Installation Problems in cmdstan 2.14 on mac: string: No such file or directory

[Lu Zhang]

Hi everyone,

    I failed to install CmdStan 2.14 on my computer. The error report I got is as follows:

g++ -I src -I stan/src -I usr/include -isystem stan/lib/stan_math/ -isystem stan/lib/stan_math/lib/eigen_3.2.9 -isystem stan/lib/stan_math/lib/boost_1.62.0 -isystem stan/lib/stan_math/lib/cvodes_2.9.0/include -Wall -DEIGEN_NO_DEBUG  -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -DFUSION_MAX_VECTOR_SIZE=12 -DNO_FPRINTF_OUTPUT -pipe  -Wno-unused-function   -c -O3 -o bin/cmdstan/stanc.o src/cmdstan/stanc.cpp

In file included from stan/src/stan/command/stanc_helper.hpp:4:0,

                 from src/cmdstan/stanc.cpp:1:

stan/src/stan/version.hpp:4:18: fatal error: string: No such file or directory

 #include <string>

                  ^

compilation terminated.

make: *** [bin/cmdstan/stanc.o] Error 1

I included folder usr/include which has string.h, but it didn't solve the problem. My operating system is OS X EI Capitan

Thanks,

Lu Zhang

[Daniel Lee]

Hi Lu, 

It looks like you don't have a complete installation. Did you git clone CmdStan? If so, you have to follow these directions: https://github.com/stan-dev/cmdstan/wiki/Getting-Started-with-CmdStan

Hopefully that's the issue. If not, perhaps tell us how you grabbed CmdStan. 

Daniel

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[Michael Betancourt]

Also, it would help to send a full report of your local computing environment

and compilers.  You’re calling g++ which already is interesting, and the string 

error often arises with compilier/core library mismatches.

[Daniel Lee]

Michael is right; I don't think I read the error correctly. 

That does look like a library issue. 

Can you type 'g++ -v' and report the result?

Daniel

[Lu Zhang]

Thank yo so much! This is the result of 'g++ -v':

s-149-142-31-228:cmdstan luzhang$ g++ -v

Using built-in specs.

COLLECT_GCC=g++

COLLECT_LTO_WRAPPER=/usr/local/libexec/gcc/x86_64-apple-darwin14.0.0/4.9.2/lto-wrapper

Target: x86_64-apple-darwin14.0.0

Configured with: ../gcc-4.9-20141029/configure --enable-languages=c++,fortran

Thread model: posix

gcc version 4.9.2 20141029 (prerelease) (GCC) 

[Daniel Lee]

I'll try to reproduce on a Windows machine today. That shouldn't be happening. 

Daniel

[Michael Betancourt]

It looks like Lu’s on a Mac, which makes the default to g++

even weirder as clang should be called be default on OS X.

[Daniel Lee]

I'm definitely not thinking straight. 

Lu, did you change anything in your make/local file?

Daniel

[Lu Zhang]

I got the same error report before I edited the makefile. Let me update my system and redo it again. I will let you know the result later. Thank you very much!

Best,

Lu Zhang

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[Lu Zhang]

Hi Daniel and Michael,

    I updated my system into macOS Sierra Version 10.12.3, Xcode into 8.3, and redo the whole process from "git clone CmdStan". But I still got the same error report. Then I changed the option CC in makefile from g++ into clang++ and finally built CmdStan successfully.  I think maybe CmdStan can only be compiled by clang++ on OS X. 

##

# Users should only need to set these three variables for use.

# - CC: The compiler to use. Expecting g++ or clang++.

# - O: Optimization level. Valid values are {0, 1, 2, 3}.

# - AR: archiver (must specify for cross-compiling)

# - OS: {mac, win, linux}. 

##

#CC = g++

CC = clang++

Thank you for all your help!

Lu Zhang

[Daniel Lee]

Hi Lu,

I don't know where you got that g++ and how it's configured. When I type `g++ -v` from the command line, I get:

$ g++ -v
Configured with: --prefix=/Library/Developer/CommandLineTools/usr --with-gxx-include-dir=/usr/include/c++/4.2.1
Apple LLVM version 8.0.0 (clang-800.0.42.1)
Target: x86_64-apple-darwin16.4.0
Thread model: posix
InstalledDir: /Library/Developer/CommandLineTools/usr/bin

This is the one installed with XCode.

Did you install your g++ 4.9.3 prerelease from homebrew or macports? Maybe `which g++` will help us find out where that is.

Daniel

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[Lu Zhang]

Hi Daniel,

    

    Yes, I remember I got g++ from homebrew. I also have macports. 

Best,

Lu Zhang

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