This is the content of ‘configure.log’ …
REPORT:
MRtrix build type requested: release version
REPORT: WARNING: anaconda/miniconda detected in PATH ("/home/amit/anaconda3/bin") - removed to avoid conflicts
REPORT: WARNING: anaconda/miniconda detected in PATH ("/home/amit/anaconda3/condabin") - removed to avoid conflicts
PATH set to: /home/amit/MRtrix3Tissue-master/bin:/usr/local/freesurfer/bin:/usr/local/freesurfer/fsfast/bin:/usr/local/freesurfer/tktools:/usr/local/fsl/bin:/usr/local/freesurfer/mni/bin:/home/amit/mrtrix3/bin:/usr/local/fsl/bin:/home/amit/bin:/home/amit/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin
REPORT:
NOTE: if you intend to build with anaconda/miniconda (not recommended), pass the -conda flag to ./configure
REPORT: Detecting OS: linux
REPORT: Looking for compiler [clang++]:
EXEC <<
CMD: clang++ --version
error invoking command "clang++": No such file or directory: 'clang++'
>>
REPORT: not found
REPORT: Looking for compiler [g++]:
EXEC <<
CMD: g++ --version
EXIT: 0
STDOUT:
g++ (Ubuntu 5.5.0-12ubuntu1~16.04) 5.5.0 20171010
Copyright (C) 2015 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
>>
REPORT: g++ (Ubuntu 5.5.0-12ubuntu1~16.04) 5.5.0 20171010
REPORT: Checking for C++11 compliance:
COMPILE /tmp/tmprw0bxzaa.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: g++ -c -std=c++11 -DMRTRIX_BUILD_TYPE="release version" -pthread -fPIC /tmp/tmprw0bxzaa.cpp -o /tmp/tmprw0bxzaa.o
EXIT: 0
>>
EXEC <<
CMD: g++ /tmp/tmprw0bxzaa.o -Wl,--sort-common,--as-needed -pthread -o a.out
EXIT: 0
>>
EXEC <<
CMD: ./a.out
EXIT: 0
>>
REPORT: ok
REPORT: Checking shared library generation:
EXEC <<
CMD: g++ -c -std=c++11 -DMRTRIX_BUILD_TYPE="release version" -pthread -fPIC /tmp/tmpw2aucflh.cpp -o /tmp/tmpw2aucflh.o
EXIT: 0
>>
EXEC <<
CMD: g++ /tmp/tmpw2aucflh.o -shared -Wl,--sort-common,--as-needed -pthread -o libtest.so
EXIT: 0
>>
REPORT: ok
REPORT: Detecting pointer size:
COMPILE /tmp/tmpuw427h6r.cpp:
---
#include <iostream>
int main() {
std::cout << sizeof(void*);
return (0);
}
---
EXEC <<
CMD: g++ -c -std=c++11 -DMRTRIX_BUILD_TYPE="release version" -pthread -fPIC /tmp/tmpuw427h6r.cpp -o /tmp/tmpuw427h6r.o
EXIT: 0
>>
EXEC <<
CMD: g++ /tmp/tmpuw427h6r.o -Wl,--sort-common,--as-needed -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/tmp3pl0z6gn.cpp:
---
int main(int argc, char* argv[]) {
int x[argc];
return 0;
}
---
EXEC <<
CMD: g++ -c -std=c++11 -DMRTRIX_BUILD_TYPE="release version" -pthread -fPIC -DMRTRIX_WORD64 /tmp/tmp3pl0z6gn.cpp -o /tmp/tmp3pl0z6gn.o
EXIT: 0
>>
EXEC <<
CMD: g++ /tmp/tmp3pl0z6gn.o -Wl,--sort-common,--as-needed -pthread -o a.out
EXIT: 0
>>
EXEC <<
CMD: ./a.out
EXIT: 0
>>
REPORT: ok
REPORT: Checking for non-POD variable-length array support:
COMPILE /tmp/tmpd6xq0tju.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 -std=c++11 -DMRTRIX_BUILD_TYPE="release version" -pthread -fPIC -DMRTRIX_WORD64 /tmp/tmpd6xq0tju.cpp -o /tmp/tmpd6xq0tju.o
EXIT: 0
>>
EXEC <<
CMD: g++ /tmp/tmpd6xq0tju.o -Wl,--sort-common,--as-needed -pthread -o a.out
EXIT: 0
>>
EXEC <<
CMD: ./a.out
EXIT: 0
>>
REPORT: ok
REPORT: Checking for ::max_align_t:
COMPILE /tmp/tmp7qmixvdy.cpp:
---
#include <iostream>
#include <cstddef>
using ::max_align_t;
int main() {
std::cout << alignof (max_align_t) << " bytes\n";
return 0;
}
---
EXEC <<
CMD: g++ -c -std=c++11 -DMRTRIX_BUILD_TYPE="release version" -pthread -fPIC -DMRTRIX_WORD64 /tmp/tmp7qmixvdy.cpp -o /tmp/tmp7qmixvdy.o
EXIT: 0
>>
EXEC <<
CMD: g++ /tmp/tmp7qmixvdy.o -Wl,--sort-common,--as-needed -pthread -o a.out
EXIT: 0
>>
EXEC <<
CMD: ./a.out
EXIT: 0
STDOUT:
16 bytes
>>
REPORT: 16 bytes
REPORT: Checking for std::max_align_t:
COMPILE /tmp/tmpay12layd.cpp:
---
#include <iostream>
#include <cstddef>
using std::max_align_t;
int main() {
std::cout << alignof (max_align_t) << " bytes\n";
return 0;
}
---
EXEC <<
CMD: g++ -c -std=c++11 -DMRTRIX_BUILD_TYPE="release version" -pthread -fPIC -DMRTRIX_WORD64 /tmp/tmpay12layd.cpp -o /tmp/tmpay12layd.o
EXIT: 0
>>
EXEC <<
CMD: g++ /tmp/tmpay12layd.o -Wl,--sort-common,--as-needed -pthread -o a.out
EXIT: 0
>>
EXEC <<
CMD: ./a.out
EXIT: 0
STDOUT:
16 bytes
>>
REPORT: 16 bytes
EXEC <<
CMD: pkg-config --cflags eigen3
EXIT: 0
STDOUT:
-I/usr/include/eigen3
>>
REPORT: Checking for Eigen3 library:
COMPILE /tmp/tmpk6p3c7js.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: g++ -c -std=c++11 -DMRTRIX_BUILD_TYPE="release version" -pthread -fPIC -DMRTRIX_WORD64 -idirafter /usr/include/eigen3 /tmp/tmpk6p3c7js.cpp -o /tmp/tmpk6p3c7js.o
EXIT: 0
>>
EXEC <<
CMD: g++ /tmp/tmpk6p3c7js.o -Wl,--sort-common,--as-needed -pthread -o a.out
EXIT: 0
>>
EXEC <<
CMD: ./a.out
EXIT: 0
STDOUT:
3.2.92
>>
REPORT: 3.2.92
REPORT: Checking for Eigen3 Unsupported:
COMPILE /tmp/tmpxn0lgjgd.cpp:
---
#include <iostream>
#include <Eigen/Core>
#include <unsupported/Eigen/SpecialFunctions>
using array_type = Eigen::Array<double, 1, 1>;
int main (int argc, char* argv[]) {
auto test = Eigen::betainc (array_type::Constant (10.0), array_type::Constant (0.5), array_type::Constant (1.0));
std::cout << "Present";
return (0);
}
---
EXEC <<
CMD: g++ -c -std=c++11 -DMRTRIX_BUILD_TYPE="release version" -pthread -fPIC -DMRTRIX_WORD64 -idirafter /usr/include/eigen3 -DEIGEN_DONT_PARALLELIZE /tmp/tmpxn0lgjgd.cpp -o /tmp/tmpxn0lgjgd.o
EXIT: 1
STDERR:
/tmp/tmpxn0lgjgd.cpp:4:46: fatal error: unsupported/Eigen/SpecialFunctions: No such file or directory
compilation terminated.
>>
error deleting temporary file "/tmp/tmpxn0lgjgd.o": No such file or directory
REPORT: not found; custom functions to be used
EXEC <<
CMD: pkg-config --cflags zlib
EXIT: 0
>>
EXEC <<
CMD: pkg-config --libs zlib
EXIT: 0
STDOUT:
-lz
>>
REPORT: Checking for zlib compression library:
COMPILE /tmp/tmp_9nte330.cpp:
---
#include <iostream>
#include <zlib.h>
int main() {
std::cout << zlibVersion();
return (0);
}
---
EXEC <<
CMD: g++ -c -std=c++11 -DMRTRIX_BUILD_TYPE="release version" -pthread -fPIC -DMRTRIX_WORD64 /tmp/tmp_9nte330.cpp -o /tmp/tmp_9nte330.o
EXIT: 0
>>
EXEC <<
CMD: g++ /tmp/tmp_9nte330.o -Wl,--sort-common,--as-needed -pthread -lz -o a.out
EXIT: 0
>>
EXEC <<
CMD: ./a.out
EXIT: 0
STDOUT:
1.2.8
>>
REPORT: 1.2.8
REPORT: Checking for "JSON for Modern C++" requirements:
COMPILE /tmp/tmpqra7vwuq.cpp:
---
#include "file/json.h"
int main (int argc, char* argv[])
{
nlohmann::json json;
json["key"] = "value";
}
---
EXEC <<
CMD: g++ -c -std=c++11 -DMRTRIX_BUILD_TYPE="release version" -pthread -fPIC -DMRTRIX_WORD64 -I/home/amit/mrtrix3/core /tmp/tmpqra7vwuq.cpp -o /tmp/tmpqra7vwuq.o
EXIT: 0
>>
EXEC <<
CMD: g++ /tmp/tmpqra7vwuq.o -Wl,--sort-common,--as-needed -pthread -lz -o a.out
EXIT: 0
>>
EXEC <<
CMD: ./a.out
EXIT: 0
>>
REPORT: ok
EXEC <<
CMD: pkg-config --cflags libtiff-4
EXIT: 1
STDERR:
Package libtiff-4 was not found in the pkg-config search path.
Perhaps you should add the directory containing `libtiff-4.pc'
to the PKG_CONFIG_PATH environment variable
No package 'libtiff-4' found
>>
error running "pkg-config --cflags libtiff-4"
EXEC <<
CMD: pkg-config --libs libtiff-4
EXIT: 1
STDERR:
Package libtiff-4 was not found in the pkg-config search path.
Perhaps you should add the directory containing `libtiff-4.pc'
to the PKG_CONFIG_PATH environment variable
No package 'libtiff-4' found
>>
error running "pkg-config --libs libtiff-4"
REPORT: Checking for TIFF library:
COMPILE /tmp/tmpqgovk224.cpp:
---
#include <iostream>
#include <tiffio.h>
int main() {
std::cout << TIFFGetVersion();
return (0);
}
---
EXEC <<
CMD: g++ -c -std=c++11 -DMRTRIX_BUILD_TYPE="release version" -pthread -fPIC -DMRTRIX_WORD64 /tmp/tmpqgovk224.cpp -o /tmp/tmpqgovk224.o
EXIT: 1
STDERR:
/tmp/tmpqgovk224.cpp:3:20: fatal error: tiffio.h: No such file or directory
compilation terminated.
>>
error deleting temporary file "/tmp/tmpqgovk224.o": No such file or directory
REPORT: not found - TIFF support disabled
EXEC <<
CMD: pkg-config --cflags libpng
EXIT: 0
STDOUT:
-I/usr/include/libpng12
>>
EXEC <<
CMD: pkg-config --libs libpng
EXIT: 0
STDOUT:
-lpng12
>>
REPORT: Checking for PNG library:
COMPILE /tmp/tmpo38czrde.cpp:
---
#include <iostream>
#include <png.h>
int main() {
std::cout << "Header: " << PNG_LIBPNG_VER_STRING << "; library: " << png_libpng_ver;
return (0);
}
---
EXEC <<
CMD: g++ -c -std=c++11 -DMRTRIX_BUILD_TYPE="release version" -pthread -fPIC -DMRTRIX_WORD64 -idirafter /usr/include/libpng12 /tmp/tmpo38czrde.cpp -o /tmp/tmpo38czrde.o
EXIT: 0
>>
EXEC <<
CMD: g++ /tmp/tmpo38czrde.o -Wl,--sort-common,--as-needed -pthread -lz -lpng12 -o a.out
EXIT: 0
>>
EXEC <<
CMD: ./a.out
EXIT: 0
STDOUT:
Header: 1.2.54; library: 1.2.54
>>
REPORT: Header: 1.2.54; library: 1.2.54
EXEC <<
CMD: pkg-config --cflags fftw3
EXIT: 0
>>
EXEC <<
CMD: pkg-config --libs fftw3
EXIT: 0
STDOUT:
-lfftw3
>>
REPORT: Checking for FFTW library:
COMPILE /tmp/tmpu2cr6l_j.cpp:
---
#include <iostream>
#include <fftw3.h>
int main() {
std::cout << fftw_version << "\n";
return (0);
}
---
EXEC <<
CMD: g++ -c -std=c++11 -DMRTRIX_BUILD_TYPE="release version" -pthread -fPIC -DMRTRIX_WORD64 -DMRTRIX_PNG_SUPPORT -idirafter /usr/include/libpng12 /tmp/tmpu2cr6l_j.cpp -o /tmp/tmpu2cr6l_j.o
EXIT: 0
>>
EXEC <<
CMD: g++ /tmp/tmpu2cr6l_j.o -Wl,--sort-common,--as-needed -pthread -lz -lpng12 -lfftw3 -o a.out
EXIT: 0
>>
EXEC <<
CMD: ./a.out
EXIT: 0
STDOUT:
fftw-3.3.4-sse2-avx
>>
REPORT: fftw-3.3.4-sse2-avx
REPORT: Checking for Qt moc:
EXEC <<
CMD: moc -v
EXIT: 0
STDOUT:
moc 5.5.1
>>
REPORT: moc (version 5.5.1)
REPORT: Checking for Qt qmake:
EXEC <<
CMD: qmake -v
EXIT: 0
STDOUT:
QMake version 3.0
Using Qt version 5.5.1 in /usr/lib/x86_64-linux-gnu
>>
REPORT: qmake (version 5.5.1)
REPORT: Checking for Qt rcc:
EXEC <<
CMD: rcc -v
EXIT: 0
STDOUT:
rcc 5.5.1
>>
REPORT: rcc (version 5.5.1)
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 network
HEADERS += qt.h
SOURCES += qt.cpp
---
EXEC <<
CMD: qmake
EXIT: 0
>>
reading Qt parameters from file 'Makefile'... ok
qt_defines: ['-DQT_NO_DEBUG', '-DQT_OPENGL_LIB', '-DQT_SVG_LIB', '-DQT_WIDGETS_LIB', '-DQT_GUI_LIB', '-DQT_NETWORK_LIB', '-DQT_CORE_LIB']
qt_includes: ['-I.', '-isystem', '/usr/include/x86_64-linux-gnu/qt5', '-isystem', '/usr/include/x86_64-linux-gnu/qt5/QtOpenGL', '-isystem', '/usr/include/x86_64-linux-gnu/qt5/QtSvg', '-isystem', '/usr/include/x86_64-linux-gnu/qt5/QtWidgets', '-isystem', '/usr/include/x86_64-linux-gnu/qt5/QtGui', '-isystem', '/usr/include/x86_64-linux-gnu/qt5/QtNetwork', '-isystem', '/usr/include/x86_64-linux-gnu/qt5/QtCore', '-I.', '-I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++-64']
qt_libs: ['$(SUBLIBS)', '-L/usr/X11R6/lib64', '-lQt5OpenGL', '-lQt5Svg', '-lQt5Widgets', '-lQt5Gui', '-lQt5Network', '-lQt5Core', '-lGL', '-lpthread']
EXEC <<
CMD: moc qt.h -o qt_moc.cpp
EXIT: 0
>>
EXEC <<
CMD: g++ -c -std=c++11 -DMRTRIX_BUILD_TYPE="release version" -pthread -fPIC -DMRTRIX_WORD64 -DMRTRIX_PNG_SUPPORT -idirafter /usr/include/libpng12 -DEIGEN_FFTW_DEFAULT -DQT_NO_DEBUG -DQT_OPENGL_LIB -DQT_SVG_LIB -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_NETWORK_LIB -DQT_CORE_LIB -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtOpenGL -isystem /usr/include/x86_64-linux-gnu/qt5/QtSvg -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtNetwork -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -idirafter /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++-64 qt.cpp -o qt.o
EXIT: 0
>>
EXEC <<
CMD: g++ -c -std=c++11 -DMRTRIX_BUILD_TYPE="release version" -pthread -fPIC -DMRTRIX_WORD64 -DMRTRIX_PNG_SUPPORT -idirafter /usr/include/libpng12 -DEIGEN_FFTW_DEFAULT -DQT_NO_DEBUG -DQT_OPENGL_LIB -DQT_SVG_LIB -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_NETWORK_LIB -DQT_CORE_LIB -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtOpenGL -isystem /usr/include/x86_64-linux-gnu/qt5/QtSvg -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtNetwork -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -idirafter /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++-64 qt_moc.cpp -o qt_moc.o
EXIT: 0
>>
EXEC <<
CMD: g++ -Wl,--sort-common,--as-needed -pthread -lz -lpng12 -lfftw3 qt_moc.o qt.o -o qt -L/usr/X11R6/lib64 -lQt5OpenGL -lQt5Svg -lQt5Widgets -lQt5Gui -lQt5Network -lQt5Core -lGL -lpthread
EXIT: 0
>>
EXEC <<
CMD: /tmp/tmpn3ikv_we/qt
EXIT: 0
STDOUT:
5.5.1
>>
REPORT: 5.5.1