[Mrtrix-discussion] Mrtrix3 install problem on mac

[Daniel Lumsden]

Dear All

I was hoping some one might have a bit of advise about installation of mrtrix3 on Max OSX 10.85.

Following the instructions on the wiki I get to the ./configure stage and then get the message below:



MRtrix build type requested: release

Checking C++ compiler [g++]: 4.2.1 - tested ok
Detecting OS: darwin
Detecting pointer size: 64 bit
Detecting byte order: little-endian
Checking for unordered_map: no


Checking for TR1 unordered_map: present
Checking for 64-bit integer type: yes
Checking for variable-length array support: yes
Checking for non-POD variable-length array support: no
Checking for zlib compression library: 1.2.5
Checking for POSIX threads: yes
Checking for GNU Scientific Library: Traceback (most recent call last):
  File "./configure", line 664, in <module>
    ''', cpp_flags + gsl_cflags, ld_flags + gsl_ldflags)
  File "./configure", line 320, in compile
    execute (cmd, CompileError)
  File "./configure", line 287, in execute
    process = subprocess.Popen (cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE, cwd=cwd)
  File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py", line 679, in __init__
    errread, errwrite)
  File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py", line 1228, in _execute_child
    raise child_exception
TypeError: execv() arg 2 must contain only strings



Can anywhere suggestion where it's going wrong? 

The full configure.log reads:


REPORT: 
MRtrix build type requested:

REPORT: release

REPORT: 

REPORT: Checking C++ compiler [g++]:
EXEC <<
CMD: g++ -dumpversion
EXIT: 0
STDOUT:
4.2.1
>>


REPORT: 4.2.1

COMPILE /var/folders/s3/4fmdnjr133j55ws3y7pl7c_h0000gn/T/tmp3BM9Ed.cpp:
---
int main() { return (0); }
---
EXEC <<
CMD: g++ -c /var/folders/s3/4fmdnjr133j55ws3y7pl7c_h0000gn/T/tmp3BM9Ed.cpp -o /var/folders/s3/4fmdnjr133j55ws3y7pl7c_h0000gn/T/tmp3BM9Ed.o
EXIT: 0
>>

EXEC <<
CMD: g++ /var/folders/s3/4fmdnjr133j55ws3y7pl7c_h0000gn/T/tmp3BM9Ed.o -o ./a.out
EXIT: 0
>>

EXEC <<
CMD: ./a.out
EXIT: 0
>>


REPORT:  - tested ok

REPORT: Detecting OS: darwin

REPORT: Detecting pointer size:

COMPILE /var/folders/s3/4fmdnjr133j55ws3y7pl7c_h0000gn/T/tmp0faCCk.cpp:
---

#include <iostream>
int main() { 
  std::cout << sizeof(void*); 
  return (0);
}

---
EXEC <<
CMD: g++ -c -DMRTRIX_MACOSX -fPIC /var/folders/s3/4fmdnjr133j55ws3y7pl7c_h0000gn/T/tmp0faCCk.cpp -o /var/folders/s3/4fmdnjr133j55ws3y7pl7c_h0000gn/T/tmp0faCCk.o
EXIT: 0
>>

EXEC <<
CMD: g++ /var/folders/s3/4fmdnjr133j55ws3y7pl7c_h0000gn/T/tmp0faCCk.o -o ./a.out
EXIT: 0
>>

EXEC <<
CMD: ./a.out
EXIT: 0
STDOUT:
8
>>


REPORT: 64 bit

REPORT: Detecting byte order:

REPORT: little-endian

REPORT: Checking for unordered_map:

COMPILE /var/folders/s3/4fmdnjr133j55ws3y7pl7c_h0000gn/T/tmpsepkJK.cpp:
---

#include <unordered_map>

int main() { 
  std::unordered_map<int,int> map; 
  return (map.size());
}

---
EXEC <<
CMD: g++ -c -DMRTRIX_MACOSX -fPIC -DMRTRIX_WORD64 /var/folders/s3/4fmdnjr133j55ws3y7pl7c_h0000gn/T/tmpsepkJK.cpp -o /var/folders/s3/4fmdnjr133j55ws3y7pl7c_h0000gn/T/tmpsepkJK.o
EXIT: 1
STDERR:
/var/folders/s3/4fmdnjr133j55ws3y7pl7c_h0000gn/T/tmpsepkJK.cpp:2:10: fatal error: 'unordered_map' file not found
#include <unordered_map>
         ^
1 error generated.
>>

error deleting temporary file "/var/folders/s3/4fmdnjr133j55ws3y7pl7c_h0000gn/T/tmpsepkJK.o": No such file or directory
REPORT: no

REPORT: Checking for TR1 unordered_map:

COMPILE /var/folders/s3/4fmdnjr133j55ws3y7pl7c_h0000gn/T/tmpmO11Nk.cpp:
---

#include <tr1/unordered_map>

int main() { 
  std::tr1::unordered_map<int,int> map; 
  return (map.size());
}

---
EXEC <<
CMD: g++ -c -DMRTRIX_MACOSX -fPIC -DMRTRIX_WORD64 /var/folders/s3/4fmdnjr133j55ws3y7pl7c_h0000gn/T/tmpmO11Nk.cpp -o /var/folders/s3/4fmdnjr133j55ws3y7pl7c_h0000gn/T/tmpmO11Nk.o
EXIT: 0
>>

EXEC <<
CMD: g++ /var/folders/s3/4fmdnjr133j55ws3y7pl7c_h0000gn/T/tmpmO11Nk.o -o ./a.out
EXIT: 0
>>

EXEC <<
CMD: ./a.out
EXIT: 0
>>


REPORT: present

REPORT: Checking for 64-bit integer type:

COMPILE /var/folders/s3/4fmdnjr133j55ws3y7pl7c_h0000gn/T/tmpBYDEbz.cpp:
---

#include <stdint.h>

int main() { 
  int64_t t = 0; 
  return (t); 
}

---
EXEC <<
CMD: g++ -c -DMRTRIX_MACOSX -fPIC -DMRTRIX_WORD64 -DMRTRIX_USE_TR1 /var/folders/s3/4fmdnjr133j55ws3y7pl7c_h0000gn/T/tmpBYDEbz.cpp -o /var/folders/s3/4fmdnjr133j55ws3y7pl7c_h0000gn/T/tmpBYDEbz.o
EXIT: 0
>>

EXEC <<
CMD: g++ /var/folders/s3/4fmdnjr133j55ws3y7pl7c_h0000gn/T/tmpBYDEbz.o -o ./a.out
EXIT: 0
>>

EXEC <<
CMD: ./a.out
EXIT: 0
>>


REPORT: yes

REPORT: Checking for variable-length array support:

COMPILE /var/folders/s3/4fmdnjr133j55ws3y7pl7c_h0000gn/T/tmpBp048Z.cpp:
---


int main(int argc, char* argv[]) { 
  int x[argc];
  return 0; 
}

---
EXEC <<
CMD: g++ -c -DMRTRIX_MACOSX -fPIC -DMRTRIX_WORD64 -DMRTRIX_USE_TR1 /var/folders/s3/4fmdnjr133j55ws3y7pl7c_h0000gn/T/tmpBp048Z.cpp -o /var/folders/s3/4fmdnjr133j55ws3y7pl7c_h0000gn/T/tmpBp048Z.o
EXIT: 0
>>

EXEC <<
CMD: g++ /var/folders/s3/4fmdnjr133j55ws3y7pl7c_h0000gn/T/tmpBp048Z.o -o ./a.out
EXIT: 0
>>

EXEC <<
CMD: ./a.out
EXIT: 0
>>


REPORT: yes

REPORT: Checking for non-POD variable-length array support:

COMPILE /var/folders/s3/4fmdnjr133j55ws3y7pl7c_h0000gn/T/tmpyT8mR_.cpp:
---

#include <string>

class X {
  int x;
  double y;
  std::string s;
};

int main(int argc, char* argv[]) { 
  X x[argc];
  return 0; 
}

---
EXEC <<
CMD: g++ -c -DMRTRIX_MACOSX -fPIC -DMRTRIX_WORD64 -DMRTRIX_USE_TR1 /var/folders/s3/4fmdnjr133j55ws3y7pl7c_h0000gn/T/tmpyT8mR_.cpp -o /var/folders/s3/4fmdnjr133j55ws3y7pl7c_h0000gn/T/tmpyT8mR_.o
EXIT: 1
STDERR:
/var/folders/s3/4fmdnjr133j55ws3y7pl7c_h0000gn/T/tmpyT8mR_.cpp:11:6: error: variable length array of non-POD element type 'X'
  X x[argc];
     ^
1 error generated.
>>

error deleting temporary file "/var/folders/s3/4fmdnjr133j55ws3y7pl7c_h0000gn/T/tmpyT8mR_.o": No such file or directory
REPORT: no

REPORT: Checking for zlib compression library:

COMPILE /var/folders/s3/4fmdnjr133j55ws3y7pl7c_h0000gn/T/tmpZp0WEo.cpp:
---

#include <iostream>
#include <zlib.h>

int main() { 
  std::cout << zlibVersion(); 
  return (0);
}

---
EXEC <<
CMD: g++ -c -DMRTRIX_MACOSX -fPIC -DMRTRIX_WORD64 -DMRTRIX_USE_TR1 -DMRTRIX_NO_NON_POD_VLA /var/folders/s3/4fmdnjr133j55ws3y7pl7c_h0000gn/T/tmpZp0WEo.cpp -o /var/folders/s3/4fmdnjr133j55ws3y7pl7c_h0000gn/T/tmpZp0WEo.o
EXIT: 0
>>

EXEC <<
CMD: g++ /var/folders/s3/4fmdnjr133j55ws3y7pl7c_h0000gn/T/tmpZp0WEo.o -lz -o ./a.out
EXIT: 0
>>

EXEC <<
CMD: ./a.out
EXIT: 0
STDOUT:
1.2.5
>>


REPORT: 1.2.5

REPORT: Checking for POSIX threads:

COMPILE /var/folders/s3/4fmdnjr133j55ws3y7pl7c_h0000gn/T/tmpVgCVmZ.cpp:
---

#include <pthread.h>

void* func (void*) { return (NULL); } 

int main() { 
  pthread_t t; 
  if (pthread_create(&t, NULL, func, NULL)) return (1);
  pthread_exit (NULL); 
  return (0); 
}

---
EXEC <<
CMD: g++ -c -DMRTRIX_MACOSX -fPIC -DMRTRIX_WORD64 -DMRTRIX_USE_TR1 -DMRTRIX_NO_NON_POD_VLA /var/folders/s3/4fmdnjr133j55ws3y7pl7c_h0000gn/T/tmpVgCVmZ.cpp -o /var/folders/s3/4fmdnjr133j55ws3y7pl7c_h0000gn/T/tmpVgCVmZ.o
EXIT: 0
>>

EXEC <<
CMD: g++ /var/folders/s3/4fmdnjr133j55ws3y7pl7c_h0000gn/T/tmpVgCVmZ.o -lz -lpthread -o ./a.out
EXIT: 0
>>

EXEC <<
CMD: ./a.out
EXIT: 0
>>


REPORT: yes

REPORT: Checking for GNU Scientific Library:
EXEC <<
CMD: gsl-config --cflags
EXIT: 0
STDOUT:
-I/opt/local/include
>>

EXEC <<
CMD: gsl-config --libs
EXIT: 0
STDOUT:
-L/opt/local/lib -lgsl -lgslcblas
>>


COMPILE /var/folders/s3/4fmdnjr133j55ws3y7pl7c_h0000gn/T/tmpb6eI_g.cpp:
---

#include <iostream>
#include <gsl/gsl_version.h>
#include <gsl/gsl_matrix.h>

int main() { 
  std::cout << gsl_version; 
  gsl_matrix* M = gsl_matrix_alloc (3,3); 
  return (M->size1 != 3);
}

---
EXEC <<
CMD: g++ -c -DMRTRIX_MACOSX -fPIC -DMRTRIX_WORD64 -DMRTRIX_USE_TR1 -DMRTRIX_NO_NON_POD_VLA -I/opt/local/include /var/folders/s3/4fmdnjr133j55ws3y7pl7c_h0000gn/T/tmpb6eI_g.cpp -o /var/folders/s3/4fmdnjr133j55ws3y7pl7c_h0000gn/T/tmpb6eI_g.o
error deleting temporary file "/var/folders/s3/4fmdnjr133j55ws3y7pl7c_h0000gn/T/tmpb6eI_g.o": No such file or directory 


Many thanks in advance and apologies for the long post

Dan
 		 	   		  
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