'lvm-g++-4.2: command not found' error after installing XCode 5.0 on Mac OS 10.8.5

[Dale]

Hi - I'm attempting to install rstan on Mac OS 10.8.5.  I installed XCode 5.0 and Command Line Tools.

> sessionInfo()

R version 3.0.2 (2013-09-25)

Platform: x86_64-apple-darwin10.8.0 (64-bit)

When I run the suggested code to test the C++ compiler ...

I get the appended error message.

Suggestions?  Thanks.  --Dale

/bin/sh: llvm-g++-4.2: command not found

make: *** [file9ec1ba6fc12.o] Error 127

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: 

 18: // user includes

 19: 

 20: 

 21: // declarations

 22: extern "C" {

 23: SEXP file9ec1ba6fc12( ) ;

 24: }

 25: 

 26: // definition

 27: 

 28: SEXP file9ec1ba6fc12(  ){

 29: BEGIN_RCPP

 30:  

 31:   std::vector<std::string> s; 

 32:   s.push_back("hello");

 33:   s.push_back("world");

 34:   return Rcpp::wrap(s);

 35: 

 36: END_RCPP

 37: }

 38: 

 39: 

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

  Compilation ERROR, function(s)/method(s) not created! /bin/sh: llvm-g++-4.2: command not found

make: *** [file9ec1ba6fc12.o] Error 127

In addition: Warning message:

running command '/Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB file9ec1ba6fc12.cpp 2> file9ec1ba6fc12.cpp.err.txt' had status 1 

> cat(hellofun(), '\n') 

Error in cat(hellofun(), "\n") : could not find function "hellofun"

/bin/sh: llvm-g++-4.2: command not found

make: *** [file9ec1ba6fc12.o] Error 127

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: 

 18: // user includes

 19: 

 20: 

 21: // declarations

 22: extern "C" {

 23: SEXP file9ec1ba6fc12( ) ;

 24: }

 25: 

 26: // definition

 27: 

 28: SEXP file9ec1ba6fc12(  ){

 29: BEGIN_RCPP

 30:  

 31:   std::vector<std::string> s; 

 32:   s.push_back("hello");

 33:   s.push_back("world");

 34:   return Rcpp::wrap(s);

 35: 

 36: END_RCPP

 37: }

 38: 

 39: 

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

  Compilation ERROR, function(s)/method(s) not created! /bin/sh: llvm-g++-4.2: command not found

make: *** [file9ec1ba6fc12.o] Error 127

In addition: Warning message:

running command '/Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB file9ec1ba6fc12.cpp 2> file9ec1ba6fc12.cpp.err.txt' had status 1 

> cat(hellofun(), '\n') 

Error in cat(hellofun(), "\n") : could not find function "hellofun"

[Bob Carpenter]

Did you turn on the command-line tools through Xcode?

If so, what happens when you run:

> which g++

This should be from a new terminal window, of course, after
the install of the command-line tools, so it'll pick up
new paths.

- Bob

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[Dale]

Not clear to me how to turn on the command-line tools through Xcode. Sounds like I must do something in addition to installing the command-line tools?

elGrande:~ dsteele$ which g++

/usr/bin/g++

elGrande:~ dsteele$ g++ -v

Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1

Apple LLVM version 5.0 (clang-500.2.76) (based on LLVM 3.3svn)

Target: x86_64-apple-darwin12.5.0

Thread model: posix

Thanks.  --Dale

[Jiqiang Guo]

The reason might be that in the c++ compiler defined in your R's default Makeconf file (its path can be found by executing R.home("etc")), it reads as follows:

CXX = llvm-g++-4.2 -arch x86_64

But in Xcode 5, this llvm-g++-4.2 does not exist any more.  You need to change it to just g++ or you can create a Makeconf file in your home directory and define CXX there.

Again, to find the file:

> R.home("etc")

[1] "/Library/Frameworks/R.framework/Resources/etc"

--

Jiqiang 

[Dale]

Thanks. 

I've edited the Makeconf in:

 /Library/Frameworks/R.framework/Resources/etc

and pasted below.  Unfortunately, same error. --Dale

# etc/Makeconf.  Generated from Makeconf.in by configure.

#

# ${R_HOME}/etc/Makeconf

#

# R was configured using the following call

# (not including env. vars and site configuration)

# configure  'CC=llvm-gcc-4.2 -arch x86_64 -std=gnu99' 'CXX=llvm-g++' 'OBJC=llvm-gcc-4.2 -arch x86_64' 'F77=gfortran-4.2 -arch x86_64' 'FC=gfortran-4.2 -arch x86_64' 'CFLAGS=-mtune=core2 -g -O2' 'CXXFLAGS=-mtune=core2 -g -O2' 'OBJCFLAGS=-mtune=core2 -g -O2' 'FCFLAGS=-g -O2' 'F77FLAGS=-g -O2' '--with-system-zlib' '--enable-memory-profiling' '--disable-openmp' '--with-tcltk=/usr/local/lib'

## This fails if it contains spaces, or if it is quoted

include $(R_SHARE_DIR)/make/vars.mk

AR = ar

## Used by packages 'maps' and 'mapdata'

AWK = awk

BLAS_LIBS = -L$(R_HOME)/lib$(R_ARCH) -lRblas

C_VISIBILITY = 

CC = llvm-gcc-4.2 -arch x86_64 -std=gnu99

CFLAGS = -mtune=core2 -g -O2 $(LTO)

CPICFLAGS = -fPIC

[Jiqiang Guo]

I did not see the definition of CXX from what you posted.  Anyway, again the CXX defined in that file should exist in your system and be a c++ compiler. 

--

Jiqiang 

[Dale]

Sorry to be dense - I've tried 'CXX=llvm-g++' and 'CXX=g++'.  Neither seems to work. In a default install of Xcode 5 - how should 'CXX=....' be defined?  Thanks.  --Dale

On Thursday, October 17, 2013 6:05:48 PM UTC-4, Jiqiang Guo wrote:

[Bob Carpenter]

It should just be "g++".

Have you installed the command-line tools along with Xcode? That
should set up the "g++" command for you. At that point, you should
be able to type:

$ g++ --version

into a terminal window and see that it's the latest version. For
me, that looks like:

$ g++ --version

Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1
Apple LLVM version 5.0 (clang-500.2.76) (based on LLVM 3.3svn)
Target: x86_64-apple-darwin12.5.0
Thread model: posix

- Bob