Issue configuring on Debian 9

installation

#1

Hello Everybody,
I have been trying to configure and build on my Debian 9 machine – and I followed all the documentation and read up on the prerequisites and dependencies and I still am having issues while trying to configure. I tried to Google anything I could relating to my errors and no luck. Was hoping someone could direct me in the right direction. Any help is greatly appreciated.

Thanks!

REPORT: 
MRtrix build type requested: release version

REPORT: Detecting OS: linux

REPORT: Looking for compiler [clang++]:
EXEC <<
CMD: clang++ --version
EXIT: 0
STDOUT:
clang version 3.8.1-24 (tags/RELEASE_381/final)
Target: x86_64-pc-linux-gnu
Thread model: posix
InstalledDir: /usr/bin
>>


REPORT: clang version 3.8.1-24 (tags/RELEASE_381/final)

REPORT: Checking for C++11 compliance:

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

EXEC <<
CMD: clang++ /tmp/tmpSLAHjU.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: clang++ -c -std=c++11 -DMRTRIX_BUILD_TYPE="release version" -pthread -fPIC /tmp/tmp941e3E.cpp -o /tmp/tmp941e3E.o
EXIT: 0
>>

EXEC <<
CMD: clang++ /tmp/tmp941e3E.o -shared -Wl,--sort-common,--as-needed -pthread -o libtest.so
EXIT: 0
>>


REPORT: ok

REPORT: Detecting pointer size:

COMPILE /tmp/tmp_TMCgJ.cpp:
---

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

---
EXEC <<
CMD: clang++ -c -std=c++11 -DMRTRIX_BUILD_TYPE="release version" -pthread -fPIC /tmp/tmp_TMCgJ.cpp -o /tmp/tmp_TMCgJ.o
EXIT: 0
>>

EXEC <<
CMD: clang++ /tmp/tmp_TMCgJ.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/tmpsFbzQK.cpp:
---

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

---
EXEC <<
CMD: clang++ -c -std=c++11 -DMRTRIX_BUILD_TYPE="release version" -pthread -fPIC -DMRTRIX_WORD64 /tmp/tmpsFbzQK.cpp -o /tmp/tmpsFbzQK.o
EXIT: 0
>>

EXEC <<
CMD: clang++ /tmp/tmpsFbzQK.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/tmp9Dlbwj.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 -DMRTRIX_BUILD_TYPE="release version" -pthread -fPIC -DMRTRIX_WORD64 /tmp/tmp9Dlbwj.cpp -o /tmp/tmp9Dlbwj.o
EXIT: 1
STDERR:
/tmp/tmp9Dlbwj.cpp:11:6: error: variable length array of non-POD element type 'X'
  X x[argc];
     ^
1 error generated.
>>

error deleting temporary file "/tmp/tmp9Dlbwj.o": No such file or directory
REPORT: not found

REPORT: Checking for ::max_align_t:

COMPILE /tmp/tmpTM41qZ.cpp:
---

#include <iostream>
#include <cstddef>
using ::max_align_t;
int main() {
  std::cout << alignof (max_align_t) << " bytes\n";
  return 0;
}

---
EXEC <<
CMD: clang++ -c -std=c++11 -DMRTRIX_BUILD_TYPE="release version" -pthread -fPIC -DMRTRIX_WORD64 -DMRTRIX_NO_NON_POD_VLA /tmp/tmpTM41qZ.cpp -o /tmp/tmpTM41qZ.o
EXIT: 0
>>

EXEC <<
CMD: clang++ /tmp/tmpTM41qZ.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/tmpfogZWg.cpp:
---

#include <iostream>
#include <cstddef>
using std::max_align_t;
int main() {
  std::cout << alignof (max_align_t) << " bytes\n";
  return 0;
}

---
EXEC <<
CMD: clang++ -c -std=c++11 -DMRTRIX_BUILD_TYPE="release version" -pthread -fPIC -DMRTRIX_WORD64 -DMRTRIX_NO_NON_POD_VLA /tmp/tmpfogZWg.cpp -o /tmp/tmpfogZWg.o
EXIT: 0
>>

EXEC <<
CMD: clang++ /tmp/tmpfogZWg.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/tmplIUS6B.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 -DMRTRIX_BUILD_TYPE="release version" -pthread -fPIC -DMRTRIX_WORD64 -DMRTRIX_NO_NON_POD_VLA -isystem /usr/include/eigen3 /tmp/tmplIUS6B.cpp -o /tmp/tmplIUS6B.o
EXIT: 0
>>

EXEC <<
CMD: clang++ /tmp/tmplIUS6B.o -Wl,--sort-common,--as-needed -pthread -o a.out
EXIT: 0
>>

EXEC <<
CMD: ./a.out
EXIT: 0
STDOUT:
3.3.2
>>


REPORT: 3.3.2
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/tmpOGXc14.cpp:
---

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

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

---
EXEC <<
CMD: clang++ -c -std=c++11 -DMRTRIX_BUILD_TYPE="release version" -pthread -fPIC -DMRTRIX_WORD64 -DMRTRIX_NO_NON_POD_VLA /tmp/tmpOGXc14.cpp -o /tmp/tmpOGXc14.o
EXIT: 0
>>

EXEC <<
CMD: clang++ /tmp/tmpOGXc14.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/tmpFOBcXS.cpp:
---

#include "file/json.h"
int main (int argc, char* argv[])
{
  nlohmann::json json;
  json["key"] = "value";
}

---
EXEC <<
CMD: clang++ -c -std=c++11 -DMRTRIX_BUILD_TYPE="release version" -pthread -fPIC -DMRTRIX_WORD64 -DMRTRIX_NO_NON_POD_VLA -I/root/mrtrix3/core /tmp/tmpFOBcXS.cpp -o /tmp/tmpFOBcXS.o
EXIT: 0
>>

EXEC <<
CMD: clang++ /tmp/tmpFOBcXS.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: 0
STDOUT:
-I/usr/include/x86_64-linux-gnu
>>

EXEC <<
CMD: pkg-config --libs libtiff-4
EXIT: 0
STDOUT:
-ltiff
>>


REPORT: Checking for TIFF library:

COMPILE /tmp/tmpcm2b1r.cpp:
---

#include <iostream>
#include <tiffio.h>

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

---
EXEC <<
CMD: clang++ -c -std=c++11 -DMRTRIX_BUILD_TYPE="release version" -pthread -fPIC -DMRTRIX_WORD64 -DMRTRIX_NO_NON_POD_VLA -isystem /usr/include/x86_64-linux-gnu /tmp/tmpcm2b1r.cpp -o /tmp/tmpcm2b1r.o
EXIT: 0
>>

EXEC <<
CMD: clang++ /tmp/tmpcm2b1r.o -Wl,--sort-common,--as-needed -pthread -lz -ltiff -o a.out
EXIT: 0
>>

EXEC <<
CMD: ./a.out
EXIT: 0
STDOUT:
LIBTIFF, Version 4.0.8
Copyright (c) 1988-1996 Sam Leffler
Copyright (c) 1991-1996 Silicon Graphics, Inc.
>>


REPORT: LIBTIFF, Version 4.0.8
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/tmpNVTqGM.cpp:
---

#include <iostream>
#include <fftw3.h>

int main() {
  std::cout << fftw_version << "\n";
  return (0);
}

---
EXEC <<
CMD: clang++ -c -std=c++11 -DMRTRIX_BUILD_TYPE="release version" -pthread -fPIC -DMRTRIX_WORD64 -DMRTRIX_NO_NON_POD_VLA -DMRTRIX_TIFF_SUPPORT -isystem /usr/include/x86_64-linux-gnu /tmp/tmpNVTqGM.cpp -o /tmp/tmpNVTqGM.o
EXIT: 0
>>

EXEC <<
CMD: clang++ /tmp/tmpNVTqGM.o -Wl,--sort-common,--as-needed -pthread -lz -ltiff -lfftw3 -o a.out
EXIT: 0
>>

EXEC <<
CMD: ./a.out
EXIT: 0
STDOUT:
fftw-3.3.5-sse2-avx
>>


REPORT: fftw-3.3.5-sse2-avx

REPORT: Checking for Qt moc:
EXEC <<
CMD: moc -v
EXIT: 1
STDERR:
Qt Meta Object Compiler version 63 (Qt 4.8.7)
>>


REPORT: moc (version 4.8.7)

REPORT: Checking for Qt qmake:
EXEC <<
CMD: qmake -v
EXIT: 0
STDOUT:
QMake version 2.01a
Using Qt version 4.8.7 in /usr/lib/x86_64-linux-gnu
>>


REPORT: qmake (version 4.8.7)

REPORT: Checking for Qt rcc:
EXEC <<
CMD: rcc -v
EXIT: 1
STDERR:
Qt Resource Compiler version 4.8.7
>>


REPORT: rcc (version 4.8.7)

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 -DMRTRIX_BUILD_TYPE="release version" -pthread -fPIC -DMRTRIX_WORD64 -DMRTRIX_NO_NON_POD_VLA -DMRTRIX_TIFF_SUPPORT -isystem /usr/include/x86_64-linux-gnu -DEIGEN_FFTW_DEFAULT -m64 -pipe -Wall -W -D_REENTRANT -DQT_NO_DEBUG -DQT_SVG_LIB -DQT_OPENGL_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -isystem /usr/share/qt4/mkspecs/linux-g++-64 -isystem /usr/include/qt4/QtCore -isystem /usr/include/qt4/QtGui -isystem /usr/include/qt4/QtOpenGL -isystem /usr/include/qt4/QtSvg -isystem /usr/include/qt4 -isystem /usr/X11R6/include qt.cpp -o qt.o
EXIT: 0
>>

EXEC <<
CMD: clang++ -c -std=c++11 -DMRTRIX_BUILD_TYPE="release version" -pthread -fPIC -DMRTRIX_WORD64 -DMRTRIX_NO_NON_POD_VLA -DMRTRIX_TIFF_SUPPORT -isystem /usr/include/x86_64-linux-gnu -DEIGEN_FFTW_DEFAULT -m64 -pipe -Wall -W -D_REENTRANT -DQT_NO_DEBUG -DQT_SVG_LIB -DQT_OPENGL_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -isystem /usr/share/qt4/mkspecs/linux-g++-64 -isystem /usr/include/qt4/QtCore -isystem /usr/include/qt4/QtGui -isystem /usr/include/qt4/QtOpenGL -isystem /usr/include/qt4/QtSvg -isystem /usr/include/qt4 -isystem /usr/X11R6/include qt_moc.cpp -o qt_moc.o
EXIT: 0
>>

EXEC <<
CMD: clang++ -Wl,--sort-common,--as-needed -pthread -lz -ltiff -lfftw3 qt_moc.o qt.o -o qt -m64 -Wl,-O1 -L/usr/lib/x86_64-linux-gnu -L/usr/X11R6/lib64 -lQtSvg -lQtOpenGL -lQtGui -lQtCore -lGL -lpthread
EXIT: 1
STDERR:
/usr/bin/ld: cannot find -lGL
clang: error: linker command failed with exit code 1 (use -v to see invocation)
>>


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.

#2

OK, this is the relevant error message:

In simple terms, this is the compiler saying it can’t find the OpenGL library, which should have the name libGL.so. A quick search for that file and Debian 9 suggests that you need to install the libgl1-mesa-dev package. Try installing it, see if it resolves the problem…


#3

Hey Jd,

I actually meant to flag this post to be closed as I was able to resolve the issue. I had libgl1-mesa-dev installed, but it was linking incorrectly. Once I changed the link it all seemed to work. Appreciate the response!


#4

Did you need to symlink libGL.so to libGL.so.1 manually…? This would suggest there’s something wrong with the Debian package…