Setup error

1

Hello there, I am having trouble setting up the configuration file.
Below is the full error log.
Could anyone perhaps assist?

REPORT: 
MRtrix build type requested:

REPORT: release

REPORT: 

REPORT: Detecting OS: darwin
EXEC <<
CMD: sw_vers -productVersion
EXIT: 0
STDOUT:
10.10.5
>>


REPORT: OS X deployment target: 10.10

REPORT: Checking for C++11 compliant compiler [clang++]:
EXEC <<
CMD: clang++ -dumpversion
EXIT: 0
STDOUT:
4.2.1
>>


REPORT: 4.2.1

COMPILE /var/folders/v3/0jc385xd2f7g023bvr5hmwjm0000gn/T/tmp4C1Psp.cpp:
---

struct Base {
    Base (int);
};
struct Derived : Base {
    using Base::Base;
};

int main() {
  Derived D (int); // check for contructor inheritance
  return (0);
}

---
EXEC <<
CMD: clang++ -c -std=c++11 -mno-avx -DMRTRIX_MACOSX -fPIC -mmacosx-version-min=10.10 /var/folders/v3/0jc385xd2f7g023bvr5hmwjm0000gn/T/tmp4C1Psp.cpp -o /var/folders/v3/0jc385xd2f7g023bvr5hmwjm0000gn/T/tmp4C1Psp.o
EXIT: 0
>>

EXEC <<
CMD: clang++ /var/folders/v3/0jc385xd2f7g023bvr5hmwjm0000gn/T/tmp4C1Psp.o -mmacosx-version-min=10.10 -o a.out
EXIT: 0
>>

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


REPORT:  - tested ok

REPORT: Detecting pointer size:

COMPILE /var/folders/v3/0jc385xd2f7g023bvr5hmwjm0000gn/T/tmp5j6oAz.cpp:
---

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

---
EXEC <<
CMD: clang++ -c -std=c++11 -mno-avx -DMRTRIX_MACOSX -fPIC -mmacosx-version-min=10.10 /var/folders/v3/0jc385xd2f7g023bvr5hmwjm0000gn/T/tmp5j6oAz.cpp -o /var/folders/v3/0jc385xd2f7g023bvr5hmwjm0000gn/T/tmp5j6oAz.o
EXIT: 0
>>

EXEC <<
CMD: clang++ /var/folders/v3/0jc385xd2f7g023bvr5hmwjm0000gn/T/tmp5j6oAz.o -mmacosx-version-min=10.10 -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 variable-length array support:

COMPILE /var/folders/v3/0jc385xd2f7g023bvr5hmwjm0000gn/T/tmpVHJSW9.cpp:
---


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

---
EXEC <<
CMD: clang++ -c -std=c++11 -mno-avx -DMRTRIX_MACOSX -fPIC -mmacosx-version-min=10.10 -DMRTRIX_WORD64 /var/folders/v3/0jc385xd2f7g023bvr5hmwjm0000gn/T/tmpVHJSW9.cpp -o /var/folders/v3/0jc385xd2f7g023bvr5hmwjm0000gn/T/tmpVHJSW9.o
EXIT: 0
>>

EXEC <<
CMD: clang++ /var/folders/v3/0jc385xd2f7g023bvr5hmwjm0000gn/T/tmpVHJSW9.o -mmacosx-version-min=10.10 -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/v3/0jc385xd2f7g023bvr5hmwjm0000gn/T/tmpp95xnh.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: clang++ -c -std=c++11 -mno-avx -DMRTRIX_MACOSX -fPIC -mmacosx-version-min=10.10 -DMRTRIX_WORD64 /var/folders/v3/0jc385xd2f7g023bvr5hmwjm0000gn/T/tmpp95xnh.cpp -o /var/folders/v3/0jc385xd2f7g023bvr5hmwjm0000gn/T/tmpp95xnh.o
EXIT: 1
STDERR:
/var/folders/v3/0jc385xd2f7g023bvr5hmwjm0000gn/T/tmpp95xnh.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/v3/0jc385xd2f7g023bvr5hmwjm0000gn/T/tmpp95xnh.o": No such file or directory
REPORT: no

REPORT: Checking for zlib compression library:

COMPILE /var/folders/v3/0jc385xd2f7g023bvr5hmwjm0000gn/T/tmpppSI6w.cpp:
---

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

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

---
EXEC <<
CMD: clang++ -c -std=c++11 -mno-avx -DMRTRIX_MACOSX -fPIC -mmacosx-version-min=10.10 -DMRTRIX_WORD64 -DMRTRIX_NO_NON_POD_VLA /var/folders/v3/0jc385xd2f7g023bvr5hmwjm0000gn/T/tmpppSI6w.cpp -o /var/folders/v3/0jc385xd2f7g023bvr5hmwjm0000gn/T/tmpppSI6w.o
EXIT: 0
>>

EXEC <<
CMD: clang++ /var/folders/v3/0jc385xd2f7g023bvr5hmwjm0000gn/T/tmpppSI6w.o -mmacosx-version-min=10.10 -lz -o a.out
EXIT: 0
>>

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


REPORT: 1.2.5

REPORT: Checking for Eigen 3 library:
EXEC <<
CMD: pkg-config --cflags eigen3
EXIT: 0
STDOUT:
-I/usr/local/Cellar/eigen/3.3.1/include/eigen3
>>


COMPILE /var/folders/v3/0jc385xd2f7g023bvr5hmwjm0000gn/T/tmpiFFBg7.cpp:
---

#include <Eigen/Core>
#include <iostream>

int main (int argc, char* argv[]) {
  std::cout << EIGEN_WORLD_VERSION << "." << EIGEN_MAJOR_VERSION << "." << EIGEN_MINOR_VERSION << "\n";
  return 0;
}

---
EXEC <<
CMD: clang++ -c -std=c++11 -mno-avx -DMRTRIX_MACOSX -fPIC -mmacosx-version-min=10.10 -DMRTRIX_WORD64 -DMRTRIX_NO_NON_POD_VLA -isystem /usr/local/Cellar/eigen/3.3.1/include/eigen3 /var/folders/v3/0jc385xd2f7g023bvr5hmwjm0000gn/T/tmpiFFBg7.cpp -o /var/folders/v3/0jc385xd2f7g023bvr5hmwjm0000gn/T/tmpiFFBg7.o
EXIT: 0
>>

EXEC <<
CMD: clang++ /var/folders/v3/0jc385xd2f7g023bvr5hmwjm0000gn/T/tmpiFFBg7.o -mmacosx-version-min=10.10 -lz -o a.out
EXIT: 0
>>

EXEC <<
CMD: ./a.out
EXIT: 0
STDOUT:
3.3.1
>>


REPORT: 3.3.1

REPORT: Checking Eigen 3 memory alignment requirements:

COMPILE /var/folders/v3/0jc385xd2f7g023bvr5hmwjm0000gn/T/tmp1iEpWI.cpp:
---

#include <iostream>
#include <Eigen/Core>

int main (int argc, char* argv[]) 
{
#ifdef EIGEN_DEFAULT_ALIGN_BYTES
  size_t default_align = std::numeric_limits<size_t>::max();
  for (size_t n = 0; n < 100; ++n) {
    struct alignas(64) X { double c[8]; };
    X* x = new X;
    size_t align = reinterpret_cast<size_t>(x) & 63U;
    if (align && align < default_align)
      default_align = align;
  }
  std::cout << "allocator memory alignment: " << default_align << ", Eigen3 needs: " << EIGEN_DEFAULT_ALIGN_BYTES << "\n";

  return default_align < EIGEN_DEFAULT_ALIGN_BYTES;
#else
  return 0;
#endif
}


---
EXEC <<
CMD: clang++ -c -v -std=c++11 -mno-avx -DMRTRIX_MACOSX -fPIC -mmacosx-version-min=10.10 -DMRTRIX_WORD64 -DMRTRIX_NO_NON_POD_VLA -isystem /usr/local/Cellar/eigen/3.3.1/include/eigen3 /var/folders/v3/0jc385xd2f7g023bvr5hmwjm0000gn/T/tmp1iEpWI.cpp -o /var/folders/v3/0jc385xd2f7g023bvr5hmwjm0000gn/T/tmp1iEpWI.o
EXIT: 0
STDERR:
Apple LLVM version 7.0.2 (clang-700.1.81)
Target: x86_64-apple-darwin14.5.0
Thread model: posix
 "/Library/Developer/CommandLineTools/usr/bin/clang" -cc1 -triple x86_64-apple-macosx10.10.0 -Wdeprecated-objc-isa-usage -Werror=deprecated-objc-isa-usage -emit-obj -mrelax-all -disable-free -disable-llvm-verifier -main-file-name tmp1iEpWI.cpp -mrelocation-model pic -pic-level 2 -mthread-model posix -mdisable-fp-elim -masm-verbose -munwind-tables -target-cpu core2 -target-feature -avx -target-linker-version 253.9 -v -dwarf-column-info -coverage-file /var/folders/v3/0jc385xd2f7g023bvr5hmwjm0000gn/T/tmp1iEpWI.o -resource-dir /Library/Developer/CommandLineTools/usr/bin/../lib/clang/7.0.2 -isystem /usr/local/Cellar/eigen/3.3.1/include/eigen3 -D MRTRIX_MACOSX -D MRTRIX_WORD64 -D MRTRIX_NO_NON_POD_VLA -stdlib=libc++ -std=c++11 -fdeprecated-macro -fdebug-compilation-dir /Users/christinapressl/mrtrix3 -ferror-limit 19 -fmessage-length 0 -stack-protector 1 -mstackrealign -fblocks -fobjc-runtime=macosx-10.10.0 -fencode-extended-block-signature -fcxx-exceptions -fexceptions -fmax-type-align=16 -fdiagnostics-show-option -o /var/folders/v3/0jc385xd2f7g023bvr5hmwjm0000gn/T/tmp1iEpWI.o -x c++ /var/folders/v3/0jc385xd2f7g023bvr5hmwjm0000gn/T/tmp1iEpWI.cpp
clang -cc1 version 7.0.2 based upon LLVM 3.7.0svn default target x86_64-apple-darwin14.5.0
ignoring nonexistent directory "/usr/include/c++/v1"
#include "..." search starts here:
#include <...> search starts here:
 /usr/local/Cellar/eigen/3.3.1/include/eigen3
 /Library/Developer/CommandLineTools/usr/bin/../include/c++/v1
 /usr/local/include
 /Library/Developer/CommandLineTools/usr/bin/../lib/clang/7.0.2/include
 /Library/Developer/CommandLineTools/usr/include
 /usr/include
 /System/Library/Frameworks (framework directory)
 /Library/Frameworks (framework directory)
End of search list.
>>

EXEC <<
CMD: clang++ /var/folders/v3/0jc385xd2f7g023bvr5hmwjm0000gn/T/tmp1iEpWI.o -mmacosx-version-min=10.10 -lz -o a.out
EXIT: 0
>>

EXEC <<
CMD: ./a.out
EXIT: 0
STDOUT:
allocator memory alignment: 32, Eigen3 needs: 16
>>


REPORT: OK

REPORT: Checking shared library generation:
EXEC <<
CMD: clang++ -c -std=c++11 -mno-avx -DMRTRIX_MACOSX -fPIC -mmacosx-version-min=10.10 -DMRTRIX_WORD64 -DMRTRIX_NO_NON_POD_VLA -isystem /usr/local/Cellar/eigen/3.3.1/include/eigen3 /var/folders/v3/0jc385xd2f7g023bvr5hmwjm0000gn/T/tmpedcV3h.cpp -o /var/folders/v3/0jc385xd2f7g023bvr5hmwjm0000gn/T/tmpedcV3h.o
EXIT: 0
>>

EXEC <<
CMD: clang++ /var/folders/v3/0jc385xd2f7g023bvr5hmwjm0000gn/T/tmpedcV3h.o -dynamiclib -install_name @rpath/LIBNAME -mmacosx-version-min=10.10 -mmacosx-version-min=10.10 -lz -o libtest.dylib
EXIT: 0
>>


REPORT: yes

REPORT: Checking for Qt moc:
EXEC <<
CMD: moc -v
EXIT: 0
STDOUT:
moc 5.7.1
>>


REPORT: moc (version 5.7.1)

REPORT: Checking for Qt qmake:
EXEC <<
CMD: qmake -v
EXIT: 0
STDOUT:
QMake version 3.0
Using Qt version 5.7.1 in /usr/local/Cellar/qt5/5.7.1_1/lib
>>


REPORT: qmake (version 5.7.1)

REPORT: Checking for Qt rcc:
EXEC <<
CMD: rcc -v
EXIT: 0
STDOUT:
rcc 5.7.1
>>


REPORT: rcc (version 5.7.1)

REPORT: Checking for Qt:

source file "qt.h":
---
#include <QObject>

class Foo: public QObject {
  Q_OBJECT;
  public:
    Foo();
    ~Foo();
  public slots:
    void setValue(int value);
  signals:
    void valueChanged (int newValue);
  private:
    int value_;
};
---

source file "qt.cpp":
---
#include <iostream>
#include "qt.h"

Foo::Foo() : value_ (42) { connect (this, SIGNAL(valueChanged(int)), this, SLOT(setValue(int))); }

Foo::~Foo() { std::cout << qVersion() << "\n"; }

void Foo::setValue (int value) { value_ = value; }

int main() { Foo f; }
---

project file "qt.pro":
---
CONFIG += c++11
QT += core gui opengl svg
HEADERS += qt.h
SOURCES += qt.cpp
QMAKE_MACOSX_DEPLOYMENT_TARGET = 10.10
---
EXEC <<
CMD: qmake
EXIT: 3
STDERR:
Project ERROR: Could not resolve SDK Path for 'macosx'
>>


ERROR: qmake returned with error:

Project ERROR: Could not resolve SDK Path for 'macosx'


ERROR: unexpected exception!

  See the file 'configure.log' for details. If this doesn't help and you need
  further assistance, please post on the MRtrix3 community forum
  (http://community.mrtrix.org/), and make sure to include the full contents of
  the 'configure.log' file.
2

I haven’t come across this one before… But the relevant error message is this one:

This indicates that Qt has trouble figuring out what settings to use on your Mac. Searching for this error, I came up with this recent post, which looks identical to your problem. It seems the solution is to use the full version of XCode rather than the stripped-down command-line tools. Does this help?

3

Hi there,

Thank you very much for the quick response.
The instructions you forwarded did help.
I simply started XCode on my machine once, which apparently performed further setup procedures and allowed me to run ./confiure

Thanks again for the help.