<p dir="ltr">Hi Michael,</p>
<p dir="ltr">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...</p>
<p dir="ltr">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...</p>
<p dir="ltr">Hope this helps,<br>
Donald<br></p>
<p dir="ltr">--<br>
Dr J-Donald Tournier (PhD)</p>
<p dir="ltr">Senior Lecturer, Biomedical Engineering<br>
Division of Imaging Sciences & Biomedical Engineering<br>
King's College London</p>
<p dir="ltr">A: Department of Perinatal Imaging & Health, 1st Floor South Wing, St Thomas' Hospital, London. SE1 7EH<br>
T: +44 (0)20 7188 7118 ext 53613<br>
W: <a href="http://www.kcl.ac.uk/medicine/research/divisions/imaging/departments/biomedengineering">http://www.kcl.ac.uk/medicine/research/divisions/imaging/departments/biomedengineering</a><br>
</p>
<div class="gmail_quote">On 17 Sep 2014 18:06, "Michael Zeineh" <<a href="mailto:mmzeineh@gmail.com">mmzeineh@gmail.com</a>> wrote:<br type="attribution"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word">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.<div><br><div>
<span style="border-collapse:separate;color:rgb(0,0,0);font-family:Helvetica;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:-webkit-auto;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;font-size:medium"><span style="border-collapse:separate;color:rgb(0,0,0);font-family:Helvetica;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:-webkit-auto;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;font-size:medium"><div style="word-wrap:break-word"><span style="border-collapse:separate;color:rgb(0,0,0);font-family:Helvetica;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:-webkit-auto;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;font-size:medium"><div style="word-wrap:break-word"><span style="border-collapse:separate;color:rgb(0,0,0);font-family:Helvetica;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:-webkit-auto;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;font-size:medium"><div style="word-wrap:break-word"><span style="border-collapse:separate;color:rgb(0,0,0);font-family:Helvetica;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:-webkit-auto;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;font-size:medium"><div style="word-wrap:break-word">Thank you.</div><div style="word-wrap:break-word"><br></div></span></div></span></div></span></div></span></span></div><div><div>On Jul 11, 2014, at 12:00 PM, <a href="mailto:mrtrix-discussion-request@www.nitrc.org" target="_blank">mrtrix-discussion-request@www.nitrc.org</a> wrote:</div><br><blockquote type="cite">Send Mrtrix-discussion mailing list submissions to<br><span style="white-space:pre-wrap"> </span><a href="mailto:mrtrix-discussion@www.nitrc.org" target="_blank">mrtrix-discussion@www.nitrc.org</a><br><br>To subscribe or unsubscribe via the World Wide Web, visit<br><span style="white-space:pre-wrap"> </span><a href="http://www.nitrc.org/mailman/listinfo/mrtrix-discussion" target="_blank">http://www.nitrc.org/mailman/listinfo/mrtrix-discussion</a><br>or, via email, send a message with subject or body 'help' to<br><span style="white-space:pre-wrap"> </span><a href="mailto:mrtrix-discussion-request@www.nitrc.org" target="_blank">mrtrix-discussion-request@www.nitrc.org</a><br><br>You can reach the person managing the list at<br><span style="white-space:pre-wrap"> </span><a href="mailto:mrtrix-discussion-owner@www.nitrc.org" target="_blank">mrtrix-discussion-owner@www.nitrc.org</a><br><br>When replying, please edit your Subject line so it is more specific<br>than "Re: Contents of Mrtrix-discussion digest..."<br><br><br>Today's Topics:<br><br> 1. Mrtrix3 install problem on mac (Daniel Lumsden)<br><br><br>----------------------------------------------------------------------<br><br>Message: 1<br>Date: Fri, 11 Jul 2014 14:51:37 +0000<br>From: Daniel Lumsden <<a href="mailto:doclumsden@hotmail.com" target="_blank">doclumsden@hotmail.com</a>><br>To: "<a href="mailto:mrtrix-discussion@www.nitrc.org" target="_blank">mrtrix-discussion@www.nitrc.org</a>"<br><span style="white-space:pre-wrap"> </span><<a href="mailto:mrtrix-discussion@www.nitrc.org" target="_blank">mrtrix-discussion@www.nitrc.org</a>><br>Subject: [Mrtrix-discussion] Mrtrix3 install problem on mac<br>Message-ID: <DUB123-W39AC1DB4E16B0111EAEB7DCF090@phx.gbl><br>Content-Type: text/plain; charset="iso-8859-1"<br><br>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><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><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><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><br>EXEC <<<br>CMD: g++ /var/folders/s3/4fmdnjr133j55ws3y7pl7c_h0000gn/T/tmp3BM9Ed.o -o ./a.out<br>EXIT: 0<br><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><br>EXEC <<<br>CMD: ./a.out<br>EXIT: 0<br><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><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><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><br>EXEC <<<br>CMD: g++ /var/folders/s3/4fmdnjr133j55ws3y7pl7c_h0000gn/T/tmp0faCCk.o -o ./a.out<br>EXIT: 0<br><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><br>EXEC <<<br>CMD: ./a.out<br>EXIT: 0<br>STDOUT:<br>8<br><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><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><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><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><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><br>EXEC <<<br>CMD: g++ /var/folders/s3/4fmdnjr133j55ws3y7pl7c_h0000gn/T/tmpmO11Nk.o -o ./a.out<br>EXIT: 0<br><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><br>EXEC <<<br>CMD: ./a.out<br>EXIT: 0<br><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><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><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><br>EXEC <<<br>CMD: g++ /var/folders/s3/4fmdnjr133j55ws3y7pl7c_h0000gn/T/tmpBYDEbz.o -o ./a.out<br>EXIT: 0<br><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><br>EXEC <<<br>CMD: ./a.out<br>EXIT: 0<br><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><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><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><br>EXEC <<<br>CMD: g++ /var/folders/s3/4fmdnjr133j55ws3y7pl7c_h0000gn/T/tmpBp048Z.o -o ./a.out<br>EXIT: 0<br><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><br>EXEC <<<br>CMD: ./a.out<br>EXIT: 0<br><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><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><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><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><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><br>EXEC <<<br>CMD: g++ /var/folders/s3/4fmdnjr133j55ws3y7pl7c_h0000gn/T/tmpZp0WEo.o -lz -o ./a.out<br>EXIT: 0<br><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><br>EXEC <<<br>CMD: ./a.out<br>EXIT: 0<br>STDOUT:<br>1.2.5<br><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><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><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><br>EXEC <<<br>CMD: g++ /var/folders/s3/4fmdnjr133j55ws3y7pl7c_h0000gn/T/tmpVgCVmZ.o -lz -lpthread -o ./a.out<br>EXIT: 0<br><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><br>EXEC <<<br>CMD: ./a.out<br>EXIT: 0<br><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><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><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><br>EXEC <<<br>CMD: gsl-config --libs<br>EXIT: 0<br>STDOUT:<br>-L/opt/local/lib -lgsl -lgslcblas<br><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><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/opt/local/include /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> <span style="white-space:pre-wrap"> </span><span style="white-space:pre-wrap"> </span> <span style="white-space:pre-wrap"> </span> <span style="white-space:pre-wrap"> </span><span style="white-space:pre-wrap"> </span> <br>-------------- next part --------------<br>An HTML attachment was scrubbed...<br>URL: <<a href="http://www.nitrc.org/pipermail/mrtrix-discussion/attachments/20140711/3f50e2de/attachment-0001.html" target="_blank">http://www.nitrc.org/pipermail/mrtrix-discussion/attachments/20140711/3f50e2de/attachment-0001.html</a>><br><br>------------------------------<br><br>_______________________________________________<br>Mrtrix-discussion mailing list<br><a href="mailto:Mrtrix-discussion@www.nitrc.org" target="_blank">Mrtrix-discussion@www.nitrc.org</a><br><a href="http://www.nitrc.org/mailman/listinfo/mrtrix-discussion" target="_blank">http://www.nitrc.org/mailman/listinfo/mrtrix-discussion</a><br><br><br>End of Mrtrix-discussion Digest, Vol 66, Issue 3<br>************************************************<br></blockquote></div><br></div></div><br>_______________________________________________<br>
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