Also, this was the contents of the configure.log file
REPORT:
MRtrix build type requested:
REPORT: release
REPORT:
REPORT: Detecting OS: darwin
EXEC <<
CMD: sw_vers -productVersion
EXIT: 0
STDOUT:
10.12.6
>>
REPORT: OS X deployment target: 10.12
REPORT: Looking for compiler [clang++]:
EXEC <<
CMD: clang++ --version
EXIT: 0
STDOUT:
Apple LLVM version 9.0.0 (clang-900.0.37)
Target: x86_64-apple-darwin16.7.0
Thread model: posix
InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin
>>
REPORT: Apple LLVM version 9.0.0 (clang-900.0.37)
REPORT: Checking for C++11 compliance:
COMPILE /var/folders/xm/01whb43d09dfb8d2qr7qq7bm0000gq/T/tmp40GMy_.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_MACOSX -fPIC -mmacosx-version-min=10.12 /var/folders/xm/01whb43d09dfb8d2qr7qq7bm0000gq/T/tmp40GMy_.cpp -o /var/folders/xm/01whb43d09dfb8d2qr7qq7bm0000gq/T/tmp40GMy_.o
EXIT: 0
>>
EXEC <<
CMD: clang++ /var/folders/xm/01whb43d09dfb8d2qr7qq7bm0000gq/T/tmp40GMy_.o -mmacosx-version-min=10.12 -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_MACOSX -fPIC -mmacosx-version-min=10.12 /var/folders/xm/01whb43d09dfb8d2qr7qq7bm0000gq/T/tmpWOEF1t.cpp -o /var/folders/xm/01whb43d09dfb8d2qr7qq7bm0000gq/T/tmpWOEF1t.o
EXIT: 0
>>
EXEC <<
CMD: clang++ /var/folders/xm/01whb43d09dfb8d2qr7qq7bm0000gq/T/tmpWOEF1t.o -dynamiclib -install_name @rpath/LIBNAME -mmacosx-version-min=10.12 -mmacosx-version-min=10.12 -o libtest.dylib
EXIT: 0
>>
REPORT: ok
REPORT: Detecting pointer size:
COMPILE /var/folders/xm/01whb43d09dfb8d2qr7qq7bm0000gq/T/tmpoRN0yn.cpp:
---
#include <iostream>
int main() {
std::cout << sizeof(void*);
return (0);
}
---
EXEC <<
CMD: clang++ -c -std=c++11 -DMRTRIX_MACOSX -fPIC -mmacosx-version-min=10.12 /var/folders/xm/01whb43d09dfb8d2qr7qq7bm0000gq/T/tmpoRN0yn.cpp -o /var/folders/xm/01whb43d09dfb8d2qr7qq7bm0000gq/T/tmpoRN0yn.o
EXIT: 1
STDERR:
In file included from /var/folders/xm/01whb43d09dfb8d2qr7qq7bm0000gq/T/tmpoRN0yn.cpp:2:
In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/iostream:38:
In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/ios:215:
In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/iosfwd:90:
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/wchar.h:133:77: error: use of undeclared identifier 'wcschr'
wchar_t* __libcpp_wcschr(const wchar_t* __s, wchar_t __c) {return (wchar_t*)wcschr(__s, __c);}
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/wchar.h:140:87: error: use of undeclared identifier 'wcspbrk'
wchar_t* __libcpp_wcspbrk(const wchar_t* __s1, const wchar_t* __s2) {return (wchar_t*)wcspbrk(__s1, __s2);}
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/wchar.h:147:78: error: use of undeclared identifier 'wcsrchr'; did you mean 'wcschr'?
wchar_t* __libcpp_wcsrchr(const wchar_t* __s, wchar_t __c) {return (wchar_t*)wcsrchr(__s, __c);}
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/wchar.h:135:16: note: 'wcschr' declared here
const wchar_t* wcschr(const wchar_t* __s, wchar_t __c) {return __libcpp_wcschr(__s, __c);}
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/wchar.h:154:86: error: use of undeclared identifier 'wcsstr'; did you mean 'wcschr'?
wchar_t* __libcpp_wcsstr(const wchar_t* __s1, const wchar_t* __s2) {return (wchar_t*)wcsstr(__s1, __s2);}
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/wchar.h:137:16: note: 'wcschr' declared here
wchar_t* wcschr( wchar_t* __s, wchar_t __c) {return __libcpp_wcschr(__s, __c);}
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/wchar.h:154:86: error: no matching function for call to 'wcschr'
wchar_t* __libcpp_wcsstr(const wchar_t* __s1, const wchar_t* __s2) {return (wchar_t*)wcsstr(__s1, __s2);}
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/wchar.h:137:16: note: candidate disabled: <no message provided>
wchar_t* wcschr( wchar_t* __s, wchar_t __c) {return __libcpp_wcschr(__s, __c);}
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/wchar.h:154:93: error: cannot initialize a parameter of type 'wchar_t *' with an lvalue of type 'const wchar_t *'
wchar_t* __libcpp_wcsstr(const wchar_t* __s1, const wchar_t* __s2) {return (wchar_t*)wcsstr(__s1, __s2);}
^~~~
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/wchar.h:137:38: note: passing argument to parameter '__s' here
wchar_t* wcschr( wchar_t* __s, wchar_t __c) {return __libcpp_wcschr(__s, __c);}
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/wchar.h:161:60: error: unknown type name 'size_t'
wchar_t* __libcpp_wmemchr(const wchar_t* __s, wchar_t __c, size_t __n) {return (wchar_t*)wmemchr(__s, __c, __n);}
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/wchar.h:163:57: error: unknown type name 'size_t'
const wchar_t* wmemchr(const wchar_t* __s, wchar_t __c, size_t __n) {return __libcpp_wmemchr(__s, __c, __n);}
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/wchar.h:165:57: error: unknown type name 'size_t'
wchar_t* wmemchr( wchar_t* __s, wchar_t __c, size_t __n) {return __libcpp_wmemchr(__s, __c, __n);}
^
In file included from /var/folders/xm/01whb43d09dfb8d2qr7qq7bm0000gq/T/tmpoRN0yn.cpp:2:
In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/iostream:38:
In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/ios:215:
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/iosfwd:176:14: error: use of undeclared identifier 'mbstate_t'
typedef fpos<mbstate_t> streampos;
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/iosfwd:177:14: error: use of undeclared identifier 'mbstate_t'
typedef fpos<mbstate_t> wstreampos;
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/iosfwd:179:14: error: use of undeclared identifier 'mbstate_t'
typedef fpos<mbstate_t> u16streampos;
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/iosfwd:180:14: error: use of undeclared identifier 'mbstate_t'
typedef fpos<mbstate_t> u32streampos;
^
In file included from /var/folders/xm/01whb43d09dfb8d2qr7qq7bm0000gq/T/tmpoRN0yn.cpp:2:
In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/iostream:38:
In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/ios:216:
In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/__locale:15:
In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/string:470:
In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/string_view:171:
In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/__string:56:
In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/algorithm:638:
In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/cstring:61:
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/string.h:74:64: error: use of undeclared identifier 'strchr'
char* __libcpp_strchr(const char* __s, int __c) {return (char*)strchr(__s, __c);}
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/string.h:81:75: error: use of undeclared identifier 'strpbrk'
char* __libcpp_strpbrk(const char* __s1, const char* __s2) {return (char*)strpbrk(__s1, __s2);}
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/string.h:88:65: error: use of undeclared identifier 'strrchr'; did you mean 'strchr'?
char* __libcpp_strrchr(const char* __s, int __c) {return (char*)strrchr(__s, __c);}
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/string.h:76:13: note: 'strchr' declared here
const char* strchr(const char* __s, int __c) {return __libcpp_strchr(__s, __c);}
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/string.h:95:76: error: use of undeclared identifier 'memchr'; did you mean 'wmemchr'?
void* __libcpp_memchr(const void* __s, int __c, size_t __n) {return (void*)memchr(__s, __c, __n);}
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/wchar.h:163:16: note: 'wmemchr' declared here
const wchar_t* wmemchr(const wchar_t* __s, wchar_t __c, size_t __n) {return __libcpp_wmemchr(__s, __c, __n);}
^
In file included from /var/folders/xm/01whb43d09dfb8d2qr7qq7bm0000gq/T/tmpoRN0yn.cpp:2:
In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/iostream:38:
In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/ios:216:
In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/__locale:15:
In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/string:470:
In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/string_view:171:
In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/__string:56:
In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/algorithm:638:
In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/cstring:61:
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/string.h:102:74: error: use of undeclared identifier 'strstr'; did you mean 'strchr'?
char* __libcpp_strstr(const char* __s1, const char* __s2) {return (char*)strstr(__s1, __s2);}
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/string.h:78:13: note: 'strchr' declared here
char* strchr( char* __s, int __c) {return __libcpp_strchr(__s, __c);}
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/string.h:102:74: error: no matching function for call to 'strchr'
char* __libcpp_strstr(const char* __s1, const char* __s2) {return (char*)strstr(__s1, __s2);}
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/string.h:78:13: note: candidate disabled: <no message provided>
char* strchr( char* __s, int __c) {return __libcpp_strchr(__s, __c);}
^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
20 errors generated.
>>
error deleting temporary file "/var/folders/xm/01whb43d09dfb8d2qr7qq7bm0000gq/T/tmpoRN0yn.o": No such file or directory
ERROR: unable to determine pointer size!
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.