ANTs install: program not found

1

Hi everyone,
I’m new to Mrtrix3 and loving it! However, I have found issues getting ANTs installed. I have followed this link and read this post.
I don’t know what I’m doing wrong but typing which ANTs doesn’t return anything. The error during the installation came at this point: ccmake …/ANTs. I’m working on a macOS Mojave 10.14.6.

This is the info in the for the CMakeError.log file:
Determining if the C compiler works failed with the following output:
Change Dir: /Users/s5110052/antsbin/CMakeFiles/CMakeTmp

Run Build Command(s):/opt/anaconda2/bin/make cmTC_a7902/fast && /opt/anaconda2/bin/make -f CMakeFiles/cmTC_a7902.dir/build.make CMakeFiles/cmTC_a7902.dir/build
make[1]: Entering directory ‘/Users/s5110052/antsbin/CMakeFiles/CMakeTmp’
Building C object CMakeFiles/cmTC_a7902.dir/testCCompiler.c.o
/opt/anaconda2/bin/x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk -o CMakeFiles/cmTC_a7902.dir/testCCompiler.c.o -c /Users/s5110052/antsbin/CMakeFiles/CMakeTmp/testCCompiler.c
Linking C executable cmTC_a7902
/usr/local/Cellar/cmake/3.18.3/bin/cmake -E cmake_link_script CMakeFiles/cmTC_a7902.dir/link.txt --verbose=1
/opt/anaconda2/bin/x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk -Wl,-search_paths_first -Wl,-headerpad_max_install_names -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs CMakeFiles/cmTC_a7902.dir/testCCompiler.c.o -o cmTC_a7902
ld: warning: ignoring file /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/lib/libSystem.tbd, file was built for unsupported file format ( 0x2D 0x2D 0x2D 0x20 0x21 0x74 0x61 0x70 0x69 0x2D 0x74 0x62 0x64 0x2D 0x76 0x33 ) which is not the architecture being linked (x86_64): /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/lib/libSystem.tbd
ld: dynamic main executables must link with libSystem.dylib for architecture x86_64
clang-4.0: error: linker command failed with exit code 1 (use -v to see invocation)
make[1]: *** [CMakeFiles/cmTC_a7902.dir/build.make:106: cmTC_a7902] Error 1
make[1]: Leaving directory ‘/Users/s5110052/antsbin/CMakeFiles/CMakeTmp’
make: *** [Makefile:140: cmTC_a7902/fast] Error 2

The info on the CMakeOutput.log:

The system is: Darwin - 18.7.0 - x86_64
Compiling the C compiler identification source file “CMakeCCompilerId.c” succeeded.
Compiler: /opt/anaconda2/bin/x86_64-apple-darwin13.4.0-clang
Build flags: -march=core2;-mtune=haswell;-mssse3;-ftree-vectorize;-fPIC;-fPIE;-fstack-protector-strong;-O2;-pipe
Id flags: -c

The output was:
0

Compilation of the C compiler identification source “CMakeCCompilerId.c” produced “CMakeCCompilerId.o”

The C compiler identification is Clang, found in “/Users/s5110052/antsbin/CMakeFiles/3.18.3/CompilerIdC/CMakeCCompilerId.o”

Compiling the CXX compiler identification source file “CMakeCXXCompilerId.cpp” succeeded.
Compiler: /opt/anaconda2/bin/x86_64-apple-darwin13.4.0-clang++
Build flags: -march=core2;-mtune=haswell;-mssse3;-ftree-vectorize;-fPIC;-fPIE;-fstack-protector-strong;-O2;-pipe;-stdlib=libc++;-fvisibility-inlines-hidden;-std=c++14;-fmessage-length=0
Id flags:

The output was:
0
ld: warning: ignoring file /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/lib/libSystem.tbd, file was built for unsupported file format ( 0x2D 0x2D 0x2D 0x20 0x21 0x74 0x61 0x70 0x69 0x2D 0x74 0x62 0x64 0x2D 0x76 0x33 ) which is not the architecture being linked (x86_64): /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/lib/libSystem.tbd

Compilation of the CXX compiler identification source “CMakeCXXCompilerId.cpp” produced “a.out”

The CXX compiler identification is Clang, found in “/Users/s5110052/antsbin/CMakeFiles/3.18.3/CompilerIdCXX/a.out”

Compiling the C compiler identification source file “CMakeCCompilerId.c” succeeded.
Compiler: /opt/anaconda2/bin/x86_64-apple-darwin13.4.0-clang
Build flags: -march=core2;-mtune=haswell;-mssse3;-ftree-vectorize;-fPIC;-fPIE;-fstack-protector-strong;-O2;-pipe
Id flags: -c

The output was:
0

Compilation of the C compiler identification source “CMakeCCompilerId.c” produced “CMakeCCompilerId.o”

The C compiler identification is Clang, found in “/Users/s5110052/antsbin/CMakeFiles/3.18.3/CompilerIdC/CMakeCCompilerId.o”

Compiling the CXX compiler identification source file “CMakeCXXCompilerId.cpp” succeeded.
Compiler: /opt/anaconda2/bin/x86_64-apple-darwin13.4.0-clang++
Build flags: -march=core2;-mtune=haswell;-mssse3;-ftree-vectorize;-fPIC;-fPIE;-fstack-protector-strong;-O2;-pipe;-stdlib=libc++;-fvisibility-inlines-hidden;-std=c++14;-fmessage-length=0
Id flags:

The output was:
0
ld: warning: ignoring file /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/lib/libSystem.tbd, file was built for unsupported file format ( 0x2D 0x2D 0x2D 0x20 0x21 0x74 0x61 0x70 0x69 0x2D 0x74 0x62 0x64 0x2D 0x76 0x33 ) which is not the architecture being linked (x86_64): /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/lib/libSystem.tbd

Compilation of the CXX compiler identification source “CMakeCXXCompilerId.cpp” produced “a.out”

The CXX compiler identification is Clang, found in “/Users/s5110052/antsbin/CMakeFiles/3.18.3/CompilerIdCXX/a.out”

Compiling the C compiler identification source file “CMakeCCompilerId.c” succeeded.
Compiler: /opt/anaconda2/bin/x86_64-apple-darwin13.4.0-clang
Build flags: -march=core2;-mtune=haswell;-mssse3;-ftree-vectorize;-fPIC;-fPIE;-fstack-protector-strong;-O2;-pipe
Id flags: -c

The output was:
0

Compilation of the C compiler identification source “CMakeCCompilerId.c” produced “CMakeCCompilerId.o”

The C compiler identification is Clang, found in “/Users/s5110052/antsbin/CMakeFiles/3.18.3/CompilerIdC/CMakeCCompilerId.o”

Compiling the CXX compiler identification source file “CMakeCXXCompilerId.cpp” succeeded.
Compiler: /opt/anaconda2/bin/x86_64-apple-darwin13.4.0-clang++
Build flags: -march=core2;-mtune=haswell;-mssse3;-ftree-vectorize;-fPIC;-fPIE;-fstack-protector-strong;-O2;-pipe;-stdlib=libc++;-fvisibility-inlines-hidden;-std=c++14;-fmessage-length=0
Id flags:

The output was:
0
ld: warning: ignoring file /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/lib/libSystem.tbd, file was built for unsupported file format ( 0x2D 0x2D 0x2D 0x20 0x21 0x74 0x61 0x70 0x69 0x2D 0x74 0x62 0x64 0x2D 0x76 0x33 ) which is not the architecture being linked (x86_64): /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/lib/libSystem.tbd

Compilation of the CXX compiler identification source “CMakeCXXCompilerId.cpp” produced “a.out”

The CXX compiler identification is Clang, found in “/Users/s5110052/antsbin/CMakeFiles/3.18.3/CompilerIdCXX/a.out”

Any ideas? Thanks a lot for your help.
Kind regards,
Eva

2

Hi Eva,

Sorry you’re having trouble with this, but to be fair, ANTs is a separate project, and this isn’t the best forum to get help… You can get help direct from the right people by asking on their forum.

However, I can probably offer a couple of pointers here. The first one is that you’re using the anaconda compiler. Our users have always had issues building MRtrix when anaconda is installed, and we’ve gone to great lengths to avoid any interference from it. I wouldn’t be surprised if that didn’t also happen with other applications.

The second point is that if you’ve got anaconda installed already, why not install the pre-compiled version of ANTs that anaconda provides? It should be a simple matter of typing:

conda install -c aramislab ants
3

Hi @jdtournier!
That has solved the issue. Thanks a lot!
Eva