ERROR: error linking Qt application! Ubuntu 22.04

[samuel2496]

Hello everyone,

I am trying to install mrtrix in ubuntu 22.04 and I am receiving errors while configuring. I have attached the configure.log file below for reference.

I have installed libqt5-opengl & libqt5-opengl-dev package but still the error persist. I have been trying various solutions from the forums but nothing is working.

Thanks

Tried Solutions:

Error Linking QT application

Yes, those instructions were suitable for a Debian derivative Linux distribution (includes Ubuntu and Linux Mint) – they use the apt package management system, with package files in .deb format. CentOS is a RedHat derivative, and as such uses a different package management system based on .rpm packages. These days, I think the recommended command to manage these packages is yum, and there will no doubt also be a graphical interface for package management somewhere. You’ll need to adjust those i…

Error Linking QT application

Well, I had already the libglvnd-dev package installed. And re-installing it didn’t help. Instead I discovered this post which concerned similar problems with NVIDIA cards and Ubuntu. As in the post, I found that I had a broken link $ ls -l /usr/lib/x86_64-linux-gnu/libGL.so lrwxrwxrwx 1 root root 14 maj 10 14:17 /usr/lib/x86_64-linux-gnu/libGL.so -> libGL.so.1.0.0 where the target /usr/lib/x86_64-linux-gnu/libGL.so.1.0.0 did not exist. The latest comment in the above post related to Ubun…

Configure error linking qt Ubuntu 16.04

Yes, that’s a similar issue. The libGL.so in /usr/lib32 is no use though: it’s the 32-bit version, but you’re compiling for 64-bit. What I can’t tell from your output is which drivers are currently installed. The ubuntu-drivers devices command lists the drivers appropriate for your device, but it doesn’t report which of them is installed. This is the first time I’ve come across this command, I’m not sure whether it should say if a driver is installed…? If so, then it looks like you don’t have an…

ERROR:
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.

REPORT:

type or paste code here
REPORT: 
MRtrix build type requested: release version
PATH set to: /home/cbdl/ANTs/bin:/usr/local/freesurfer/bin:/usr/local/freesurfer/fsfast/bin:/usr/local/freesurfer/tktools:/usr/local/fsl/bin:/usr/local/fsl/share/fsl/bin:/usr/local/freesurfer/mni/bin:/usr/local/fsl/share/fsl/bin:/usr/local/fsl/share/fsl/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/snap/bin
REPORT: Detecting OS: linux

REPORT: Looking for compiler [clang++]:
EXEC <<
CMD: clang++ --version
EXIT: 0
STDOUT:
Ubuntu clang version 14.0.0-1ubuntu1
Target: x86_64-pc-linux-gnu
Thread model: posix
InstalledDir: /usr/bin
>>


REPORT: Ubuntu clang version 14.0.0-1ubuntu1

REPORT: Checking for C++11 compliance:

COMPILE /tmp/tmp5qzb6zso.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 -DMRTRIX_BUILD_TYPE="release version" -pthread -fPIC /tmp/tmp5qzb6zso.cpp -o /tmp/tmp5qzb6zso.o
EXIT: 1
STDERR:
/tmp/tmp5qzb6zso.cpp:2:10: fatal error: 'cstddef' file not found
#include <cstddef>
         ^~~~~~~~~
1 error generated.
>>

error deleting temporary file "/tmp/tmp5qzb6zso.o": No such file or directory
REPORT: test failed (see configure.log for details)

REPORT: Looking for compiler [g++]:
EXEC <<
CMD: g++ --version
EXIT: 0
STDOUT:
g++ (conda-forge gcc 11.3.0-19) 11.3.0
Copyright (C) 2021 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++ (conda-forge gcc 11.3.0-19) 11.3.0

REPORT: Checking for C++11 compliance:

COMPILE /tmp/tmpx_znw5ri.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/tmpx_znw5ri.cpp -o /tmp/tmpx_znw5ri.o
EXIT: 0
>>

EXEC <<
CMD: g++ /tmp/tmpx_znw5ri.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/tmph_q2dkzc.cpp -o /tmp/tmph_q2dkzc.o
EXIT: 0
>>

EXEC <<
CMD: g++ /tmp/tmph_q2dkzc.o -shared -Wl,--sort-common,--as-needed -pthread -o libtest.so
EXIT: 0
>>


REPORT: ok

REPORT: Detecting pointer size:

COMPILE /tmp/tmprcv620_l.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/tmprcv620_l.cpp -o /tmp/tmprcv620_l.o
EXIT: 0
>>

EXEC <<
CMD: g++ /tmp/tmprcv620_l.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/tmpwdyhz31e.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/tmpwdyhz31e.cpp -o /tmp/tmpwdyhz31e.o
EXIT: 0
>>

EXEC <<
CMD: g++ /tmp/tmpwdyhz31e.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/tmpwaeth5b7.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/tmpwaeth5b7.cpp -o /tmp/tmpwaeth5b7.o
EXIT: 0
>>

EXEC <<
CMD: g++ /tmp/tmpwaeth5b7.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/tmpxywg2v0p.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/tmpxywg2v0p.cpp -o /tmp/tmpxywg2v0p.o
EXIT: 0
>>

EXEC <<
CMD: g++ /tmp/tmpxywg2v0p.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/tmpn_9m4t5a.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/tmpn_9m4t5a.cpp -o /tmp/tmpn_9m4t5a.o
EXIT: 0
>>

EXEC <<
CMD: g++ /tmp/tmpn_9m4t5a.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/local/fsl/include/eigen3
>>


REPORT: Checking for Eigen3 library:

COMPILE /tmp/tmpznfrkcfm.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/local/fsl/include/eigen3 /tmp/tmpznfrkcfm.cpp -o /tmp/tmpznfrkcfm.o
EXIT: 0
>>

EXEC <<
CMD: g++ /tmp/tmpznfrkcfm.o -Wl,--sort-common,--as-needed -pthread -o a.out
EXIT: 0
>>

EXEC <<
CMD: ./a.out
EXIT: 0
STDOUT:
3.4.0
>>


REPORT: 3.4.0

REPORT: Checking for Eigen3 Unsupported:

COMPILE /tmp/tmpl1cf66od.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/local/fsl/include/eigen3 -DEIGEN_DONT_PARALLELIZE /tmp/tmpl1cf66od.cpp -o /tmp/tmpl1cf66od.o
EXIT: 0
>>

EXEC <<
CMD: g++ /tmp/tmpl1cf66od.o -Wl,--sort-common,--as-needed -pthread -o a.out
EXIT: 0
>>

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


REPORT: Present
EXEC <<
CMD: pkg-config --cflags zlib
EXIT: 0
STDOUT:
-I/usr/local/fsl/include
>>

EXEC <<
CMD: pkg-config --libs zlib
EXIT: 0
STDOUT:
-L/usr/local/fsl/lib -lz
>>


REPORT: Checking for zlib compression library:

COMPILE /tmp/tmpzhy640t5.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 -DMRTRIX_HAVE_EIGEN_UNSUPPORTED_SPECIAL_FUNCTIONS -idirafter /usr/local/fsl/include /tmp/tmpzhy640t5.cpp -o /tmp/tmpzhy640t5.o
EXIT: 0
>>

EXEC <<
CMD: g++ /tmp/tmpzhy640t5.o -Wl,--sort-common,--as-needed -pthread -L/usr/local/fsl/lib -lz -o a.out
EXIT: 0
>>

EXEC <<
CMD: ./a.out
EXIT: 0
STDOUT:
1.2.13
>>


REPORT: 1.2.13

REPORT: Checking for "JSON for Modern C++" requirements:

COMPILE /tmp/tmpodwylycg.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 -DMRTRIX_HAVE_EIGEN_UNSUPPORTED_SPECIAL_FUNCTIONS -idirafter /usr/local/fsl/include -I/home/cbdl/mrtrix3/core /tmp/tmpodwylycg.cpp -o /tmp/tmpodwylycg.o
EXIT: 0
>>

EXEC <<
CMD: g++ /tmp/tmpodwylycg.o -Wl,--sort-common,--as-needed -pthread -L/usr/local/fsl/lib -lz -o a.out
EXIT: 0
>>

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


REPORT: ok
EXEC <<
CMD: pkg-config --cflags libtiff-4
EXIT: 0
STDOUT:
-I/usr/local/fsl/include
>>

EXEC <<
CMD: pkg-config --libs libtiff-4
EXIT: 0
STDOUT:
-L/usr/local/fsl/lib -ltiff
>>


REPORT: Checking for TIFF library:

COMPILE /tmp/tmpxvn37frz.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 -DMRTRIX_HAVE_EIGEN_UNSUPPORTED_SPECIAL_FUNCTIONS -idirafter /usr/local/fsl/include -idirafter /usr/local/fsl/include /tmp/tmpxvn37frz.cpp -o /tmp/tmpxvn37frz.o
EXIT: 0
>>

EXEC <<
CMD: g++ /tmp/tmpxvn37frz.o -Wl,--sort-common,--as-needed -pthread -L/usr/local/fsl/lib -lz -L/usr/local/fsl/lib -ltiff -o a.out
EXIT: 0
>>

EXEC <<
CMD: ./a.out
EXIT: 0
STDOUT:
LIBTIFF, Version 4.4.0
Copyright (c) 1988-1996 Sam Leffler
Copyright (c) 1991-1996 Silicon Graphics, Inc.
>>


REPORT: LIBTIFF, Version 4.4.0
EXEC <<
CMD: pkg-config --cflags libpng
EXIT: 0
STDOUT:
-I/usr/local/fsl/include/libpng16 -I/usr/local/fsl/include
>>

EXEC <<
CMD: pkg-config --libs libpng
EXIT: 0
STDOUT:
-L/usr/local/fsl/lib -lpng16
>>


REPORT: Checking for PNG library:

COMPILE /tmp/tmpuk9zf5bj.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 -DMRTRIX_HAVE_EIGEN_UNSUPPORTED_SPECIAL_FUNCTIONS -idirafter /usr/local/fsl/include -DMRTRIX_TIFF_SUPPORT -idirafter /usr/local/fsl/include -idirafter /usr/local/fsl/include/libpng16 -idirafter /usr/local/fsl/include /tmp/tmpuk9zf5bj.cpp -o /tmp/tmpuk9zf5bj.o
EXIT: 0
>>

EXEC <<
CMD: g++ /tmp/tmpuk9zf5bj.o -Wl,--sort-common,--as-needed -pthread -L/usr/local/fsl/lib -lz -L/usr/local/fsl/lib -ltiff -L/usr/local/fsl/lib -lpng16 -o a.out
EXIT: 0
>>

EXEC <<
CMD: ./a.out
EXIT: 0
STDOUT:
Header: 1.6.39; library: 1.6.39
>>


REPORT: Header: 1.6.39; library: 1.6.39
EXEC <<
CMD: pkg-config --cflags fftw3
EXIT: 0
STDOUT:
-I/usr/local/fsl/include
>>

EXEC <<
CMD: pkg-config --libs fftw3
EXIT: 0
STDOUT:
-L/usr/local/fsl/lib -lfftw3
>>


REPORT: Checking for FFTW library:

COMPILE /tmp/tmpkkstmkov.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_HAVE_EIGEN_UNSUPPORTED_SPECIAL_FUNCTIONS -idirafter /usr/local/fsl/include -DMRTRIX_TIFF_SUPPORT -idirafter /usr/local/fsl/include -DMRTRIX_PNG_SUPPORT -idirafter /usr/local/fsl/include/libpng16 -idirafter /usr/local/fsl/include -idirafter /usr/local/fsl/include /tmp/tmpkkstmkov.cpp -o /tmp/tmpkkstmkov.o
EXIT: 0
>>

EXEC <<
CMD: g++ /tmp/tmpkkstmkov.o -Wl,--sort-common,--as-needed -pthread -L/usr/local/fsl/lib -lz -L/usr/local/fsl/lib -ltiff -L/usr/local/fsl/lib -lpng16 -L/usr/local/fsl/lib -lfftw3 -o a.out
EXIT: 0
>>

EXEC <<
CMD: ./a.out
EXIT: 0
STDOUT:
fftw-3.3.10-sse2-avx
>>


REPORT: fftw-3.3.10-sse2-avx

REPORT: Checking for Qt moc:
EXEC <<
CMD: moc -v
EXIT: 0
STDOUT:
moc 5.15.6
>>


REPORT: moc (version 5.15.6)

REPORT: Checking for Qt qmake:
EXEC <<
CMD: qmake -v
EXIT: 0
STDOUT:
QMake version 3.1
Using Qt version 5.15.6 in /usr/local/fsl/lib
>>


REPORT: qmake (version 5.15.6)

REPORT: Checking for Qt rcc:
EXEC <<
CMD: rcc -v
EXIT: 0
STDOUT:
rcc 5.15.6
>>


REPORT: rcc (version 5.15.6)

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
STDOUT:
Info: creating stash file /tmp/tmpt2yqmhi4/.qmake.stash
>>

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.', '-I/usr/local/fsl/include/qt', '-I/usr/local/fsl/include/qt/QtOpenGL', '-I/usr/local/fsl/include/qt/QtSvg', '-I/usr/local/fsl/include/qt/QtWidgets', '-I/usr/local/fsl/include/qt/QtGui', '-I/usr/local/fsl/include/qt/QtNetwork', '-I/usr/local/fsl/include/qt/QtCore', '-I.', '-I/usr/local/fsl/include', '-I/usr/include/libdrm', '-I$(CONDA_BUILD_SYSROOT)/usr/include', '-I/usr/local/fsl/mkspecs/linux-g++']
  qt_libs: ['$(SUBLIBS)', '/usr/local/fsl/lib/libQt5OpenGL.so', '/usr/local/fsl/lib/libQt5Svg.so', '/usr/local/fsl/lib/libQt5Widgets.so', '/usr/local/fsl/lib/libQt5Gui.so', '/usr/local/fsl/lib/libQt5Network.so', '/usr/local/fsl/lib/libQt5Core.so', '-L/usr/lib64', '-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_HAVE_EIGEN_UNSUPPORTED_SPECIAL_FUNCTIONS -idirafter /usr/local/fsl/include -DMRTRIX_TIFF_SUPPORT -idirafter /usr/local/fsl/include -DMRTRIX_PNG_SUPPORT -idirafter /usr/local/fsl/include/libpng16 -idirafter /usr/local/fsl/include -DEIGEN_FFTW_DEFAULT -idirafter /usr/local/fsl/include -DQT_NO_DEBUG -DQT_OPENGL_LIB -DQT_SVG_LIB -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_NETWORK_LIB -DQT_CORE_LIB -idirafter /usr/local/fsl/include/qt -idirafter /usr/local/fsl/include/qt/QtOpenGL -idirafter /usr/local/fsl/include/qt/QtSvg -idirafter /usr/local/fsl/include/qt/QtWidgets -idirafter /usr/local/fsl/include/qt/QtGui -idirafter /usr/local/fsl/include/qt/QtNetwork -idirafter /usr/local/fsl/include/qt/QtCore -idirafter /usr/local/fsl/include -idirafter /usr/include/libdrm -idirafter $(CONDA_BUILD_SYSROOT)/usr/include -idirafter /usr/local/fsl/mkspecs/linux-g++ qt.cpp -o qt.o
EXIT: 0
>>

EXEC <<
CMD: g++ -c -std=c++11 -DMRTRIX_BUILD_TYPE="release version" -pthread -fPIC -DMRTRIX_WORD64 -DMRTRIX_HAVE_EIGEN_UNSUPPORTED_SPECIAL_FUNCTIONS -idirafter /usr/local/fsl/include -DMRTRIX_TIFF_SUPPORT -idirafter /usr/local/fsl/include -DMRTRIX_PNG_SUPPORT -idirafter /usr/local/fsl/include/libpng16 -idirafter /usr/local/fsl/include -DEIGEN_FFTW_DEFAULT -idirafter /usr/local/fsl/include -DQT_NO_DEBUG -DQT_OPENGL_LIB -DQT_SVG_LIB -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_NETWORK_LIB -DQT_CORE_LIB -idirafter /usr/local/fsl/include/qt -idirafter /usr/local/fsl/include/qt/QtOpenGL -idirafter /usr/local/fsl/include/qt/QtSvg -idirafter /usr/local/fsl/include/qt/QtWidgets -idirafter /usr/local/fsl/include/qt/QtGui -idirafter /usr/local/fsl/include/qt/QtNetwork -idirafter /usr/local/fsl/include/qt/QtCore -idirafter /usr/local/fsl/include -idirafter /usr/include/libdrm -idirafter $(CONDA_BUILD_SYSROOT)/usr/include -idirafter /usr/local/fsl/mkspecs/linux-g++ qt_moc.cpp -o qt_moc.o
EXIT: 0
>>

EXEC <<
CMD: g++ -Wl,--sort-common,--as-needed -pthread -L/usr/local/fsl/lib -lz -L/usr/local/fsl/lib -ltiff -L/usr/local/fsl/lib -lpng16 -L/usr/local/fsl/lib -lfftw3 qt_moc.o qt.o -o qt /usr/local/fsl/lib/libQt5OpenGL.so /usr/local/fsl/lib/libQt5Svg.so /usr/local/fsl/lib/libQt5Widgets.so /usr/local/fsl/lib/libQt5Gui.so /usr/local/fsl/lib/libQt5Network.so /usr/local/fsl/lib/libQt5Core.so -L/usr/lib64 -lGL -lpthread
EXIT: 1
STDERR:
/usr/local/fsl/bin/../lib/gcc/x86_64-conda-linux-gnu/11.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: cannot find -lGL: No such file or directory
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.

Output of dpkg -l | grep nvidia

type or paste code hereii  libnvidia-cfg1-470:amd64                   470.161.03-0ubuntu0.22.04.1             amd64        NVIDIA binary OpenGL/GLX configuration library
ii  libnvidia-common-470                       470.161.03-0ubuntu0.22.04.1             all          Shared files used by the NVIDIA libraries
ii  libnvidia-compute-470:amd64                470.161.03-0ubuntu0.22.04.1             amd64        NVIDIA libcompute package
ii  libnvidia-compute-470:i386                 470.161.03-0ubuntu0.22.04.1             i386         NVIDIA libcompute package
ii  libnvidia-decode-470:amd64                 470.161.03-0ubuntu0.22.04.1             amd64        NVIDIA Video Decoding runtime libraries
ii  libnvidia-decode-470:i386                  470.161.03-0ubuntu0.22.04.1             i386         NVIDIA Video Decoding runtime libraries
ii  libnvidia-egl-wayland1:amd64               1:1.1.9-1.1                             amd64        Wayland EGL External Platform library -- shared library
ii  libnvidia-encode-470:amd64                 470.161.03-0ubuntu0.22.04.1             amd64        NVENC Video Encoding runtime library
ii  libnvidia-encode-470:i386                  470.161.03-0ubuntu0.22.04.1             i386         NVENC Video Encoding runtime library
ii  libnvidia-extra-470:amd64                  470.161.03-0ubuntu0.22.04.1             amd64        Extra libraries for the NVIDIA driver
ii  libnvidia-fbc1-470:amd64                   470.161.03-0ubuntu0.22.04.1             amd64        NVIDIA OpenGL-based Framebuffer Capture runtime library
ii  libnvidia-fbc1-470:i386                    470.161.03-0ubuntu0.22.04.1             i386         NVIDIA OpenGL-based Framebuffer Capture runtime library
ii  libnvidia-gl-470:amd64                     470.161.03-0ubuntu0.22.04.1             amd64        NVIDIA OpenGL/GLX/EGL/GLES GLVND libraries and Vulkan ICD
ii  libnvidia-gl-470:i386                      470.161.03-0ubuntu0.22.04.1             i386         NVIDIA OpenGL/GLX/EGL/GLES GLVND libraries and Vulkan ICD
ii  libnvidia-ifr1-470:amd64                   470.161.03-0ubuntu0.22.04.1             amd64        NVIDIA OpenGL-based Inband Frame Readback runtime library
ii  libnvidia-ifr1-470:i386                    470.161.03-0ubuntu0.22.04.1             i386         NVIDIA OpenGL-based Inband Frame Readback runtime library
rc  linux-modules-nvidia-470-5.15.0-43-generic 5.15.0-43.46+1                          amd64        Linux kernel nvidia modules for version 5.15.0-43
ii  linux-modules-nvidia-470-5.15.0-60-generic 5.15.0-60.66                            amd64        Linux kernel nvidia modules for version 5.15.0-60
ii  linux-modules-nvidia-470-generic-hwe-22.04 5.15.0-60.66                            amd64        Extra drivers for nvidia-470 for the generic-hwe-22.04 flavour
ii  linux-objects-nvidia-470-5.15.0-43-generic 5.15.0-43.46+1                          amd64        Linux kernel nvidia modules for version 5.15.0-43 (objects)
ii  linux-objects-nvidia-470-5.15.0-60-generic 5.15.0-60.66                            amd64        Linux kernel nvidia modules for version 5.15.0-60 (objects)
ii  linux-signatures-nvidia-5.15.0-43-generic  5.15.0-43.46+1                          amd64        Linux kernel signatures for nvidia modules for version 5.15.0-43-generic
ii  linux-signatures-nvidia-5.15.0-60-generic  5.15.0-60.66                            amd64        Linux kernel signatures for nvidia modules for version 5.15.0-60-generic
ii  nvidia-compute-utils-470                   470.161.03-0ubuntu0.22.04.1             amd64        NVIDIA compute utilities
ii  nvidia-driver-470                          470.161.03-0ubuntu0.22.04.1             amd64        NVIDIA driver metapackage
ii  nvidia-kernel-common-470                   470.161.03-0ubuntu0.22.04.1             amd64        Shared files used with the kernel module
ii  nvidia-kernel-source-470                   470.161.03-0ubuntu0.22.04.1             amd64        NVIDIA kernel source package
ii  nvidia-prime                               0.8.17.1                                all          Tools to enable NVIDIA's Prime
ii  nvidia-settings                            510.47.03-0ubuntu1                      amd64        Tool for configuring the NVIDIA graphics driver
ii  nvidia-utils-470                           470.161.03-0ubuntu0.22.04.1             amd64        NVIDIA driver support binaries
ii  screen-resolution-extra                    0.18.2                                  all          Extension for the nvidia-settings control panel
ii  xserver-xorg-video-nvidia-470              470.161.03-0ubuntu0.22.04.1             amd64        NVIDIA binary Xorg d

[jdtournier]

Main issue probably stems from interference from two separate sources, both of which could cause trouble: FSL and conda.

---

First, it’s using the conda compiler, which invariably causes trouble – especially for GUI / OpenGL applications:

@samuel2496

REPORT: Looking for compiler [g++]:
EXEC <<
CMD: g++ --version
EXIT: 0
STDOUT:
g++ (conda-forge gcc 11.3.0-19) 11.3.0
Copyright (C) 2021 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.
>>

I’m not sure why that would be, we normally try to remove anything conda-related from the configuration to avoid these kinds of issues – but I can’t see anything in your PATH that makes any mention of conda, so it’s possible you’ve installed it in a non-standard location where the name ‘conda’ doesn’t feature, which would fool our naive attempts at dealing with this… (?)

---

Second, you’re using non-system packages installed in /usr/local/fsl.

EXEC <<
CMD: pkg-config --cflags eigen3
EXIT: 0
STDOUT:
-I/usr/local/fsl/include/eigen3
>>

I expect the reason these are being included may be because it’s using a version of pkg-config installed in that location, rather than the system-supplied one (you can check with which pkg-config – system-supplied version should be in /usr/bin).

I’ve no idea whether you installed these packages manually at this location, or whether these came as part of FSL. We’ve not previously come across issues of this sort with FSL, so I suspect the former (?)

---

To fix both issues, it may be sufficient to set your PATH to a more bare-bones version that doesn’t include any 3rd party packages (at least not FSL or conda). Something like this ought to be enough, which I’ve obtained by stripping out anything non-standard from the PATH reported at the head of your configure.log:

export PATH=/usr/sbin:/usr/bin:/sbin:/bin:/snap/bin
./configure

Note that you may now find that some of the packages that you thought were installed are now no longer found, if it was previously relying on the non-standard versions installed in /usr/local/fsl. If that’s the case, it should just be a matter of using apt to install the expected system-supplied version, as suggested in our docs.

Hope this sorts out the problem…
Cheers,
Donald.

[samuel2496]

Hi

Thank you for your assistance. The solution worked.

Regarding FSL:
I did not install it manually, it came as part of FSL itself. I think it might have changed in the recent versions.

Thanks again

[bjeurissen]

It have a feeling that current FSL installation instructions/distribution have an issue.

Only yesterday, a colleague of mine freshly installed FSL and ended up with a “broken” compiler because the FSL installation bundles clang++ and adds it to the front of the PATH variable.

[jdtournier]

Ok, that’s an … interesting decision they made there. I have a feeling they’re going to start getting a fair bit of pushback about this, it’s going to break quite a lot of users’ workflows…

[raz27289]

I am facing the problem with linking Qt application. I have installed libqt5-opengl & libqt5-opengl-dev package but still the error persist. I have been trying various solutions from the forums but nothing is working. I tried all the solution as mentioned above but still stuck up with the same error.

REPORT: 
MRtrix build type requested: release version

REPORT: WARNING: anaconda/miniconda detected in PATH ("/usr/local/fsl/condabin") - removed to avoid conflicts
PATH set to: /usr/local/fsl/bin:/usr/sbin:/usr/bin:/sbin:/bin:/snap/bin
REPORT: WARNING: anaconda/miniconda compiler set by CXX environment variable - ignored to avoid conflicts

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
>>


REPORT: not found

REPORT: Looking for compiler [g++]:
EXEC <<
CMD: g++ --version
EXIT: 0
STDOUT:
g++ (conda-forge gcc 12.3.0-11) 12.3.0
Copyright (C) 2022 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++ (conda-forge gcc 12.3.0-11) 12.3.0

REPORT: Checking for C++11 compliance:

COMPILE /tmp/tmpjyv6gsaz.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 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /usr/local/fsl/include /tmp/tmpjyv6gsaz.cpp -o /tmp/tmpjyv6gsaz.o
EXIT: 0
>>

EXEC <<
CMD: g++ /tmp/tmpjyv6gsaz.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 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /usr/local/fsl/include /tmp/tmpys3l_6j0.cpp -o /tmp/tmpys3l_6j0.o
EXIT: 0
>>

EXEC <<
CMD: g++ /tmp/tmpys3l_6j0.o -shared -Wl,--sort-common,--as-needed -pthread -o libtest.so
EXIT: 0
>>


REPORT: ok

REPORT: Detecting pointer size:

COMPILE /tmp/tmph7nrsoj5.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 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /usr/local/fsl/include /tmp/tmph7nrsoj5.cpp -o /tmp/tmph7nrsoj5.o
EXIT: 0
>>

EXEC <<
CMD: g++ /tmp/tmph7nrsoj5.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/tmpe4w22ryh.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 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /usr/local/fsl/include -DMRTRIX_WORD64 /tmp/tmpe4w22ryh.cpp -o /tmp/tmpe4w22ryh.o
EXIT: 0
>>

EXEC <<
CMD: g++ /tmp/tmpe4w22ryh.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/tmpobq81e7n.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 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /usr/local/fsl/include -DMRTRIX_WORD64 /tmp/tmpobq81e7n.cpp -o /tmp/tmpobq81e7n.o
EXIT: 0
>>

EXEC <<
CMD: g++ /tmp/tmpobq81e7n.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/tmpes83nmk7.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 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /usr/local/fsl/include -DMRTRIX_WORD64 /tmp/tmpes83nmk7.cpp -o /tmp/tmpes83nmk7.o
EXIT: 0
>>

EXEC <<
CMD: g++ /tmp/tmpes83nmk7.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/tmpgl3lpwm2.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 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /usr/local/fsl/include -DMRTRIX_WORD64 /tmp/tmpgl3lpwm2.cpp -o /tmp/tmpgl3lpwm2.o
EXIT: 0
>>

EXEC <<
CMD: g++ /tmp/tmpgl3lpwm2.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/local/fsl/include/eigen3
>>


REPORT: Checking for Eigen3 library:

COMPILE /tmp/tmphqbu6azl.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 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /usr/local/fsl/include -DMRTRIX_WORD64 -isystem /usr/local/fsl/include/eigen3 /tmp/tmphqbu6azl.cpp -o /tmp/tmphqbu6azl.o
EXIT: 0
>>

EXEC <<
CMD: g++ /tmp/tmphqbu6azl.o -Wl,--sort-common,--as-needed -pthread -o a.out
EXIT: 0
>>

EXEC <<
CMD: ./a.out
EXIT: 0
STDOUT:
3.4.0
>>


REPORT: 3.4.0

REPORT: Checking for Eigen3 Unsupported:

COMPILE /tmp/tmpc_a0a4o6.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 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /usr/local/fsl/include -DMRTRIX_WORD64 -isystem /usr/local/fsl/include/eigen3 -DEIGEN_DONT_PARALLELIZE /tmp/tmpc_a0a4o6.cpp -o /tmp/tmpc_a0a4o6.o
EXIT: 0
>>

EXEC <<
CMD: g++ /tmp/tmpc_a0a4o6.o -Wl,--sort-common,--as-needed -pthread -o a.out
EXIT: 0
>>

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


REPORT: Present
EXEC <<
CMD: pkg-config --cflags zlib
EXIT: 0
STDOUT:
-I/usr/local/fsl/include
>>

EXEC <<
CMD: pkg-config --libs zlib
EXIT: 0
STDOUT:
-L/usr/local/fsl/lib -lz
>>


REPORT: Checking for zlib compression library:

COMPILE /tmp/tmp796cg7kz.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 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /usr/local/fsl/include -DMRTRIX_WORD64 -DMRTRIX_HAVE_EIGEN_UNSUPPORTED_SPECIAL_FUNCTIONS -isystem /usr/local/fsl/include /tmp/tmp796cg7kz.cpp -o /tmp/tmp796cg7kz.o
EXIT: 0
>>

EXEC <<
CMD: g++ /tmp/tmp796cg7kz.o -Wl,--sort-common,--as-needed -pthread -L/usr/local/fsl/lib -lz -o a.out
EXIT: 0
>>

EXEC <<
CMD: ./a.out
EXIT: 0
STDOUT:
1.2.13
>>


REPORT: 1.2.13

REPORT: Checking for "JSON for Modern C++" requirements:

COMPILE /tmp/tmpli9c4apv.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 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /usr/local/fsl/include -DMRTRIX_WORD64 -DMRTRIX_HAVE_EIGEN_UNSUPPORTED_SPECIAL_FUNCTIONS -isystem /usr/local/fsl/include -I/home/vboxuser/mrtrix3/core /tmp/tmpli9c4apv.cpp -o /tmp/tmpli9c4apv.o
EXIT: 0
>>

EXEC <<
CMD: g++ /tmp/tmpli9c4apv.o -Wl,--sort-common,--as-needed -pthread -L/usr/local/fsl/lib -lz -o a.out
EXIT: 0
>>

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


REPORT: ok
EXEC <<
CMD: pkg-config --cflags libtiff-4
EXIT: 0
STDOUT:
-I/usr/local/fsl/include -I/usr/local/fsl/include/webp -I/usr/local/fsl/include
>>

EXEC <<
CMD: pkg-config --libs libtiff-4
EXIT: 0
STDOUT:
-L/usr/local/fsl/lib -ltiff
>>


REPORT: Checking for TIFF library:

COMPILE /tmp/tmphg3w9p2o.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 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /usr/local/fsl/include -DMRTRIX_WORD64 -DMRTRIX_HAVE_EIGEN_UNSUPPORTED_SPECIAL_FUNCTIONS -isystem /usr/local/fsl/include -isystem /usr/local/fsl/include -isystem /usr/local/fsl/include/webp -isystem /usr/local/fsl/include /tmp/tmphg3w9p2o.cpp -o /tmp/tmphg3w9p2o.o
EXIT: 0
>>

EXEC <<
CMD: g++ /tmp/tmphg3w9p2o.o -Wl,--sort-common,--as-needed -pthread -L/usr/local/fsl/lib -lz -L/usr/local/fsl/lib -ltiff -o a.out
EXIT: 1
STDERR:
/usr/local/fsl/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /usr/local/fsl/lib/liblzma.so.5: undefined reference to `memcpy@GLIBC_2.14'
/usr/local/fsl/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /usr/local/fsl/lib/liblzma.so.5: undefined reference to `clock_gettime@GLIBC_2.17'
collect2: error: ld returned 1 exit status
>>

error deleting temporary file "a.out": No such file or directory
REPORT: not found - TIFF support disabled
EXEC <<
CMD: pkg-config --cflags libpng
EXIT: 0
STDOUT:
-I/usr/local/fsl/include/libpng16 -I/usr/local/fsl/include
>>

EXEC <<
CMD: pkg-config --libs libpng
EXIT: 0
STDOUT:
-L/usr/local/fsl/lib -lpng16
>>


REPORT: Checking for PNG library:

COMPILE /tmp/tmpadtiomy2.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 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /usr/local/fsl/include -DMRTRIX_WORD64 -DMRTRIX_HAVE_EIGEN_UNSUPPORTED_SPECIAL_FUNCTIONS -isystem /usr/local/fsl/include -isystem /usr/local/fsl/include/libpng16 -isystem /usr/local/fsl/include /tmp/tmpadtiomy2.cpp -o /tmp/tmpadtiomy2.o
EXIT: 0
>>

EXEC <<
CMD: g++ /tmp/tmpadtiomy2.o -Wl,--sort-common,--as-needed -pthread -L/usr/local/fsl/lib -lz -L/usr/local/fsl/lib -lpng16 -o a.out
EXIT: 0
>>

EXEC <<
CMD: ./a.out
EXIT: 0
STDOUT:
Header: 1.6.43; library: 1.6.43
>>


REPORT: Header: 1.6.43; library: 1.6.43
EXEC <<
CMD: pkg-config --cflags fftw3
EXIT: 0
STDOUT:
-I/usr/local/fsl/include
>>

EXEC <<
CMD: pkg-config --libs fftw3
EXIT: 0
STDOUT:
-L/usr/local/fsl/lib -lfftw3
>>


REPORT: Checking for FFTW library:

COMPILE /tmp/tmpvqwrnxa3.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 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /usr/local/fsl/include -DMRTRIX_WORD64 -DMRTRIX_HAVE_EIGEN_UNSUPPORTED_SPECIAL_FUNCTIONS -isystem /usr/local/fsl/include -DMRTRIX_PNG_SUPPORT -isystem /usr/local/fsl/include/libpng16 -isystem /usr/local/fsl/include -isystem /usr/local/fsl/include /tmp/tmpvqwrnxa3.cpp -o /tmp/tmpvqwrnxa3.o
EXIT: 0
>>

EXEC <<
CMD: g++ /tmp/tmpvqwrnxa3.o -Wl,--sort-common,--as-needed -pthread -L/usr/local/fsl/lib -lz -L/usr/local/fsl/lib -lpng16 -L/usr/local/fsl/lib -lfftw3 -o a.out
EXIT: 0
>>

EXEC <<
CMD: ./a.out
EXIT: 0
STDOUT:
fftw-3.3.10-sse2-avx
>>


REPORT: fftw-3.3.10-sse2-avx

REPORT: Checking for Qt moc:
EXEC <<
CMD: moc -v
EXIT: 0
STDOUT:
moc 5.15.8
>>


REPORT: moc (version 5.15.8)

REPORT: Checking for Qt qmake:
EXEC <<
CMD: qmake -v
EXIT: 0
STDOUT:
QMake version 3.1
Using Qt version 5.15.8 in /usr/local/fsl/lib
>>


REPORT: qmake (version 5.15.8)

REPORT: Checking for Qt rcc:
EXEC <<
CMD: rcc -v
EXIT: 0
STDOUT:
rcc 5.15.8
>>


REPORT: rcc (version 5.15.8)

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
STDOUT:
Info: creating stash file /tmp/tmpmow5qyd5/.qmake.stash
>>

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.', '-I/usr/local/fsl/include/qt', '-I/usr/local/fsl/include/qt/QtOpenGL', '-I/usr/local/fsl/include/qt/QtSvg', '-I/usr/local/fsl/include/qt/QtWidgets', '-I/usr/local/fsl/include/qt/QtGui', '-I/usr/local/fsl/include/qt/QtNetwork', '-I/usr/local/fsl/include/qt/QtCore', '-I.', '-I/usr/local/fsl/include', '-I/usr/include/libdrm', '-I/usr/local/fsl/mkspecs/linux-g++']
  qt_libs: ['$(SUBLIBS)', '/usr/local/fsl/lib/libQt5OpenGL.so', '/usr/local/fsl/lib/libQt5Svg.so', '/usr/local/fsl/lib/libQt5Widgets.so', '/usr/local/fsl/lib/libQt5Gui.so', '/usr/local/fsl/lib/libQt5Network.so', '/usr/local/fsl/lib/libQt5Core.so', '-L/usr/lib64', '-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 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /usr/local/fsl/include -DMRTRIX_WORD64 -DMRTRIX_HAVE_EIGEN_UNSUPPORTED_SPECIAL_FUNCTIONS -isystem /usr/local/fsl/include -DMRTRIX_PNG_SUPPORT -isystem /usr/local/fsl/include/libpng16 -isystem /usr/local/fsl/include -DEIGEN_FFTW_DEFAULT -isystem /usr/local/fsl/include -DQT_NO_DEBUG -DQT_OPENGL_LIB -DQT_SVG_LIB -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_NETWORK_LIB -DQT_CORE_LIB -isystem /usr/local/fsl/include/qt -isystem /usr/local/fsl/include/qt/QtOpenGL -isystem /usr/local/fsl/include/qt/QtSvg -isystem /usr/local/fsl/include/qt/QtWidgets -isystem /usr/local/fsl/include/qt/QtGui -isystem /usr/local/fsl/include/qt/QtNetwork -isystem /usr/local/fsl/include/qt/QtCore -isystem /usr/local/fsl/include -isystem /usr/include/libdrm -isystem /usr/local/fsl/mkspecs/linux-g++ qt.cpp -o qt.o
EXIT: 0
>>

EXEC <<
CMD: g++ -c -std=c++11 -DMRTRIX_BUILD_TYPE="release version" -pthread -fPIC -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /usr/local/fsl/include -DMRTRIX_WORD64 -DMRTRIX_HAVE_EIGEN_UNSUPPORTED_SPECIAL_FUNCTIONS -isystem /usr/local/fsl/include -DMRTRIX_PNG_SUPPORT -isystem /usr/local/fsl/include/libpng16 -isystem /usr/local/fsl/include -DEIGEN_FFTW_DEFAULT -isystem /usr/local/fsl/include -DQT_NO_DEBUG -DQT_OPENGL_LIB -DQT_SVG_LIB -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_NETWORK_LIB -DQT_CORE_LIB -isystem /usr/local/fsl/include/qt -isystem /usr/local/fsl/include/qt/QtOpenGL -isystem /usr/local/fsl/include/qt/QtSvg -isystem /usr/local/fsl/include/qt/QtWidgets -isystem /usr/local/fsl/include/qt/QtGui -isystem /usr/local/fsl/include/qt/QtNetwork -isystem /usr/local/fsl/include/qt/QtCore -isystem /usr/local/fsl/include -isystem /usr/include/libdrm -isystem /usr/local/fsl/mkspecs/linux-g++ qt_moc.cpp -o qt_moc.o
EXIT: 0
>>

EXEC <<
CMD: g++ -Wl,--sort-common,--as-needed -pthread -L/usr/local/fsl/lib -lz -L/usr/local/fsl/lib -lpng16 -L/usr/local/fsl/lib -lfftw3 qt_moc.o qt.o -o qt /usr/local/fsl/lib/libQt5OpenGL.so /usr/local/fsl/lib/libQt5Svg.so /usr/local/fsl/lib/libQt5Widgets.so /usr/local/fsl/lib/libQt5Gui.so /usr/local/fsl/lib/libQt5Network.so /usr/local/fsl/lib/libQt5Core.so -L/usr/lib64 -lGL -lpthread
EXIT: 1
STDERR:
/usr/local/fsl/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: cannot find -lGL: No such file or directory
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.

[jdtournier]

Hi @raz27289,

This seems like the same issue as in this post:

ERROR: no suitable compiler found!

Ok, it looks like you’ve got anaconda installed, and that’s the likely problem. We’ve removed it from the path, since it’s actually really difficult to use anaconda for this, so it’s best avoided. But in your case, you’ve probably still got the CXX and/or LD variables set to point to the anaconda versions – which are no longer in the path… To get this working, you’ll need to use the XCode compiler. Assuming you have it installed, try unsetting the variables I mentioned before issuing ./configur…

Try the suggested solution, see if that helps…

Donald