Help installing in macos mojave 10.14.2

Gari · January 18, 2019, 7:00am

Hi,
I updated my Mac Book Pro and went from a 10.14.2 installation to another 10.14.2 installation. But mrtrix (at least mrview) was not working in the new laptop.

I tried to install it by compiling, by using brew (I even uninstalled the whole homebrew and started from scratch, but to no avail).

This is the error I get:
(this is when using ./configure)

Detecting OS: darwin
OS X deployment target: 10.14
Looking for compiler [clang++]: Apple LLVM version 10.0.0 (clang-1000.11.45.5)
Checking for C++11 compliance: ok
Checking shared library generation: ok
Detecting pointer size:
ERROR: unable to determine pointer size!

I then made use gcc instead of clang like this:

export CXX=/usr/local/Cellar/gcc/8.2.0/bin/g++-8
export CC=/usr/local/Cellar/gcc/8.2.0/bin/gcc-8

But then this is the error I get:

Detecting OS: darwin
OS X deployment target: 10.14
Looking for compiler [/usr/local/Cellar/gcc/8.2.0/bin/g++-8]: g++-8 (Homebrew GCC 8.2.0) 8.2.0
Checking for C++11 compliance: ok
Checking shared library generation: ok
Detecting pointer size: 64 bit
Detecting byte order: little-endian
Checking for variable-length array support: ok
Checking for non-POD variable-length array support: ok
Checking for ::max_align_t: 16 bytes
Checking for std::max_align_t: 16 bytes
Checking for Eigen3 library: 3.3.7
Checking for zlib compression library: 1.2.11
Checking for "JSON for Modern C++" requirements: ok
Checking for TIFF library: LIBTIFF, Version 4.0.10
Checking for FFTW library: fftw-3.3.8-sse2
Checking for Qt moc: moc (version 5.12.0)
Checking for Qt qmake: qmake (version 5.12.0)
Checking for Qt rcc: rcc (version 5.12.0)
Checking for Qt:
ERROR: error compiling Qt application!

Looking in the configure.log I see that the problem is this option which is for clang…

g++-8: error: unrecognized command line option '-stdlib=libc++'

So, I do not know what else to try right now… any help will be welcome!
Thanks,
Gari

jdtournier · January 18, 2019, 12:29pm

OK, I think the best thing is to figure out why the default using clang++ doesn’t work. It’s failing at the ‘detecting pointer size’ stage, which is only asking it to compile and run a very simple snippet of code. Can you try again, and copy/paste the full configure.log output here? That might give us a clue.

Gari · January 18, 2019, 6:58pm

Thanks!! here you have it:

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/tmpuUR5k8.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/tmpuUR5k8.cpp -o /var/folders/nw/l98kcbl53l1dl5t8wy__3k300000gq/T/tmpuUR5k8.o
EXIT: 0
>>

EXEC <<
CMD: clang++ /var/folders/nw/l98kcbl53l1dl5t8wy__3k300000gq/T/tmpuUR5k8.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/tmpRZD9TM.cpp -o /var/folders/nw/l98kcbl53l1dl5t8wy__3k300000gq/T/tmpRZD9TM.o
EXIT: 0
>>

EXEC <<
CMD: clang++ /var/folders/nw/l98kcbl53l1dl5t8wy__3k300000gq/T/tmpRZD9TM.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/tmpzL6dVz.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/tmpzL6dVz.cpp -o /var/folders/nw/l98kcbl53l1dl5t8wy__3k300000gq/T/tmpzL6dVz.o
EXIT: 1
STDERR:
In file included from /var/folders/nw/l98kcbl53l1dl5t8wy__3k300000gq/T/tmpzL6dVz.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 /usr/local/include/stdint.h:59:
In file included from /usr/local/include/stdint.h:59:
In file included from /usr/local/include/stdint.h:59:
In file included from /usr/local/include/stdint.h:59:
In file included from /usr/local/include/stdint.h:59:
In file included from /usr/local/include/stdint.h:59:
In file included from /usr/local/include/stdint.h:59:
In file included from /usr/local/include/stdint.h:59:
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In file included from /usr/local/include/stdint.h:59:
In file included from /usr/local/include/stdint.h:59:
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In file included from /usr/local/include/stdint.h:59:
In file included from /usr/local/include/stdint.h:59:
In file included from /usr/local/include/stdint.h:59:
In file included from /usr/local/include/stdint.h:59:
In file included from /usr/local/include/stdint.h:59:
In file included from /usr/local/include/stdint.h:59:
In file included from /usr/local/include/stdint.h:59:
In file included from /usr/local/include/stdint.h:59:
In file included from /usr/local/include/stdint.h:59:
In file included from /usr/local/include/stdint.h:59:
In file included from /usr/local/include/stdint.h:59:
In file included from /usr/local/include/stdint.h:59:
In file included from /usr/local/include/stdint.h:59:
In file included from /usr/local/include/stdint.h:59:
In file included from /usr/local/include/stdint.h:59:
In file included from /usr/local/include/stdint.h:59:
In file included from /usr/local/include/stdint.h:59:
In file included from /usr/local/include/stdint.h:59:
/usr/local/include/stdint.h:2:10: error: #include nested too deeply
#include <stddef.h>
         ^
/usr/local/include/stdint.h:59:11: error: #include nested too deeply
# include <stdint.h>
          ^
/usr/local/include/stdint.h:72:11: error: #include nested too deeply
# include <sys/types.h>
          ^
/usr/local/include/stdint.h:76:10: error: #include nested too deeply
#include <limits.h>
         ^
/usr/local/include/stdint.h:82:11: error: #include nested too deeply
# include <inttypes.h>
          ^
In file included from /var/folders/nw/l98kcbl53l1dl5t8wy__3k300000gq/T/tmpzL6dVz.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;
     ~~^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/cstdint:173:8: error: no member named 'int_fast8_t' in the global namespace
using::int_fast8_t;
     ~~^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/cstdint:174:8: error: no member named 'int_fast16_t' in the global namespace
using::int_fast16_t;
     ~~^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/cstdint:175:8: error: no member named 'int_fast32_t' in the global namespace
using::int_fast32_t;
     ~~^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/cstdint:176:8: error: no member named 'int_fast64_t' in the global namespace
using::int_fast64_t;
     ~~^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/cstdint:178:8: error: no member named 'uint_fast8_t' in the global namespace
using::uint_fast8_t;
     ~~^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
20 errors generated.
>>

error deleting temporary file "/var/folders/nw/l98kcbl53l1dl5t8wy__3k300000gq/T/tmpzL6dVz.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.

jdtournier · January 18, 2019, 10:25pm

Wow, looks like clang has got itself seriously messed up… From what I can tell, the issue is that at some point, clang starts including files from a different compiler, using headers located in /usr/local/include rather than the XCode folder:

...
In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/cstdint:145:
In file included from /usr/local/include/stdint.h:59:
...

This is most likely due to interference from your gcc install (presumably installed via homebrew?). I expect things would work just fine if you got rid of it…

Gari · January 19, 2019, 1:55am

Thanks!
Well, the thing is that gcc is a requirement for fftw, see here:

glerma@axial:/Users/glerma/soft/mrtrix3:(master)$
# brew uninstall fftw
Uninstalling /usr/local/Cellar/fftw/3.3.8... (52 files, 10.9MB)
glerma@axial:/Users/glerma/soft/mrtrix3:(master)$
# brew uninstall gcc
Uninstalling /usr/local/Cellar/gcc/8.2.0... (1,413 files, 295.9MB)
glerma@axial:/Users/glerma/soft/mrtrix3:(master)$
# brew install fftw
Updating Homebrew...
==> Auto-updated Homebrew!
Updated 1 tap (homebrew/core).
==> New Formulae
ahoy                                                                                       opencv@3
==> Updated Formulae
ansible           carla             embulk            fonttools         libgpg-error      mpd               pulumi            swiftlint         vips              zabbix
audacious         checkbashisms     fauna-shell       gearman           mongodb           mpv               scummvm           typescript        wtf               zeromq
bower             dosbox-x          fluid-synth       imagemagick       mongodb@3.6       open-babel        sphinx            urbit             yara
==> Deleted Formulae
cputhrottle

==> Installing dependencies for fftw: gcc
==> Installing fftw dependency: gcc
==> Downloading https://homebrew.bintray.com/bottles/gcc-8.2.0.mojave.bottle.2.tar.gz
Already downloaded: /Users/glerma/Library/Caches/Homebrew/downloads/5e336edb977168e21c1c3d0e1d374b76c39a8780ccee6b1e2d81a832a3f01118--gcc-8.2.0.mojave.bottle.2.tar.gz
==> Pouring gcc-8.2.0.mojave.bottle.2.tar.gz
🍺  /usr/local/Cellar/gcc/8.2.0: 1,413 files, 295.9MB
==> Installing fftw
==> Downloading https://homebrew.bintray.com/bottles/fftw-3.3.8.mojave.bottle.tar.gz
Already downloaded: /Users/glerma/Library/Caches/Homebrew/downloads/3421e4a325c9d0baafe341cc32a1b0df238231473fde94c47f6b28256db41683--fftw-3.3.8.mojave.bottle.tar.gz
==> Pouring fftw-3.3.8.mojave.bottle.tar.gz
🍺  /usr/local/Cellar/fftw/3.3.8: 52 files, 10.9MB

The same happens if we try to install brew install mrtrix3, the same files are installed as dependencies…
I uninstalled again fftw and gcc and used ./configure again and I have the same

ERROR: unable to determine pointer size!

I tried to brew uninstall gcc and then manually installing fftw, but when I do ./configure I get a similar error regarding the pointer size.

Can you think in something I could try that does not involve reinstalling the whole operating system again?

thanks!
Gari

jdtournier · January 19, 2019, 10:00am

Is this a new thing, @maxpietsch…?

maxpietsch · January 19, 2019, 11:42am

gcc has been a requirement for fftw for a while. It does not need it if fftw is installed with the --without-fortran but without the --with-openmp option (link) but gcc is likely required for other homebrew packages anyway.

gcc 8.2.0 works on my machine (High Sierra). Unfortunately, my macbook is too old to upgrade to mojave so I can not test this but I’d guess it’s your Xcode command line tools that are not properly set up. This stackoverflow answer might help?

If that doesn’t solve it, you can still use our release candidate formula instead: brew install mrtrix3_0rc3

Gari · January 19, 2019, 8:47pm

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

maxpietsch · January 20, 2019, 11:23pm

You should not need the compiler to work to install the rc3 homebrew recipe. What is the error message?

You might want to check homebrew with homebrew doctor. For troubleshooting see here.

If that does not fix it, what I would try (in that order, check if the installation works after each):

xcode-select --install
xcode-select --reset
`mv /Library/Developer/CommandLineTools /Library/Developer/CommandLineTools_old && xcode-select --install # remove /Library/Developer/CommandLineTools_old after that
mv /usr/local/include to /usr/local/include_old # this might be a bit drastic but seems necessary in some cases.

Gari · January 21, 2019, 3:39am

Many thanks for your help!

You were right, I don’t know what was the error for the rc3 installation, I run it again and it worked.
Steps: I did brew install mrtrix3 after every step, and only after the last one it worked the compilation, BUT, when I execute mrview it does not work, this is what it said at the end

[...]
(504/505) [LB] bin/mrview
(505/505) [LB] bin/amp2sh
==> mkdir /usr/local/Cellar/mrtrix3/3.0_RC3-51-g52a2540d/lib
Installation done. MRtrix3 lives in /usr/local/Cellar/mrtrix3/3.0_RC3-51-g52a2540d
For more information go to http://mrtrix.readthedocs.io
Warning: mrtrix3/mrtrix3/mrtrix3 dependency gcc was built with a different C++ standard
library (libstdc++ from clang). This may cause problems at runtime.
🍺  /usr/local/Cellar/mrtrix3/3.0_RC3-51-g52a2540d: 211 files, 56.2MB, built in 6 minutes 3 seconds

OK, we are getting closer, then I tried using ./configure again, but it failed, because now eigen3 is in the moved /usr/local/include, to solve it I added the EIGEN_CFLAGS to /usr/local/Cellar/eigen/3.3.7/include/eigen3 and then it compiled ok again.

But, the same error, the mrview screen is black:

So, I removed mrtrix3 from the path again and used the RC3 without compiling… it would be great if you could upgrade it to the latest version…

Now it is working nicely (at least mrview):

Thanks again for your help!

Gari