[Mrtrix-discussion] Mrtrix-discussion Digest, Vol 66, Issue 3
Michael Zeineh
mmzeineh at gmail.com
Wed Sep 17 10:06:35 PDT 2014
Just checking if anyone has figure the problem with installation of 0.3 on a mac out, I run into the same problem on 10.7.5.
Thank you.
On Jul 11, 2014, at 12:00 PM, mrtrix-discussion-request at www.nitrc.org wrote:
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> 1. Mrtrix3 install problem on mac (Daniel Lumsden)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 11 Jul 2014 14:51:37 +0000
> From: Daniel Lumsden <doclumsden at hotmail.com>
> To: "mrtrix-discussion at www.nitrc.org"
> <mrtrix-discussion at www.nitrc.org>
> Subject: [Mrtrix-discussion] Mrtrix3 install problem on mac
> Message-ID: <DUB123-W39AC1DB4E16B0111EAEB7DCF090 at phx.gbl>
> Content-Type: text/plain; charset="iso-8859-1"
>
> 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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