Hello,
I’m having difficulty resolving the errors listed at the bottom of my configure.log file, of which I’ve pasted the contents below. One error indicates that Xcode is not verified, which is likely true, as every time I try to open Xcode it seems to be incredibly slow/ lagging in the verification process. The other error only indicates that I should resolve the issue in the configure.log file, but I can’t find where exactly the error would be.
I realize this issue is probably quite basic/ simple to resolve. All help is appreciated!
REPORT:
MRtrix build type requested:
REPORT: release
REPORT:
REPORT: Detecting OS: darwin
EXEC <<
CMD: sw_vers -productVersion
EXIT: 0
STDOUT:
10.11.6
>>
REPORT: OS X deployment target: 10.11
REPORT: Checking for C++11 compliant compiler [clang++]:
EXEC <<
CMD: clang++ -dumpversion
EXIT: 0
STDOUT:
4.2.1
>>
REPORT: 4.2.1
COMPILE /var/folders/md/r653q57n37zbxz5bnwz1g8cm0000gp/T/tmpe13dk0di.cpp:
---
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 -mno-avx -DMRTRIX_MACOSX -fPIC -mmacosx-version-min=10.11 /var/folders/md/r653q57n37zbxz5bnwz1g8cm0000gp/T/tmpe13dk0di.cpp -o /var/folders/md/r653q57n37zbxz5bnwz1g8cm0000gp/T/tmpe13dk0di.o
EXIT: 0
>>
EXEC <<
CMD: clang++ /var/folders/md/r653q57n37zbxz5bnwz1g8cm0000gp/T/tmpe13dk0di.o -mmacosx-version-min=10.11 -o a.out
EXIT: 0
>>
EXEC <<
CMD: ./a.out
EXIT: 0
>>
REPORT: - tested ok
REPORT: Detecting pointer size:
COMPILE /var/folders/md/r653q57n37zbxz5bnwz1g8cm0000gp/T/tmpasm0awb_.cpp:
---
#include <iostream>
int main() {
std::cout << sizeof(void*);
return (0);
}
---
EXEC <<
CMD: clang++ -c -std=c++11 -mno-avx -DMRTRIX_MACOSX -fPIC -mmacosx-version-min=10.11 /var/folders/md/r653q57n37zbxz5bnwz1g8cm0000gp/T/tmpasm0awb_.cpp -o /var/folders/md/r653q57n37zbxz5bnwz1g8cm0000gp/T/tmpasm0awb_.o
EXIT: 0
>>
EXEC <<
CMD: clang++ /var/folders/md/r653q57n37zbxz5bnwz1g8cm0000gp/T/tmpasm0awb_.o -mmacosx-version-min=10.11 -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 /var/folders/md/r653q57n37zbxz5bnwz1g8cm0000gp/T/tmpif9yaj26.cpp:
---
int main(int argc, char* argv[]) {
int x[argc];
return 0;
}
---
EXEC <<
CMD: clang++ -c -std=c++11 -mno-avx -DMRTRIX_MACOSX -fPIC -mmacosx-version-min=10.11 -DMRTRIX_WORD64 /var/folders/md/r653q57n37zbxz5bnwz1g8cm0000gp/T/tmpif9yaj26.cpp -o /var/folders/md/r653q57n37zbxz5bnwz1g8cm0000gp/T/tmpif9yaj26.o
EXIT: 0
>>
EXEC <<
CMD: clang++ /var/folders/md/r653q57n37zbxz5bnwz1g8cm0000gp/T/tmpif9yaj26.o -mmacosx-version-min=10.11 -o a.out
EXIT: 0
>>
EXEC <<
CMD: ./a.out
EXIT: 0
>>
REPORT: yes
REPORT: Checking for non-POD variable-length array support:
COMPILE /var/folders/md/r653q57n37zbxz5bnwz1g8cm0000gp/T/tmp6bhqfudn.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 -mno-avx -DMRTRIX_MACOSX -fPIC -mmacosx-version-min=10.11 -DMRTRIX_WORD64 /var/folders/md/r653q57n37zbxz5bnwz1g8cm0000gp/T/tmp6bhqfudn.cpp -o /var/folders/md/r653q57n37zbxz5bnwz1g8cm0000gp/T/tmp6bhqfudn.o
EXIT: 1
STDERR:
/var/folders/md/r653q57n37zbxz5bnwz1g8cm0000gp/T/tmp6bhqfudn.cpp:11:6: error: variable length array of non-POD element type 'X'
X x[argc];
^
1 error generated.
>>
error deleting temporary file "/var/folders/md/r653q57n37zbxz5bnwz1g8cm0000gp/T/tmp6bhqfudn.o": No such file or directory
REPORT: no
REPORT: Checking for zlib compression library:
COMPILE /var/folders/md/r653q57n37zbxz5bnwz1g8cm0000gp/T/tmp10i_l4su.cpp:
---
#include <iostream>
#include <zlib.h>
int main() {
std::cout << zlibVersion();
return (0);
}
---
EXEC <<
CMD: clang++ -c -std=c++11 -mno-avx -DMRTRIX_MACOSX -fPIC -mmacosx-version-min=10.11 -DMRTRIX_WORD64 -DMRTRIX_NO_NON_POD_VLA /var/folders/md/r653q57n37zbxz5bnwz1g8cm0000gp/T/tmp10i_l4su.cpp -o /var/folders/md/r653q57n37zbxz5bnwz1g8cm0000gp/T/tmp10i_l4su.o
EXIT: 0
>>
EXEC <<
CMD: clang++ /var/folders/md/r653q57n37zbxz5bnwz1g8cm0000gp/T/tmp10i_l4su.o -mmacosx-version-min=10.11 -lz -o a.out
EXIT: 0
>>
EXEC <<
CMD: ./a.out
EXIT: 0
STDOUT:
1.2.5
>>
REPORT: 1.2.5
REPORT: Checking for Eigen 3 library:
EXEC <<
CMD: pkg-config --cflags eigen3
EXIT: 0
STDOUT:
-I/usr/local/Cellar/eigen/3.3.1/include/eigen3
>>
COMPILE /var/folders/md/r653q57n37zbxz5bnwz1g8cm0000gp/T/tmpm7hea6v9.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: clang++ -c -std=c++11 -mno-avx -DMRTRIX_MACOSX -fPIC -mmacosx-version-min=10.11 -DMRTRIX_WORD64 -DMRTRIX_NO_NON_POD_VLA -isystem /usr/local/Cellar/eigen/3.3.1/include/eigen3 /var/folders/md/r653q57n37zbxz5bnwz1g8cm0000gp/T/tmpm7hea6v9.cpp -o /var/folders/md/r653q57n37zbxz5bnwz1g8cm0000gp/T/tmpm7hea6v9.o
EXIT: 0
>>
EXEC <<
CMD: clang++ /var/folders/md/r653q57n37zbxz5bnwz1g8cm0000gp/T/tmpm7hea6v9.o -mmacosx-version-min=10.11 -lz -o a.out
EXIT: 0
>>
EXEC <<
CMD: ./a.out
EXIT: 0
STDOUT:
3.3.1
>>
REPORT: 3.3.1
REPORT: Checking Eigen 3 memory alignment requirements:
COMPILE /var/folders/md/r653q57n37zbxz5bnwz1g8cm0000gp/T/tmpywrpnz1r.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: clang++ -c -v -std=c++11 -mno-avx -DMRTRIX_MACOSX -fPIC -mmacosx-version-min=10.11 -DMRTRIX_WORD64 -DMRTRIX_NO_NON_POD_VLA -isystem /usr/local/Cellar/eigen/3.3.1/include/eigen3 /var/folders/md/r653q57n37zbxz5bnwz1g8cm0000gp/T/tmpywrpnz1r.cpp -o /var/folders/md/r653q57n37zbxz5bnwz1g8cm0000gp/T/tmpywrpnz1r.o
EXIT: 0
STDERR:
Apple LLVM version 7.3.0 (clang-703.0.31)
Target: x86_64-apple-darwin15.6.0
Thread model: posix
InstalledDir: /Library/Developer/CommandLineTools/usr/bin
"/Library/Developer/CommandLineTools/usr/bin/clang" -cc1 -triple x86_64-apple-macosx10.11.0 -Wdeprecated-objc-isa-usage -Werror=deprecated-objc-isa-usage -emit-obj -mrelax-all -disable-free -disable-llvm-verifier -main-file-name tmpywrpnz1r.cpp -mrelocation-model pic -pic-level 2 -mthread-model posix -mdisable-fp-elim -masm-verbose -munwind-tables -target-cpu core2 -target-feature -avx -target-linker-version 264.3.102 -v -dwarf-column-info -coverage-file /var/folders/md/r653q57n37zbxz5bnwz1g8cm0000gp/T/tmpywrpnz1r.o -resource-dir /Library/Developer/CommandLineTools/usr/bin/../lib/clang/7.3.0 -isystem /usr/local/Cellar/eigen/3.3.1/include/eigen3 -D MRTRIX_MACOSX -D MRTRIX_WORD64 -D MRTRIX_NO_NON_POD_VLA -stdlib=libc++ -std=c++11 -fdeprecated-macro -fdebug-compilation-dir /Users/rbaraka/mrtrix3 -ferror-limit 19 -fmessage-length 0 -stack-protector 1 -fblocks -fobjc-runtime=macosx-10.11.0 -fencode-extended-block-signature -fcxx-exceptions -fexceptions -fmax-type-align=16 -fdiagnostics-show-option -o /var/folders/md/r653q57n37zbxz5bnwz1g8cm0000gp/T/tmpywrpnz1r.o -x c++ /var/folders/md/r653q57n37zbxz5bnwz1g8cm0000gp/T/tmpywrpnz1r.cpp
clang -cc1 version 7.3.0 (clang-703.0.31) default target x86_64-apple-darwin15.6.0
ignoring nonexistent directory "/usr/include/c++/v1"
#include "..." search starts here:
#include <...> search starts here:
/usr/local/Cellar/eigen/3.3.1/include/eigen3
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1
/usr/local/include
/Library/Developer/CommandLineTools/usr/bin/../lib/clang/7.3.0/include
/Library/Developer/CommandLineTools/usr/include
/usr/include
/System/Library/Frameworks (framework directory)
/Library/Frameworks (framework directory)
End of search list.
>>
EXEC <<
CMD: clang++ /var/folders/md/r653q57n37zbxz5bnwz1g8cm0000gp/T/tmpywrpnz1r.o -mmacosx-version-min=10.11 -lz -o a.out
EXIT: 0
>>
EXEC <<
CMD: ./a.out
EXIT: 0
STDOUT:
allocator memory alignment: 48, Eigen3 needs: 16
>>
REPORT: OK
REPORT: Checking shared library generation:
EXEC <<
CMD: clang++ -c -std=c++11 -mno-avx -DMRTRIX_MACOSX -fPIC -mmacosx-version-min=10.11 -DMRTRIX_WORD64 -DMRTRIX_NO_NON_POD_VLA -isystem /usr/local/Cellar/eigen/3.3.1/include/eigen3 /var/folders/md/r653q57n37zbxz5bnwz1g8cm0000gp/T/tmp_fxop1wc.cpp -o /var/folders/md/r653q57n37zbxz5bnwz1g8cm0000gp/T/tmp_fxop1wc.o
EXIT: 0
>>
EXEC <<
CMD: clang++ /var/folders/md/r653q57n37zbxz5bnwz1g8cm0000gp/T/tmp_fxop1wc.o -dynamiclib -install_name @rpath/LIBNAME -mmacosx-version-min=10.11 -mmacosx-version-min=10.11 -lz -o libtest.dylib
EXIT: 0
>>
REPORT: yes
REPORT: Checking for Qt moc:
EXEC <<
CMD: moc -v
EXIT: 0
STDOUT:
moc 5.6.0
>>
REPORT: moc (version 5.6.0)
REPORT: Checking for Qt qmake:
EXEC <<
CMD: qmake -v
EXIT: 0
STDOUT:
QMake version 3.0
Using Qt version 5.6.0 in /Users/rbaraka/anaconda/lib
>>
REPORT: qmake (version 5.6.0)
REPORT: Checking for Qt rcc:
EXEC <<
CMD: rcc -v
EXIT: 0
STDOUT:
rcc 5.6.0
>>
REPORT: rcc (version 5.6.0)
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
QMAKE_MACOSX_DEPLOYMENT_TARGET = 10.11
---
EXEC <<
CMD: qmake
EXIT: 3
STDERR:
Project ERROR: Xcode not set up properly. You may need to confirm the license agreement by running /usr/bin/xcodebuild.
>>
ERROR: qmake returned with error:
Project ERROR: Xcode not set up properly. You may need to confirm the license agreement by running /usr/bin/xcodebuild.
ERROR: unexpected exception!
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.