Sorry for this basic installation question, see configure.log below.
Has anyone come across this already?
Is it to do with my qt-installation? Already tried it with both qt4 and qt5. The latest version seems to be 5.8, which I also downloaded and installed, but configure doesn’t seem to recognize it? Anyway, maybe it’s not qt?
Thanks for your help, Samuel
REPORT:
MRtrix build type requested:
REPORT: release
REPORT:
REPORT: Detecting OS: linux
REPORT: Checking for C++11 compliant compiler [g++]:
EXEC <<
CMD: g++ -dumpversion
EXIT: 0
STDOUT:
5.4.0
>>
REPORT: 5.4.0
COMPILE /tmp/tmpS3LJ9e.cpp:
---
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 -mno-avx -pthread -fPIC -march=native /tmp/tmpS3LJ9e.cpp -o /tmp/tmpS3LJ9e.o
EXIT: 0
>>
EXEC <<
CMD: g++ /tmp/tmpS3LJ9e.o -pthread -o a.out
EXIT: 0
>>
EXEC <<
CMD: ./a.out
EXIT: 0
>>
REPORT: - tested ok
REPORT: Detecting pointer size:
COMPILE /tmp/tmp8PbqLK.cpp:
---
#include <iostream>
int main() {
std::cout << sizeof(void*);
return (0);
}
---
EXEC <<
CMD: g++ -c -std=c++11 -mno-avx -pthread -fPIC -march=native /tmp/tmp8PbqLK.cpp -o /tmp/tmp8PbqLK.o
EXIT: 0
>>
EXEC <<
CMD: g++ /tmp/tmp8PbqLK.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/tmpSL1MIc.cpp:
---
int main(int argc, char* argv[]) {
int x[argc];
return 0;
}
---
EXEC <<
CMD: g++ -c -std=c++11 -mno-avx -pthread -fPIC -march=native -DMRTRIX_WORD64 /tmp/tmpSL1MIc.cpp -o /tmp/tmpSL1MIc.o
EXIT: 0
>>
EXEC <<
CMD: g++ /tmp/tmpSL1MIc.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/tmpCHtXtj.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 -mno-avx -pthread -fPIC -march=native -DMRTRIX_WORD64 /tmp/tmpCHtXtj.cpp -o /tmp/tmpCHtXtj.o
EXIT: 0
>>
EXEC <<
CMD: g++ /tmp/tmpCHtXtj.o -pthread -o a.out
EXIT: 0
>>
EXEC <<
CMD: ./a.out
EXIT: 0
>>
REPORT: yes
REPORT: Checking for zlib compression library:
COMPILE /tmp/tmpp9KOCA.cpp:
---
#include <iostream>
#include <zlib.h>
int main() {
std::cout << zlibVersion();
return (0);
}
---
EXEC <<
CMD: g++ -c -std=c++11 -mno-avx -pthread -fPIC -march=native -DMRTRIX_WORD64 /tmp/tmpp9KOCA.cpp -o /tmp/tmpp9KOCA.o
EXIT: 0
>>
EXEC <<
CMD: g++ /tmp/tmpp9KOCA.o -pthread -lz -o a.out
EXIT: 0
>>
EXEC <<
CMD: ./a.out
EXIT: 0
STDOUT:
1.2.8
>>
REPORT: 1.2.8
REPORT: Checking for Eigen 3 library:
EXEC <<
CMD: pkg-config --cflags eigen3
EXIT: 0
STDOUT:
-I/usr/include/eigen3
>>
COMPILE /tmp/tmpscNVO9.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: g++ -c -std=c++11 -mno-avx -pthread -fPIC -march=native -DMRTRIX_WORD64 -isystem /usr/include/eigen3 /tmp/tmpscNVO9.cpp -o /tmp/tmpscNVO9.o
EXIT: 0
>>
EXEC <<
CMD: g++ /tmp/tmpscNVO9.o -pthread -lz -o a.out
EXIT: 0
>>
EXEC <<
CMD: ./a.out
EXIT: 0
STDOUT:
3.2.92
>>
REPORT: 3.2.92
REPORT: Checking Eigen 3 memory alignment requirements:
COMPILE /tmp/tmpUCStpy.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: g++ -c -v -std=c++11 -mno-avx -pthread -fPIC -march=native -DMRTRIX_WORD64 -isystem /usr/include/eigen3 /tmp/tmpUCStpy.cpp -o /tmp/tmpUCStpy.o
EXIT: 0
STDERR:
Using built-in specs.
COLLECT_GCC=g++
Target: x86_64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Ubuntu 5.4.0-6ubuntu1~16.04.4' --with-bugurl=file:///usr/share/doc/gcc-5/README.Bugs --enable-languages=c,ada,c++,java,go,d,fortran,objc,obj-c++ --prefix=/usr --program-suffix=-5 --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --with-sysroot=/ --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-libmpx --enable-plugin --with-system-zlib --disable-browser-plugin --enable-java-awt=gtk --enable-gtk-cairo --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-5-amd64/jre --enable-java-home --with-jvm-root-dir=/usr/lib/jvm/java-1.5.0-gcj-5-amd64 --with-jvm-jar-dir=/usr/lib/jvm-exports/java-1.5.0-gcj-5-amd64 --with-arch-directory=amd64 --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --enable-objc-gc --enable-multiarch --disable-werror --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu
Thread model: posix
gcc version 5.4.0 20160609 (Ubuntu 5.4.0-6ubuntu1~16.04.4)
COLLECT_GCC_OPTIONS='-c' '-v' '-std=c++11' '-mno-avx' '-pthread' '-fPIC' '-march=native' '-D' 'MRTRIX_WORD64' '-isystem' '/usr/include/eigen3' '-o' '/tmp/tmpUCStpy.o' '-shared-libgcc'
/usr/lib/gcc/x86_64-linux-gnu/5/cc1plus -quiet -v -imultiarch x86_64-linux-gnu -D_GNU_SOURCE -D_REENTRANT -D MRTRIX_WORD64 -isystem /usr/include/eigen3 /tmp/tmpUCStpy.cpp -march=broadwell -mmmx -mno-3dnow -msse -msse2 -msse3 -mssse3 -mno-sse4a -mcx16 -msahf -mmovbe -maes -mno-sha -mpclmul -mpopcnt -mabm -mno-lwp -mfma -mno-fma4 -mno-xop -mbmi -mbmi2 -mno-tbm -mavx -mavx2 -msse4.2 -msse4.1 -mlzcnt -mrtm -mhle -mrdrnd -mf16c -mfsgsbase -mrdseed -mprfchw -madx -mfxsr -mxsave -mxsaveopt -mno-avx512f -mno-avx512er -mno-avx512cd -mno-avx512pf -mno-prefetchwt1 -mclflushopt -mxsavec -mxsaves -mno-avx512dq -mno-avx512bw -mno-avx512vl -mno-avx512ifma -mno-avx512vbmi -mno-clwb -mno-pcommit -mno-mwaitx --param l1-cache-size=32 --param l1-cache-line-size=64 --param l2-cache-size=8192 -mtune=generic -quiet -dumpbase tmpUCStpy.cpp -mno-avx -auxbase-strip /tmp/tmpUCStpy.o -std=c++11 -version -fPIC -fstack-protector-strong -Wformat -Wformat-security -o /tmp/cc03qFRv.s
GNU C++11 (Ubuntu 5.4.0-6ubuntu1~16.04.4) version 5.4.0 20160609 (x86_64-linux-gnu)
compiled by GNU C version 5.4.0 20160609, GMP version 6.1.0, MPFR version 3.1.4, MPC version 1.0.3
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
ignoring duplicate directory "/usr/include/x86_64-linux-gnu/c++/5"
ignoring nonexistent directory "/usr/local/include/x86_64-linux-gnu"
ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/5/../../../../x86_64-linux-gnu/include"
#include "..." search starts here:
#include <...> search starts here:
/usr/include/eigen3
/usr/include/c++/5
/usr/include/x86_64-linux-gnu/c++/5
/usr/include/c++/5/backward
/usr/lib/gcc/x86_64-linux-gnu/5/include
/usr/local/include
/usr/lib/gcc/x86_64-linux-gnu/5/include-fixed
/usr/include/x86_64-linux-gnu
/usr/include
End of search list.
GNU C++11 (Ubuntu 5.4.0-6ubuntu1~16.04.4) version 5.4.0 20160609 (x86_64-linux-gnu)
compiled by GNU C version 5.4.0 20160609, GMP version 6.1.0, MPFR version 3.1.4, MPC version 1.0.3
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
Compiler executable checksum: c3fdb80f2154421ceaf9e22c85325a8d
COLLECT_GCC_OPTIONS='-c' '-v' '-std=c++11' '-mno-avx' '-pthread' '-fPIC' '-march=native' '-D' 'MRTRIX_WORD64' '-isystem' '/usr/include/eigen3' '-o' '/tmp/tmpUCStpy.o' '-shared-libgcc'
as -v --64 -o /tmp/tmpUCStpy.o /tmp/cc03qFRv.s
GNU assembler version 2.26.1 (x86_64-linux-gnu) using BFD version (GNU Binutils for Ubuntu) 2.26.1
COMPILER_PATH=/usr/lib/gcc/x86_64-linux-gnu/5/:/usr/lib/gcc/x86_64-linux-gnu/5/:/usr/lib/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/5/:/usr/lib/gcc/x86_64-linux-gnu/
LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/5/:/usr/lib/gcc/x86_64-linux-gnu/5/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/5/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/5/../../../:/lib/:/usr/lib/
COLLECT_GCC_OPTIONS='-c' '-v' '-std=c++11' '-mno-avx' '-pthread' '-fPIC' '-march=native' '-D' 'MRTRIX_WORD64' '-isystem' '/usr/include/eigen3' '-o' '/tmp/tmpUCStpy.o' '-shared-libgcc'
>>
EXEC <<
CMD: g++ /tmp/tmpUCStpy.o -pthread -lz -o a.out
EXIT: 0
>>
EXEC <<
CMD: ./a.out
EXIT: 0
STDOUT:
allocator memory alignment: 16, Eigen3 needs: 16
>>
REPORT: OK
REPORT: Checking shared library generation:
EXEC <<
CMD: g++ -c -std=c++11 -mno-avx -pthread -fPIC -march=native -DMRTRIX_WORD64 -isystem /usr/include/eigen3 /tmp/tmp6AIz58.cpp -o /tmp/tmp6AIz58.o
EXIT: 0
>>
EXEC <<
CMD: g++ /tmp/tmp6AIz58.o -pthread -shared -pthread -lz -o libtest.so
EXIT: 0
>>
REPORT: yes
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
HEADERS += qt.h
SOURCES += qt.cpp
---
EXEC <<
CMD: qmake
EXIT: 0
>>
EXEC <<
CMD: moc qt.h -o qt_moc.cpp
EXIT: 0
>>
EXEC <<
CMD: g++ -c -std=c++11 -mno-avx -pthread -fPIC -march=native -DMRTRIX_WORD64 -isystem /usr/include/eigen3 -m64 -pipe -O2 -std=c++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/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/QtCore -isystem /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 -mno-avx -pthread -fPIC -march=native -DMRTRIX_WORD64 -isystem /usr/include/eigen3 -m64 -pipe -O2 -std=c++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/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/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++-64 qt_moc.cpp -o qt_moc.o
EXIT: 0
>>
EXEC <<
CMD: g++ -pthread -lz qt_moc.o qt.o -o qt -m64 -Wl,-O1 -L/usr/X11R6/lib64 -lQt5OpenGL -lQt5Svg -lQt5Widgets -lQt5Gui -lQt5Core -lGL -lpthread
EXIT: 1
STDERR:
/usr/bin/ld: cannot find -lGL
collect2: error: ld returned 1 exit status
>>
ERROR: error linking 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.