compiler;C:\\Program Files (x86)\\Python3.4.3\\;C:\\Program Files (x86)\\Python3.4.3\\Scripts;C:\\ProgramData\\Oracle\\Java\\javapath;C:\\Program Files (x86)\\Calibre2\\;D:\\CTEX\\UserData\\miktex\\bin;D:\\CTEX\\MiKTeX\\miktex\\bin;D:\\CTEX\\CTeX\\ctex\\bin;D:\\CTEX\\CTeX\\cct\\bin;D:\\CTEX\\CTeX\\ty\\bin;D:\\CTEX\\Ghostscript\\gs9.05\\bin;D:\\CTEX\\GSview\\gsview;D:\\CTEX\\WinEdt;C:\\Program Files (x86)\\Skype\\Phone\\;D:\\gbk2uni;C:\\Program Files (x86)\\SAS\\SharedFiles\\Formats;D:\\ggobi"

> system("g++ -v")

Using built-in specs.

COLLECT_GCC=c:\Rtools\GCC-46~1.3\bin\G__~1.EXE

COLLECT_LTO_WRAPPER=c:/rtools/gcc-46~1.3/bin/../libexec/gcc/i686-w64-mingw32/4.6.3/lto-wrapper.exe

Target: i686-w64-mingw32

Configured with: /data/gannet/ripley/Sources/mingw-test3/src/gcc/configure --host=i686-w64-mingw32 --build=x86_64-linux-gnu --target=i686-w64-mingw32 --with-sysroot=/data/gannet/ripley/Sources/mingw-test3/mingw32mingw32/mingw32 --prefix=/data/gannet/ripley/Sources/mingw-test3/mingw32mingw32/mingw32 --with-gmp=/data/gannet/ripley/Sources/mingw-test3/mingw32mingw32/prereq_install --with-mpfr=/data/gannet/ripley/Sources/mingw-test3/mingw32mingw32/prereq_install --with-mpc=/data/gannet/ripley/Sources/mingw-test3/mingw32mingw32/prereq_install --disable-shared --enable-static --enable-targets=all --enable-languages=c,c++,fortran --enable-libgomp --enable-sjlj-exceptions --enable-fully-dynamic-string --disable-nls --disable-werror --enable-checking=release --disable-win32-registry --disable-rpath --disable-werror CFLAGS='-O2 -mtune=core2 -fomit-frame-pointer' LDFLAGS=

Thread model: win32

gcc version 4.6.3 20111208 (prerelease) (GCC) 

> system("where make")

c:\Rtools\bin\make.exe

> cat(readLines(M), sep = "\n")

CXXFLAGS=-O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function

CXXFLAGS += -Wno-ignored-attributes -Wno-deprecated-declarations

[Ben Goodrich]

On Tuesday, September 13, 2016 at 12:17:15 AM UTC-4, Ding Zhou wrote:

I've reinstalled R, but it still didn't work.  My installation info is as follows.  Could you please help me solve this problem?  Thanks a lot!

OS: Windows 8 (64 bit)

R version: 3.3.1

RStudio version: 0.99.903

C++ compilar version: Rtools 33 

gcc version: 4.6.3

For R 3.3.x and Rtools33 you should be using gcc 4.9.x. Did you do the part of the instructions that says to execute

cat('Sys.setenv(BINPREF = "C:/Rtools/mingw_$(WIN)/bin/")',
    file = file.path(Sys.getenv("HOME"), ".Rprofile"), 
    sep = "\n", append = TRUE)

Ben

[Ding Zhou]

Dear Ben,

Yes, I executed that codes, and here is what in my file.path(Sys.getenv("HOME"), ".Rprofile") file:

Sys.setenv(BINPREF = "C:/Rtools/mingw_$(WIN)/bin/")

But it still showed the error when tested functions: Error in compileCode(f, code, language = language, verbose = verbose) : Compilation ERROR, function(s)/method(s) not created!

 

How can I renew my gcc version?  Thanks a lot!

Best Regards,

Ding

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[Ben Goodrich]

On Tuesday, September 13, 2016 at 8:14:52 AM UTC-4, Ding Zhou wrote:

Dear Ben,

Yes, I executed that codes, and here is what in my file.path(Sys.getenv("HOME"), ".Rprofile") file:

Sys.setenv(BINPREF = "C:/Rtools/mingw_$(WIN)/bin/")

But it still showed the error when tested functions: Error in compileCode(f, code, language = language, verbose = verbose) : Compilation ERROR, function(s)/method(s) not created!

 

How can I renew my gcc version?  Thanks a lot!

We need to see the whole error message. Can you call inline::cxxfunction() with verbose = TRUE?

Ben

[Ding Zhou]

Hi Ben,

I call the following function:

> fx <- inline::cxxfunction( signature(x = "integer", y = "numeric"),'return ScalarReal( INTEGER(x)[0] * REAL(y)[0] )',verbose=TRUE)

And the whole error is:

 >> Program source :

   1 : 

   2 : // includes from the plugin

   3 : #include <R.h>

   4 : #include <Rdefines.h>

   5 : #include <R_ext/Error.h>

   6 : 

   7 : 

   8 : // user includes

   9 : 

  10 : 

  11 : // declarations

  12 : extern "C" {

  13 : SEXP fileabc6684483e( SEXP x, SEXP y) ;

  14 : }

  15 : 

  16 : // definition

  17 : 

  18 : SEXP fileabc6684483e( SEXP x, SEXP y ){

  19 : return ScalarReal( INTEGER(x)[0] * REAL(y)[0] ) 

  20 : Rf_warning("your C++ program does not return anything"); 

  21 :  return R_NilValue ; 

  22 : }

  23 : 

  24 : 

Compilation argument:

 C:/R/R-3.3.1/bin/x64/R CMD SHLIB fileabc6684483e.cpp 2> fileabc6684483e.cpp.err.txt 

C:/Rtools/mingw_64/bin/g++  -I"C:/R/R-33~1.1/include" -DNDEBUG     -I"d:/Compiler/gcc-4.9.3/local330/include"     -O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function -c fileabc6684483e.cpp -o fileabc6684483e.o

fileabc6684483e.cpp: In function 'SEXPREC* fileabc6684483e(SEXP, SEXP)':

fileabc6684483e.cpp:20:1: error: expected ';' before 'Rf_warning'

 Rf_warning("your C++ program does not return anything"); 

 ^

make: *** [fileabc6684483e.o] Error 1

Warning message:

Run 'make -f "C:/R/R-33~1.1/etc/x64/Makeconf" -f "C:/R/R-33~1.1/share/make/winshlib.mk" -f "C:\Users\DELL\Documents/.R/Makevars" SHLIB_LDFLAGS='$(SHLIB_CXXLDFLAGS)' SHLIB_LD='$(SHLIB_CXXLD)' SHLIB="fileabc6684483e.dll" WIN=64 TCLBIN=64 OBJECTS="fileabc6684483e.o"' condition is 2. 

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

Program source:

  1: 

  2: // includes from the plugin

  3: #include <R.h>

  4: #include <Rdefines.h>

  5: #include <R_ext/Error.h>

  6: 

  7: 

  8: // user includes

  9: 

 10: 

 11: // declarations

 12: extern "C" {

 13: SEXP fileabc6684483e( SEXP x, SEXP y) ;

 14: }

 15: 

 16: // definition

 17: 

 18: SEXP fileabc6684483e( SEXP x, SEXP y ){

 19: return ScalarReal( INTEGER(x)[0] * REAL(y)[0] ) 

 20: Rf_warning("your C++ program does not return anything"); 

 21:  return R_NilValue ; 

 22: }

 23: 

 24: 

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

  Compilation ERROR, function(s)/method(s) not created! fileabc6684483e.cpp: In function 'SEXPREC* fileabc6684483e(SEXP, SEXP)':

fileabc6684483e.cpp:20:1: error: expected ';' before 'Rf_warning'

 Rf_warning("your C++ program does not return anything"); 

 ^

make: *** [fileabc6684483e.o] Error 1

Warning message:

Run 'make -f "C:/R/R-33~1.1/etc/x64/Makeconf" -f "C:/R/R-33~1.1/share/make/winshlib.mk" -f "C:\Users\DELL\Documents/.R/Makevars" SHLIB_LDFLAGS='$(SHLIB_CXXLDFLAGS)' SHLIB_LD='$(SHLIB_CXXLD)' SHLIB="fileabc6684483e.dll" WIN=64 TCLBIN=64 OBJECTS="fileabc6684483e.o"' condition is 2

Warning message:

Run 'C:/R/R-3.3.1/bin/x64/R CMD SHLIB fileabc6684483e.cpp 2> fileabc6684483e.cpp.err.txt' condition is 1.

Thanks for your help!

Best Regards,

Ding

[Ben Goodrich]

On Tuesday, September 13, 2016 at 10:30:35 AM UTC-4, Ding Zhou wrote:

 16: // definition

 17: 

 18: SEXP fileabc6684483e( SEXP x, SEXP y ){

 19: return ScalarReal( INTEGER(x)[0] * REAL(y)[0] ) 

 20: Rf_warning("your C++ program does not return anything"); 

 21:  return R_NilValue ; 

 22: }

For some reason, your R code yields a C++ function that is missing the terminating semi-colon on line 19. Are you sure you pasted in exactly

fx <- inline::cxxfunction( signature(x = "integer", y = "numeric" ) , '

    return ScalarReal( INTEGER(x)[0] * REAL(y)[0] ) ;
' )
fx( 2L, 5 ) # should be 10

Otherwise, I don't know why it would do that. Maybe try reinstalling Rcpp. Or it could be something with the language settings on your computer.

Ben

[Ding Zhou]

Hi Ben,

Sorry, I do miss a semi-colon and now I change it and run again.  It still has error.  Also this time I reinstall Rtools34, and now the gcc version is 4.9.3.

> system('g++ -v')

Using built-in specs.

COLLECT_GCC=c:\Rtools\mingw_32\bin\G__~1.EXE

COLLECT_LTO_WRAPPER=c:/Rtools/mingw_32/bin/../libexec/gcc/i686-w64-mingw32/4.9.3/lto-wrapper.exe

Target: i686-w64-mingw32

Configured with: ../../../src/gcc-4.9.3/configure --host=i686-w64-mingw32 --build=i686-w64-mingw32 --target=i686-w64-mingw32 --prefix=/mingw32 --with-sysroot=/home/Jeroen/mingw-gcc-4.9.3/i686-493-posix-dwarf-rt_v3-s/mingw32 --with-gxx-include-dir=/mingw32/i686-w64-mingw32/include/c++ --enable-static --disable-shared --disable-multilib --enable-languages=c,c++,fortran,lto --enable-libstdcxx-time=yes --enable-threads=posix --enable-libgomp --enable-libatomic --enable-lto --enable-graphite --enable-checking=release --enable-fully-dynamic-string --enable-version-specific-runtime-libs --disable-sjlj-exceptions --with-dwarf2 --disable-isl-version-check --disable-cloog-version-check --disable-libstdcxx-pch --disable-libstdcxx-debug --enable-bootstrap --disable-rpath --disable-win32-registry --disable-nls --disable-werror --disable-symvers --with-gnu-as --with-gnu-ld --with-arch=i686 --with-tune=generic --with-libiconv --with-system-zlib --with-gmp=/home/Jeroen/mingw-gcc-4.9.3/prerequisites/i686-w64-mingw32-static --with-mpfr=/home/Jeroen/mingw-gcc-4.9.3/prerequisites/i686-w64-mingw32-static --with-mpc=/home/Jeroen/mingw-gcc-4.9.3/prerequisites/i686-w64-mingw32-static --with-isl=/home/Jeroen/mingw-gcc-4.9.3/prerequisites/i686-w64-mingw32-static --with-cloog=/home/Jeroen/mingw-gcc-4.9.3/prerequisites/i686-w64-mingw32-static --enable-cloog-backend=isl --with-pkgversion='i686-posix-dwarf, Built by MinGW-W64 project' --with-bugurl=http://sourceforge.net/projects/mingw-w64 CFLAGS='-O2 -pipe -I/home/Jeroen/mingw-gcc-4.9.3/i686-493-posix-dwarf-rt_v3-s/mingw32/opt/include -I/home/Jeroen/mingw-gcc-4.9.3/prerequisites/i686-zlib-static/include -I/home/Jeroen/mingw-gcc-4.9.3/prerequisites/i686-w64-mingw32-static/include' CXXFLAGS='-O2 -pipe -I/home/Jeroen/mingw-gcc-4.9.3/i686-493-posix-dwarf-rt_v3-s/mingw32/opt/include -I/home/Jeroen/mingw-gcc-4.9.3/prerequisites/i686-zlib-static/include -I/home/Jeroen/mingw-gcc-4.9.3/prerequisites/i686-w64-mingw32-static/include' CPPFLAGS= LDFLAGS='-pipe -L/home/Jeroen/mingw-gcc-4.9.3/i686-493-posix-dwarf-rt_v3-s/mingw32/opt/lib -L/home/Jeroen/mingw-gcc-4.9.3/prerequisites/i686-zlib-static/lib -L/home/Jeroen/mingw-gcc-4.9.3/prerequisites/i686-w64-mingw32-static/lib -Wl,--large-address-aware'

Thread model: posix

gcc version 4.9.3 (i686-posix-dwarf, Built by MinGW-W64 project) 

Here is the error:   

> fx <- inline::cxxfunction( signature(x = "integer", y = "numeric" ) , 'return ScalarReal( INTEGER(x)[0] * REAL(y)[0] ) ;', verbose=TRUE)

 >> Program source :

   1 : 

   2 : // includes from the plugin

   3 : #include <R.h>

   4 : #include <Rdefines.h>

   5 : #include <R_ext/Error.h>

   6 : 

   7 : 

   8 : // user includes

   9 : 

  10 : 

  11 : // declarations

  12 : extern "C" {

  13 : SEXP file55c40933844( SEXP x, SEXP y) ;

  14 : }

  15 : 

  16 : // definition

  17 : 

  18 : SEXP file55c40933844( SEXP x, SEXP y ){

  19 : return ScalarReal( INTEGER(x)[0] * REAL(y)[0] ) ; 

  20 : Rf_warning("your C++ program does not return anything"); 

  21 :  return R_NilValue ; 

  22 : }

  23 : 

  24 : 

Compilation argument:

 C:/R/R-3.3.1/bin/x64/R CMD SHLIB file55c40933844.cpp 2> file55c40933844.cpp.err.txt 

C:/Rtools/mingw_64/bin/g++  -I"C:/R/R-33~1.1/include" -DNDEBUG     -I"d:/Compiler/gcc-4.9.3/local330/include"     -O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function -Wno-ignored-attributes -Wno-deprecated-declarations -c file55c40933844.cpp -o file55c40933844.o

C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o file55c40933844.dll tmp.def file55c40933844.o -Ld:/Compiler/gcc-4.9.3/local330/lib/x64 -Ld:/Compiler/gcc-4.9.3/local330/lib -LC:/R/R-33~1.1/bin/x64 -lR

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

Program source:

  1: 

  2: // includes from the plugin

  3: #include <R.h>

  4: #include <Rdefines.h>

  5: #include <R_ext/Error.h>

  6: 

  7: 

  8: // user includes

  9: 

 10: 

 11: // declarations

 12: extern "C" {

 13: SEXP file55c40933844( SEXP x, SEXP y) ;

 14: }

 15: 

 16: // definition

 17: 

 18: SEXP file55c40933844( SEXP x, SEXP y ){

 19: return ScalarReal( INTEGER(x)[0] * REAL(y)[0] ) ; 

 20: Rf_warning("your C++ program does not return anything"); 

 21:  return R_NilValue ; 

 22: }

 23: 

 24: 

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

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

Thank you for your help!

Best,

Ding

[Daniel Lee]

Hi Ding,

Your R version needs to match your RTools version. You're on R 3.3 and RTools 3.4. Either upgrade R or downgrade RTools. (I think Ben would suggest you upgrade R.)

Daniel

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[Ding Zhou]

Hi Daniel,

At first, I tried Rtools33, and it didn't work either.  It had the same error: ERROR(s) during compilation: source code errors or compiler configuration errors! as now.  And at that time, R version was 3.3.1, gcc version was 4.6.3.  Ben told me that for R 3.3.x and Rtools33, I should be using gcc 4.9.x.  Therefore I upgrade to Rtools34, and the gcc version is 4.9.3 now.  But it still doesn't work.

Best,

Ding

[Ben Goodrich]

On Tuesday, September 13, 2016 at 11:54:23 AM UTC-4, Ding Zhou wrote:

At first, I tried Rtools33, and it didn't work either.  It had the same error: ERROR(s) during compilation: source code errors or compiler configuration errors! as now.  And at that time, R version was 3.3.1, gcc version was 4.6.3.  Ben told me that for R 3.3.x and Rtools33, I should be using gcc 4.9.x.  Therefore I upgrade to Rtools34, and the gcc version is 4.9.3 now.  But it still doesn't work.

RTools 3.4 is ostensibly legal but it is not frozen, so I would try to get it working with RTools33. The C++ code inline::cxxfunction is generating is now valid, so it must be a problem with how the compiler is configured.

Ben

[Ding Zhou]

Hi Ben and Daniel,

The problem has been solved now.  A folder for temporary variables in R is in wrong place.  Now both RTools33 and 34 work on my computer.  Thanks a lot for all your help during my debug procedure!

Best Regards,

Ding

[Daniel Lee]

Hi Ding,

I'm happy your problem was solved!

Could I ask how the folder was changed? How you knew that was the problem? And how you fixed it?

It might help other users in the future. 

Daniel

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[Ding Zhou]

Hi Daniel,

Sure!  I'm lucky to find that I keep a copy of all the error during the debugging.  

About one month ago, I changed the TEMP and TMP environment variables in User Variables from disk-C to D, but I miswrote the folder path.  It should be D:\USERTemp, but I wrote it as D:USERTemp.  (My computer somehow works well after that!)  

My classmate help me find this problem.  We could find it because when I ran the test stan function twice or more times, it would show the following error: Error in file(file, ifelse(append, "a", "w")) : cannot open the connection In addition: Warning message: In file(file, ifelse(append, "a", "w")) : cannot open file 'D:USERTemp/RtmpUrLY8M/file1a905e30692b.cpp': No such file or directory.  (If I just ran the test function once, it showed error as: Error in compileCode(f, code, language = language, verbose = verbose) : Compilation ERROR, function(s)/method(s) not created!)  It seemed that R cannot find the location of temporary cpp file, hence I changed the folder path, and the problem was settled!

This is how the whole thing goes on.  Hope it can help other users.  Please tell me if any detail unclear.

Best Regards,

Ding

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[Daniel Lee]

Thank you! That is really helpful.