Thanks!
the rc3 is not working either, I reinstalled according the stackoverflow link and now the configure.log is different. Just in case I did brew uninstall fftw and brew uninstall gcc before I did ./configure, but the error is the same…
REPORT:
MRtrix build type requested: release version
REPORT: WARNING: Anaconda removed from PATH to avoid conflicts
REPORT: Detecting OS: darwin
EXEC <<
CMD: sw_vers -productVersion
EXIT: 0
STDOUT:
10.14.2
>>
REPORT: OS X deployment target: 10.14
REPORT: Looking for compiler [clang++]:
EXEC <<
CMD: clang++ --version
EXIT: 0
STDOUT:
Apple LLVM version 10.0.0 (clang-1000.11.45.5)
Target: x86_64-apple-darwin18.2.0
Thread model: posix
InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin
>>
REPORT: Apple LLVM version 10.0.0 (clang-1000.11.45.5)
REPORT: Checking for C++11 compliance:
COMPILE /var/folders/nw/l98kcbl53l1dl5t8wy__3k300000gq/T/tmpoyhQaC.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" -DMRTRIX_MACOSX -fPIC -mmacosx-version-min=10.14 /var/folders/nw/l98kcbl53l1dl5t8wy__3k300000gq/T/tmpoyhQaC.cpp -o /var/folders/nw/l98kcbl53l1dl5t8wy__3k300000gq/T/tmpoyhQaC.o
EXIT: 0
>>
EXEC <<
CMD: clang++ /var/folders/nw/l98kcbl53l1dl5t8wy__3k300000gq/T/tmpoyhQaC.o -mmacosx-version-min=10.14 -L/usr/local/opt/qt/lib -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" -DMRTRIX_MACOSX -fPIC -mmacosx-version-min=10.14 /var/folders/nw/l98kcbl53l1dl5t8wy__3k300000gq/T/tmpcgC2TT.cpp -o /var/folders/nw/l98kcbl53l1dl5t8wy__3k300000gq/T/tmpcgC2TT.o
EXIT: 0
>>
EXEC <<
CMD: clang++ /var/folders/nw/l98kcbl53l1dl5t8wy__3k300000gq/T/tmpcgC2TT.o -dynamiclib -install_name @rpath/LIBNAME -mmacosx-version-min=10.14 -L/usr/local/opt/qt/lib -o libtest.dylib
EXIT: 0
>>
REPORT: ok
REPORT: Detecting pointer size:
COMPILE /var/folders/nw/l98kcbl53l1dl5t8wy__3k300000gq/T/tmpBVuy3v.cpp:
---
#include <iostream>
int main() {
std::cout << sizeof(void*);
return (0);
}
---
EXEC <<
CMD: clang++ -c -std=c++11 -DMRTRIX_BUILD_TYPE="release version" -DMRTRIX_MACOSX -fPIC -mmacosx-version-min=10.14 /var/folders/nw/l98kcbl53l1dl5t8wy__3k300000gq/T/tmpBVuy3v.cpp -o /var/folders/nw/l98kcbl53l1dl5t8wy__3k300000gq/T/tmpBVuy3v.o
EXIT: 1
STDERR:
In file included from /var/folders/nw/l98kcbl53l1dl5t8wy__3k300000gq/T/tmpBVuy3v.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:477:
In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/string_view:176:
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:642:
In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/utility:203:
In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/cstdint:145:
In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/stdint.h:119:
In file included from /usr/local/include/stdint.h:82:
In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/inttypes.h:247:
In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/10.0.0/include/inttypes.h:30:
/usr/include/inttypes.h:235:8: error: unknown type name 'intmax_t'
extern intmax_t
^
/usr/include/inttypes.h:236:9: error: unknown type name 'intmax_t'
imaxabs(intmax_t j);
^
/usr/include/inttypes.h:240:2: error: unknown type name 'intmax_t'
intmax_t quot;
^
/usr/include/inttypes.h:241:2: error: unknown type name 'intmax_t'
intmax_t rem;
^
/usr/include/inttypes.h:246:9: error: unknown type name 'intmax_t'
imaxdiv(intmax_t __numer, intmax_t __denom);
^
/usr/include/inttypes.h:246:27: error: unknown type name 'intmax_t'
imaxdiv(intmax_t __numer, intmax_t __denom);
^
/usr/include/inttypes.h:250:8: error: unknown type name 'intmax_t'
extern intmax_t
^
/usr/include/inttypes.h:256:8: error: unknown type name 'uintmax_t'; did you mean 'uintptr_t'?
extern uintmax_t
^
/usr/include/sys/_types/_uintptr_t.h:30:24: note: 'uintptr_t' declared here
typedef unsigned long uintptr_t;
^
In file included from /var/folders/nw/l98kcbl53l1dl5t8wy__3k300000gq/T/tmpBVuy3v.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:477:
In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/string_view:176:
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:642:
In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/utility:203:
In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/cstdint:145:
In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/stdint.h:119:
In file included from /usr/local/include/stdint.h:82:
In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/inttypes.h:247:
In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/10.0.0/include/inttypes.h:30:
/usr/include/inttypes.h:263:8: error: unknown type name 'intmax_t'
extern intmax_t
^
/usr/include/inttypes.h:269:8: error: unknown type name 'uintmax_t'; did you mean 'uintptr_t'?
extern uintmax_t
^
/usr/include/sys/_types/_uintptr_t.h:30:24: note: 'uintptr_t' declared here
typedef unsigned long uintptr_t;
^
In file included from /var/folders/nw/l98kcbl53l1dl5t8wy__3k300000gq/T/tmpBVuy3v.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:477:
In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/string_view:176:
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:642:
In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/utility:203:
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/cstdint:161:8: error: no member named 'uint64_t' in the global namespace
using::uint64_t;
~~^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/cstdint:163:8: error: no member named 'int_least8_t' in the global namespace
using::int_least8_t;
~~^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/cstdint:164:8: error: no member named 'int_least16_t' in the global namespace
using::int_least16_t;
~~^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/cstdint:165:8: error: no member named 'int_least32_t' in the global namespace
using::int_least32_t;
~~^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/cstdint:166:8: error: no member named 'int_least64_t' in the global namespace
using::int_least64_t;
~~^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/cstdint:168:8: error: no member named 'uint_least8_t' in the global namespace
using::uint_least8_t;
~~^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/cstdint:169:8: error: no member named 'uint_least16_t' in the global namespace
using::uint_least16_t;
~~^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/cstdint:170:8: error: no member named 'uint_least32_t' in the global namespace
using::uint_least32_t;
~~^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/cstdint:171:8: error: no member named 'uint_least64_t' in the global namespace
using::uint_least64_t;
~~^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
20 errors generated.
>>
error deleting temporary file "/var/folders/nw/l98kcbl53l1dl5t8wy__3k300000gq/T/tmpBVuy3v.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.
The strange thing for me is that I migrated from an old 10.14.2 laptop to a new 10.14.2 laptop. mrtrix is working in the old laptop, but it is not working in the new one. If I remember correclty the first time I tried to launch mrview it ask to change permissions to /usr/local/Cellar, I did and it did not work and I think that then I tried to do a git pull and ./configure and until now…
Any other test or way to explore what to do now?
thanks again for your help