I got a lot of errors during the ./configure step, and passed all of them except this one:
MRtrix build type requested: release
Detecting OS: linux
Looking for compiler [clang++]: clang version 3.4.2 (tags/RELEASE_34/dot2-final)
Checking for C++11 compliance: ok
Checking for ::max_align_t: ok
Checking for std::max_align_t: not found
Detecting pointer size: 64 bit
Detecting byte order: little-endian
Checking for variable-length array support: yes
Checking for non-POD variable-length array support: no
Checking for zlib compression library: 1.2.7
Checking for TIFF library: LIBTIFF, Version 4.0.3
Checking for Eigen 3 library: 3.2.5
Checking for FFTW library: fftw-3.3.3-sse2
Checking JSON for Modern C++ requirements: OK
Checking shared library generation: yes
Checking for Qt moc: moc (version 5.6.1)
Checking for Qt qmake: qmake (version 5.6.1)
Checking for Qt rcc: rcc (version 5.6.1)
Checking for Qt:
ERROR: error compiling Qt application!
here is the full configure.log file, please help
REPORT:
MRtrix build type requested:
REPORT: release
REPORT:
REPORT: Detecting OS: linux
REPORT: Looking for compiler [clang++]:
EXEC <<
CMD: clang++ --version
EXIT: 0
STDOUT:
clang version 3.4.2 (tags/RELEASE_34/dot2-final)
Target: x86_64-redhat-linux-gnu
Thread model: posix
>>
REPORT: clang version 3.4.2 (tags/RELEASE_34/dot2-final)
REPORT: Checking for C++11 compliance:
COMPILE /tmp/tmpARJI7S.cpp:
---
#include <cstddef>
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 -pthread -fPIC /tmp/tmpARJI7S.cpp -o /tmp/tmpARJI7S.o
EXIT: 0
>>
EXEC <<
CMD: clang++ /tmp/tmpARJI7S.o -pthread -o a.out
EXIT: 0
>>
EXEC <<
CMD: ./a.out
EXIT: 0
>>
REPORT: ok
REPORT: Checking for ::max_align_t:
COMPILE /tmp/tmphPUO0L.cpp:
---
#include <cstddef>
using ::max_align_t;
int main() {
return 0;
}
---
EXEC <<
CMD: clang++ -c -std=c++11 -pthread -fPIC /tmp/tmphPUO0L.cpp -o /tmp/tmphPUO0L.o
EXIT: 0
>>
EXEC <<
CMD: clang++ /tmp/tmphPUO0L.o -pthread -o a.out
EXIT: 0
>>
EXEC <<
CMD: ./a.out
EXIT: 0
>>
REPORT: ok
REPORT: Checking for std::max_align_t:
COMPILE /tmp/tmpfk3ODh.cpp:
---
#include <cstddef>
using std::max_align_t;
int main() {
return 0;
}
---
EXEC <<
CMD: clang++ -c -std=c++11 -pthread -fPIC /tmp/tmpfk3ODh.cpp -o /tmp/tmpfk3ODh.o
EXIT: 1
STDERR:
/tmp/tmpfk3ODh.cpp:3:7: error: no member named 'max_align_t' in namespace 'std'; did you mean '::max_align_t'?
using std::max_align_t;
^~~~~~~~~~~~~~~~
::max_align_t
/usr/bin/../lib/clang/3.4.2/include/stddef.h:94:3: note: '::max_align_t' declared here
} max_align_t;
^
1 error generated.
>>
error deleting temporary file "/tmp/tmpfk3ODh.o": No such file or directory
REPORT: not found
REPORT: Detecting pointer size:
COMPILE /tmp/tmpHMj3Bi.cpp:
---
#include <iostream>
int main() {
std::cout << sizeof(void*);
return (0);
}
---
EXEC <<
CMD: clang++ -c -std=c++11 -pthread -fPIC -DMRTRIX_STD_MAX_ALIGN_T_NOT_DEFINED /tmp/tmpHMj3Bi.cpp -o /tmp/tmpHMj3Bi.o
EXIT: 0
>>
EXEC <<
CMD: clang++ /tmp/tmpHMj3Bi.o -pthread -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 /tmp/tmpxZtzC6.cpp:
---
int main(int argc, char* argv[]) {
int x[argc];
return 0;
}
---
EXEC <<
CMD: clang++ -c -std=c++11 -pthread -fPIC -DMRTRIX_STD_MAX_ALIGN_T_NOT_DEFINED -DMRTRIX_WORD64 /tmp/tmpxZtzC6.cpp -o /tmp/tmpxZtzC6.o
EXIT: 0
>>
EXEC <<
CMD: clang++ /tmp/tmpxZtzC6.o -pthread -o a.out
EXIT: 0
>>
EXEC <<
CMD: ./a.out
EXIT: 0
>>
REPORT: yes
REPORT: Checking for non-POD variable-length array support:
COMPILE /tmp/tmpHToDbo.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 -pthread -fPIC -DMRTRIX_STD_MAX_ALIGN_T_NOT_DEFINED -DMRTRIX_WORD64 /tmp/tmpHToDbo.cpp -o /tmp/tmpHToDbo.o
EXIT: 1
STDERR:
/tmp/tmpHToDbo.cpp:11:6: error: variable length array of non-POD element type 'X'
X x[argc];
^
1 error generated.
>>
error deleting temporary file "/tmp/tmpHToDbo.o": No such file or directory
REPORT: no
REPORT: Checking for zlib compression library:
COMPILE /tmp/tmpOxih2d.cpp:
---
#include <iostream>
#include <zlib.h>
int main() {
std::cout << zlibVersion();
return (0);
}
---
EXEC <<
CMD: clang++ -c -std=c++11 -pthread -fPIC -DMRTRIX_STD_MAX_ALIGN_T_NOT_DEFINED -DMRTRIX_WORD64 -DMRTRIX_NO_NON_POD_VLA /tmp/tmpOxih2d.cpp -o /tmp/tmpOxih2d.o
EXIT: 0
>>
EXEC <<
CMD: clang++ /tmp/tmpOxih2d.o -pthread -lz -o a.out
EXIT: 0
>>
EXEC <<
CMD: ./a.out
EXIT: 0
STDOUT:
1.2.7
>>
REPORT: 1.2.7
REPORT: Checking for TIFF library:
COMPILE /tmp/tmp90HoOB.cpp:
---
#include <iostream>
#include <tiffio.h>
int main() {
std::cout << TIFFGetVersion();
return (0);
}
---
EXEC <<
CMD: clang++ -c -std=c++11 -pthread -fPIC -DMRTRIX_STD_MAX_ALIGN_T_NOT_DEFINED -DMRTRIX_WORD64 -DMRTRIX_NO_NON_POD_VLA /tmp/tmp90HoOB.cpp -o /tmp/tmp90HoOB.o
EXIT: 0
>>
EXEC <<
CMD: clang++ /tmp/tmp90HoOB.o -pthread -lz -ltiff -o a.out
EXIT: 0
>>
EXEC <<
CMD: ./a.out
EXIT: 0
STDOUT:
LIBTIFF, Version 4.0.3
Copyright (c) 1988-1996 Sam Leffler
Copyright (c) 1991-1996 Silicon Graphics, Inc.
>>
REPORT: LIBTIFF, Version 4.0.3
REPORT: Checking for Eigen 3 library:
EXEC <<
CMD: pkg-config --cflags eigen3
EXIT: 0
STDOUT:
-I/usr/include/eigen3
>>
COMPILE /tmp/tmpeHMcV4.cpp:
---
#include <cstddef>
#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 -pthread -fPIC -DMRTRIX_STD_MAX_ALIGN_T_NOT_DEFINED -DMRTRIX_WORD64 -DMRTRIX_NO_NON_POD_VLA -DMRTRIX_TIFF_SUPPORT -isystem /usr/include/eigen3 /tmp/tmpeHMcV4.cpp -o /tmp/tmpeHMcV4.o
EXIT: 0
>>
EXEC <<
CMD: clang++ /tmp/tmpeHMcV4.o -pthread -lz -ltiff -o a.out
EXIT: 0
>>
EXEC <<
CMD: ./a.out
EXIT: 0
STDOUT:
3.2.5
>>
REPORT: 3.2.5
REPORT: Checking for FFTW library:
COMPILE /tmp/tmphmwIsj.cpp:
---
#include <iostream>
#include <fftw3.h>
int main() {
std::cout << fftw_version << "\n";
return (0);
}
---
EXEC <<
CMD: clang++ -c -std=c++11 -pthread -fPIC -DMRTRIX_STD_MAX_ALIGN_T_NOT_DEFINED -DMRTRIX_WORD64 -DMRTRIX_NO_NON_POD_VLA -DMRTRIX_TIFF_SUPPORT /tmp/tmphmwIsj.cpp -o /tmp/tmphmwIsj.o
EXIT: 0
>>
EXEC <<
CMD: clang++ /tmp/tmphmwIsj.o -pthread -lz -ltiff -lfftw3 -o a.out
EXIT: 0
>>
EXEC <<
CMD: ./a.out
EXIT: 0
STDOUT:
fftw-3.3.3-sse2
>>
REPORT: fftw-3.3.3-sse2
REPORT: Checking JSON for Modern C++ requirements:
COMPILE /tmp/tmpn0FRTH.cpp:
---
#include "file/json.h"
int main (int argc, char* argv[])
{
nlohmann::json json;
json["key"] = "value";
}
---
EXEC <<
CMD: clang++ -c -std=c++11 -pthread -fPIC -DMRTRIX_STD_MAX_ALIGN_T_NOT_DEFINED -DMRTRIX_WORD64 -DMRTRIX_NO_NON_POD_VLA -DMRTRIX_TIFF_SUPPORT -DEIGEN_FFTW_DEFAULT -I/home/synapse.1/mrtrix3/core /tmp/tmpn0FRTH.cpp -o /tmp/tmpn0FRTH.o
EXIT: 0
>>
EXEC <<
CMD: clang++ /tmp/tmpn0FRTH.o -pthread -lz -ltiff -lfftw3 -o a.out
EXIT: 0
>>
EXEC <<
CMD: ./a.out
EXIT: 0
>>
REPORT: OK
REPORT: Checking shared library generation:
EXEC <<
CMD: clang++ -c -std=c++11 -pthread -fPIC -DMRTRIX_STD_MAX_ALIGN_T_NOT_DEFINED -DMRTRIX_WORD64 -DMRTRIX_NO_NON_POD_VLA -DMRTRIX_TIFF_SUPPORT -DEIGEN_FFTW_DEFAULT /tmp/tmp5MXjAI.cpp -o /tmp/tmp5MXjAI.o
EXIT: 0
>>
EXEC <<
CMD: clang++ /tmp/tmp5MXjAI.o -pthread -shared -pthread -lz -ltiff -lfftw3 -o libtest.so
EXIT: 0
>>
REPORT: yes
REPORT: Checking for Qt moc:
EXEC <<
CMD: moc -v
EXIT: 0
STDOUT:
moc 5.6.1
>>
REPORT: moc (version 5.6.1)
REPORT: Checking for Qt qmake:
EXEC <<
CMD: qmake -v
EXIT: 0
STDOUT:
QMake version 3.0
Using Qt version 5.6.1 in /usr/lib64
>>
REPORT: qmake (version 5.6.1)
REPORT: Checking for Qt rcc:
EXEC <<
CMD: rcc -v
EXIT: 0
STDOUT:
rcc 5.6.1
>>
REPORT: rcc (version 5.6.1)
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
---
EXEC <<
CMD: qmake
EXIT: 0
>>
EXEC <<
CMD: moc qt.h -o qt_moc.cpp
EXIT: 0
>>
EXEC <<
CMD: clang++ -c -std=c++11 -pthread -fPIC -DMRTRIX_STD_MAX_ALIGN_T_NOT_DEFINED -DMRTRIX_WORD64 -DMRTRIX_NO_NON_POD_VLA -DMRTRIX_TIFF_SUPPORT -DEIGEN_FFTW_DEFAULT -pipe -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -std=gnu++0x -Wall -W -D_REENTRANT -fPIC -DQT_NO_DEBUG -DQT_OPENGL_LIB -DQT_SVG_LIB -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_CORE_LIB -isystem /usr/include/qt5 -isystem /usr/include/qt5/QtOpenGL -isystem /usr/include/qt5/QtSvg -isystem /usr/include/qt5/QtWidgets -isystem /usr/include/qt5/QtGui -isystem /usr/include/qt5/QtCore -isystem /usr/lib64/qt5/mkspecs/linux-g++ qt.cpp -o qt.o
EXIT: 1
STDERR:
clang: error: unknown argument: '-fstack-protector-strong'
>>
ERROR: error compiling Qt application!
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.