Mac ARM Installation failed #92
Description
I try to install on ARM Mac but I got
benjamin@MacBook-Pro-de-Benjamin cmake-3.31.7 % which cmake
/usr/local/bin/cmake
benjamin@MacBook-Pro-de-Benjamin cmake-3.31.7 % kb compile all --overwrite
[2025-04-28 14:43:31,256] INFO [compile] Downloading kallisto source from https://api.github.com/repos/pachterlab/kallisto/tarball/v0.51.1
100%|█████████████████████████████████████████████████████████████████████████| 5.68M/5.68M [00:02<00:00, 2.29MB/s]
[2025-04-28 14:43:36,384] INFO [compile] Compiling `kallisto` binary from source at /Users/benjamin/Downloads/cmake-3.31.7/tmp/tmp4q5go_jq/pachterlab-kallisto-0397342 to /opt/homebrew/lib/python3.12/site-packages/kb_python/bins/compiled/kallisto/kallisto. This requires `autoheader`, `autoconf`, `cmake` and `make` to be executable from the command-line, as well as zlib development headers. See https://pachterlab.github.io/kallisto/source for more information.
[2025-04-28 14:43:42,921] ERROR [compile] [ 3%] Creating directories for 'bifrost'
[ 7%] No download step for 'bifrost'
[ 11%] No update step for 'bifrost'
[ 15%] No patch step for 'bifrost'
[ 19%] Performing configure step for 'bifrost'
CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required):
Compatibility with CMake < 3.10 will be removed from a future version of
CMake.
Update the VERSION argument <min> value. Or, use the <min>...<max> syntax
to tell CMake that the project requires at least <min> but has been updated
to work with policies introduced by <max> or earlier.
-- The C compiler identification is AppleClang 17.0.0.17000013
-- The CXX compiler identification is AppleClang 17.0.0.17000013
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /Library/Developer/CommandLineTools/usr/bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /Library/Developer/CommandLineTools/usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success
-- Found Threads: TRUE
Disabling AVX2 instructions on arm64
Disabling native architecture compilation (including AVX2)
Disabling AVX2 instructions
Build type: Release
Maximum k-mer size: 31
Maximum g-mer size: 31
-- Found ZLIB: /Library/Developer/CommandLineTools/SDKs/MacOSX15.4.sdk/usr/lib/libz.tbd (found version "1.2.12")
-- Configuring done (0.6s)
-- Generating done (0.0s)
-- Build files have been written to: /Users/benjamin/Downloads/cmake-3.31.7/tmp/tmp4q5go_jq/pachterlab-kallisto-0397342/ext/bifrost/build
[ 23%] Performing build step for 'bifrost'
[ 3%] Building CXX object src/CMakeFiles/bifrost_static.dir/Bifrost.cpp.o
c++: error: unsupported option '-mno-avx2' for target 'arm64-apple-darwin24.4.0'
make[5]: *** [src/CMakeFiles/bifrost_static.dir/Bifrost.cpp.o] Error 1
make[4]: *** [src/CMakeFiles/bifrost_static.dir/all] Error 2
make[3]: *** [all] Error 2
make[2]: *** [/Users/benjamin/Downloads/cmake-3.31.7/tmp/tmp4q5go_jq/pachterlab-kallisto-0397342/ext/bifrost/src/bifrost-stamp/bifrost-build] Error 2
make[1]: *** [CMakeFiles/bifrost.dir/all] Error 2
make: *** [all] Error 2
[2025-04-28 14:43:42,923] ERROR [main] An exception occurred
Traceback (most recent call last):
File "/opt/homebrew/lib/python3.12/site-packages/kb_python/main.py", line 1926, in main
COMMAND_TO_FUNCTION[args.command](parser, args, temp_dir=temp_dir)
File "/opt/homebrew/lib/python3.12/site-packages/kb_python/main.py", line 188, in parse_compile
compile(
File "/opt/homebrew/lib/python3.12/site-packages/ngs_tools/logging.py", line 62, in inner
return func(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^
File "/opt/homebrew/lib/python3.12/site-packages/kb_python/compile.py", line 251, in compile
binary_path = compile_kallisto(
^^^^^^^^^^^^^^^^^
File "/opt/homebrew/lib/python3.12/site-packages/kb_python/utils.py", line 921, in wrapper
return func(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^
File "/opt/homebrew/lib/python3.12/site-packages/kb_python/compile.py", line 150, in compile_kallisto
run_executable(['make'])
File "/opt/homebrew/lib/python3.12/site-packages/kb_python/dry/__init__.py", line 25, in inner
return func(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^
File "/opt/homebrew/lib/python3.12/site-packages/kb_python/utils.py", line 203, in run_executable
raise sp.CalledProcessError(p.returncode, ' '.join(command))
subprocess.CalledProcessError: Command 'make' returned non-zero exit status 2.
benjamin@MacBook-Pro-de-Benjamin cmake-3.31.7 % git clone https://github.com/pmelsted/bifrost.git
cd bifrost && mkdir build && cd build
cmake ..
make
sudo make install
Cloning into 'bifrost'...
remote: Enumerating objects: 4759, done.
remote: Counting objects: 100% (757/757), done.
remote: Compressing objects: 100% (314/314), done.
remote: Total 4759 (delta 525), reused 632 (delta 443), pack-reused 4002 (from 1)
Receiving objects: 100% (4759/4759), 5.28 MiB | 6.87 MiB/s, done.
Resolving deltas: 100% (3358/3358), done.
CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required):
Compatibility with CMake < 3.10 will be removed from a future version of
CMake.
Update the VERSION argument <min> value. Or, use the <min>...<max> syntax
to tell CMake that the project requires at least <min> but has been updated
to work with policies introduced by <max> or earlier.
-- The C compiler identification is AppleClang 17.0.0.17000013
-- The CXX compiler identification is AppleClang 17.0.0.17000013
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /Library/Developer/CommandLineTools/usr/bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /Library/Developer/CommandLineTools/usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success
-- Found Threads: TRUE
Disabling AVX2 instructions on arm64
Disabling native architecture compilation (including AVX2)
Disabling AVX2 instructions
Build type: Release
Maximum k-mer size: 31
Maximum g-mer size: 31
-- Found ZLIB: /Library/Developer/CommandLineTools/SDKs/MacOSX15.4.sdk/usr/lib/libz.tbd (found version "1.2.12")
-- Configuring done (0.7s)
-- Generating done (0.0s)
-- Build files have been written to: /Users/benjamin/Downloads/cmake-3.31.7/bifrost/build
[ 3%] Building CXX object src/CMakeFiles/bifrost_static.dir/Bifrost.cpp.o
c++: error: unsupported option '-mno-avx2' for target 'arm64-apple-darwin24.4.0'
make[2]: *** [src/CMakeFiles/bifrost_static.dir/Bifrost.cpp.o] Error 1
make[1]: *** [src/CMakeFiles/bifrost_static.dir/all] Error 2
make: *** [all] Error 2
[ 3%] Building CXX object src/CMakeFiles/bifrost_static.dir/Bifrost.cpp.o
c++: error: unsupported option '-mno-avx2' for target 'arm64-apple-darwin24.4.0'
make[2]: *** [src/CMakeFiles/bifrost_static.dir/Bifrost.cpp.o] Error 1
make[1]: *** [src/CMakeFiles/bifrost_static.dir/all] Error 2
make: *** [all] Error 2
benjamin@MacBook-Pro-de-Benjamin build %