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<body class='hmmessage'><div dir='ltr'>Dear All<br><br>I was hoping some one might have a bit of advise about installation of mrtrix3 on Max OSX 10.85.<br><br>Following the instructions on the wiki I get to the ./configure stage and then get the message below:<br><br><br><br>MRtrix build type requested: release<br><br>Checking C++ compiler [g++]: 4.2.1 - tested ok<br>Detecting OS: darwin<br>Detecting pointer size: 64 bit<br>Detecting byte order: little-endian<br>Checking for unordered_map: no<br><br><br>Checking for TR1 unordered_map: present<br>Checking for 64-bit integer type: yes<br>Checking for variable-length array support: yes<br>Checking for non-POD variable-length array support: no<br>Checking for zlib compression library: 1.2.5<br>Checking for POSIX threads: yes<br>Checking for GNU Scientific Library: Traceback (most recent call last):<br> File "./configure", line 664, in <module><br> ''', cpp_flags + gsl_cflags, ld_flags + gsl_ldflags)<br> File "./configure", line 320, in compile<br> execute (cmd, CompileError)<br> File "./configure", line 287, in execute<br> process = subprocess.Popen (cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE, cwd=cwd)<br> File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py", line 679, in __init__<br> errread, errwrite)<br> File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py", line 1228, in _execute_child<br> raise child_exception<br>TypeError: execv() arg 2 must contain only strings<br><br><br><br>Can anywhere suggestion where it's going wrong? <br><br>The full configure.log reads:<br><br><br>REPORT: <br>MRtrix build type requested:<br><br>REPORT: release<br><br>REPORT: <br><br>REPORT: Checking C++ compiler [g++]:<br>EXEC <<<br>CMD: g++ -dumpversion<br>EXIT: 0<br>STDOUT:<br>4.2.1<br>>><br><br><br>REPORT: 4.2.1<br><br>COMPILE /var/folders/s3/4fmdnjr133j55ws3y7pl7c_h0000gn/T/tmp3BM9Ed.cpp:<br>---<br>int main() { return (0); }<br>---<br>EXEC <<<br>CMD: g++ -c /var/folders/s3/4fmdnjr133j55ws3y7pl7c_h0000gn/T/tmp3BM9Ed.cpp -o /var/folders/s3/4fmdnjr133j55ws3y7pl7c_h0000gn/T/tmp3BM9Ed.o<br>EXIT: 0<br>>><br><br>EXEC <<<br>CMD: g++ /var/folders/s3/4fmdnjr133j55ws3y7pl7c_h0000gn/T/tmp3BM9Ed.o -o ./a.out<br>EXIT: 0<br>>><br><br>EXEC <<<br>CMD: ./a.out<br>EXIT: 0<br>>><br><br><br>REPORT: - tested ok<br><br>REPORT: Detecting OS: darwin<br><br>REPORT: Detecting pointer size:<br><br>COMPILE /var/folders/s3/4fmdnjr133j55ws3y7pl7c_h0000gn/T/tmp0faCCk.cpp:<br>---<br><br>#include <iostream><br>int main() { <br> std::cout << sizeof(void*); <br> return (0);<br>}<br><br>---<br>EXEC <<<br>CMD: g++ -c -DMRTRIX_MACOSX -fPIC /var/folders/s3/4fmdnjr133j55ws3y7pl7c_h0000gn/T/tmp0faCCk.cpp -o /var/folders/s3/4fmdnjr133j55ws3y7pl7c_h0000gn/T/tmp0faCCk.o<br>EXIT: 0<br>>><br><br>EXEC <<<br>CMD: g++ /var/folders/s3/4fmdnjr133j55ws3y7pl7c_h0000gn/T/tmp0faCCk.o -o ./a.out<br>EXIT: 0<br>>><br><br>EXEC <<<br>CMD: ./a.out<br>EXIT: 0<br>STDOUT:<br>8<br>>><br><br><br>REPORT: 64 bit<br><br>REPORT: Detecting byte order:<br><br>REPORT: little-endian<br><br>REPORT: Checking for unordered_map:<br><br>COMPILE /var/folders/s3/4fmdnjr133j55ws3y7pl7c_h0000gn/T/tmpsepkJK.cpp:<br>---<br><br>#include <unordered_map><br><br>int main() { <br> std::unordered_map<int,int> map; <br> return (map.size());<br>}<br><br>---<br>EXEC <<<br>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<br>EXIT: 1<br>STDERR:<br>/var/folders/s3/4fmdnjr133j55ws3y7pl7c_h0000gn/T/tmpsepkJK.cpp:2:10: fatal error: 'unordered_map' file not found<br>#include <unordered_map><br> ^<br>1 error generated.<br>>><br><br>error deleting temporary file "/var/folders/s3/4fmdnjr133j55ws3y7pl7c_h0000gn/T/tmpsepkJK.o": No such file or directory<br>REPORT: no<br><br>REPORT: Checking for TR1 unordered_map:<br><br>COMPILE /var/folders/s3/4fmdnjr133j55ws3y7pl7c_h0000gn/T/tmpmO11Nk.cpp:<br>---<br><br>#include <tr1/unordered_map><br><br>int main() { <br> std::tr1::unordered_map<int,int> map; <br> return (map.size());<br>}<br><br>---<br>EXEC <<<br>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<br>EXIT: 0<br>>><br><br>EXEC <<<br>CMD: g++ /var/folders/s3/4fmdnjr133j55ws3y7pl7c_h0000gn/T/tmpmO11Nk.o -o ./a.out<br>EXIT: 0<br>>><br><br>EXEC <<<br>CMD: ./a.out<br>EXIT: 0<br>>><br><br><br>REPORT: present<br><br>REPORT: Checking for 64-bit integer type:<br><br>COMPILE /var/folders/s3/4fmdnjr133j55ws3y7pl7c_h0000gn/T/tmpBYDEbz.cpp:<br>---<br><br>#include <stdint.h><br><br>int main() { <br> int64_t t = 0; <br> return (t); <br>}<br><br>---<br>EXEC <<<br>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<br>EXIT: 0<br>>><br><br>EXEC <<<br>CMD: g++ /var/folders/s3/4fmdnjr133j55ws3y7pl7c_h0000gn/T/tmpBYDEbz.o -o ./a.out<br>EXIT: 0<br>>><br><br>EXEC <<<br>CMD: ./a.out<br>EXIT: 0<br>>><br><br><br>REPORT: yes<br><br>REPORT: Checking for variable-length array support:<br><br>COMPILE /var/folders/s3/4fmdnjr133j55ws3y7pl7c_h0000gn/T/tmpBp048Z.cpp:<br>---<br><br><br>int main(int argc, char* argv[]) { <br> int x[argc];<br> return 0; <br>}<br><br>---<br>EXEC <<<br>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<br>EXIT: 0<br>>><br><br>EXEC <<<br>CMD: g++ /var/folders/s3/4fmdnjr133j55ws3y7pl7c_h0000gn/T/tmpBp048Z.o -o ./a.out<br>EXIT: 0<br>>><br><br>EXEC <<<br>CMD: ./a.out<br>EXIT: 0<br>>><br><br><br>REPORT: yes<br><br>REPORT: Checking for non-POD variable-length array support:<br><br>COMPILE /var/folders/s3/4fmdnjr133j55ws3y7pl7c_h0000gn/T/tmpyT8mR_.cpp:<br>---<br><br>#include <string><br><br>class X {<br> int x;<br> double y;<br> std::string s;<br>};<br><br>int main(int argc, char* argv[]) { <br> X x[argc];<br> return 0; <br>}<br><br>---<br>EXEC <<<br>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<br>EXIT: 1<br>STDERR:<br>/var/folders/s3/4fmdnjr133j55ws3y7pl7c_h0000gn/T/tmpyT8mR_.cpp:11:6: error: variable length array of non-POD element type 'X'<br> X x[argc];<br> ^<br>1 error generated.<br>>><br><br>error deleting temporary file "/var/folders/s3/4fmdnjr133j55ws3y7pl7c_h0000gn/T/tmpyT8mR_.o": No such file or directory<br>REPORT: no<br><br>REPORT: Checking for zlib compression library:<br><br>COMPILE /var/folders/s3/4fmdnjr133j55ws3y7pl7c_h0000gn/T/tmpZp0WEo.cpp:<br>---<br><br>#include <iostream><br>#include <zlib.h><br><br>int main() { <br> std::cout << zlibVersion(); <br> return (0);<br>}<br><br>---<br>EXEC <<<br>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<br>EXIT: 0<br>>><br><br>EXEC <<<br>CMD: g++ /var/folders/s3/4fmdnjr133j55ws3y7pl7c_h0000gn/T/tmpZp0WEo.o -lz -o ./a.out<br>EXIT: 0<br>>><br><br>EXEC <<<br>CMD: ./a.out<br>EXIT: 0<br>STDOUT:<br>1.2.5<br>>><br><br><br>REPORT: 1.2.5<br><br>REPORT: Checking for POSIX threads:<br><br>COMPILE /var/folders/s3/4fmdnjr133j55ws3y7pl7c_h0000gn/T/tmpVgCVmZ.cpp:<br>---<br><br>#include <pthread.h><br><br>void* func (void*) { return (NULL); } <br><br>int main() { <br> pthread_t t; <br> if (pthread_create(&t, NULL, func, NULL)) return (1);<br> pthread_exit (NULL); <br> return (0); <br>}<br><br>---<br>EXEC <<<br>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<br>EXIT: 0<br>>><br><br>EXEC <<<br>CMD: g++ /var/folders/s3/4fmdnjr133j55ws3y7pl7c_h0000gn/T/tmpVgCVmZ.o -lz -lpthread -o ./a.out<br>EXIT: 0<br>>><br><br>EXEC <<<br>CMD: ./a.out<br>EXIT: 0<br>>><br><br><br>REPORT: yes<br><br>REPORT: Checking for GNU Scientific Library:<br>EXEC <<<br>CMD: gsl-config --cflags<br>EXIT: 0<br>STDOUT:<br>-I/opt/local/include<br>>><br><br>EXEC <<<br>CMD: gsl-config --libs<br>EXIT: 0<br>STDOUT:<br>-L/opt/local/lib -lgsl -lgslcblas<br>>><br><br><br>COMPILE /var/folders/s3/4fmdnjr133j55ws3y7pl7c_h0000gn/T/tmpb6eI_g.cpp:<br>---<br><br>#include <iostream><br>#include <gsl/gsl_version.h><br>#include <gsl/gsl_matrix.h><br><br>int main() { <br> std::cout << gsl_version; <br> gsl_matrix* M = gsl_matrix_alloc (3,3); <br> return (M->size1 != 3);<br>}<br><br>---<br>EXEC <<<br>CMD: g++ -c -DMRTRIX_MACOSX -fPIC -DMRTRIX_WORD64 -DMRTRIX_USE_TR1 -DMRTRIX_NO_NON_POD_VLA - I / o p t / l o c a l / i n c l u d e /var/folders/s3/4fmdnjr133j55ws3y7pl7c_h0000gn/T/tmpb6eI_g.cpp -o /var/folders/s3/4fmdnjr133j55ws3y7pl7c_h0000gn/T/tmpb6eI_g.o<br>error deleting temporary file "/var/folders/s3/4fmdnjr133j55ws3y7pl7c_h0000gn/T/tmpb6eI_g.o": No such file or directory <br><br><br>Many thanks in advance and apologies for the long post<br><br>Dan<br> </div></body>
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