[Mrtrix-discussion] Mrtrix-discussion Digest, Vol 66, Issue 3

J-Donald Tournier jdtournier at gmail.com
Wed Sep 17 12:11:57 PDT 2014 

Hi Michael,

Yes, this is a weird one. In my experience, this one is due to gsl-config
returning non-ASCII characters - from what I've seen it returns 16 bit wide
characters, which then causes an issue for the subsequent command. I don't
really know how to get around it, but people have had some success using a
different version of python. One person simply installed the 64 bit version
of python instead, and that fixed it for some mysterious reason, but
personally I think it's probably a matter of choosing one compiled with the
right options. I'm guessing this'll change between macports, fink,
homebrew, etc., which may be why some versions work and others don't...

If you do get to the bottom of it, please report back, we'll try to include
a fix for it. I just haven't had the chance to investigate - the Mac I'm
using for testing doesn't have this issue...

Hope this helps,
Donald

--
Dr J-Donald Tournier (PhD)

Senior Lecturer, Biomedical Engineering
Division of Imaging Sciences & Biomedical Engineering
King's College London

A: Department of Perinatal Imaging & Health, 1st Floor South Wing, St
Thomas' Hospital, London. SE1 7EH
T: +44 (0)20 7188 7118 ext 53613
W:
http://www.kcl.ac.uk/medicine/research/divisions/imaging/departments/biomedengineering

On 17 Sep 2014 18:06, "Michael Zeineh" <mmzeineh at gmail.com> wrote:

> 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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> Today's Topics:
>
>   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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