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M1 compilation issue #1154

@xianantwist

Description

@xianantwist

I have trouble compiling nanopolish on M1 chip. (Ventura 13.5.1 OS)
make CC=gcc-11 CXX=g++-11 CPP=cpp-11 arm_neon=1
This is log file that i got. Thanks in advance!

if [ ! -e hdf5-1.13.3.tar.gz ]; then
version_major_minor=echo "1.13.3" | sed -E 's/\.[0-9]+$//';
wget https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-${version_major_minor}/hdf5-1.13.3/src/hdf5-1.13.3.tar.gz;
fi
tar -xzf hdf5-1.13.3.tar.gz || exit 255
cd hdf5-1.13.3 &&
./configure CFLAGS="-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -L/usr/lib" CPPFLAGS="-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -L/usr/lib" --enable-threadsafe --disable-hl --libdir=pwd/../lib --includedir=pwd/../include --prefix=pwd/.. || exit 255
checking for a BSD-compatible install... /opt/homebrew/bin/ginstall -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /opt/homebrew/bin/gmkdir -p
checking for gawk... no
checking for mawk... no
checking for nawk... no
checking for awk... awk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking whether make supports nested variables... (cached) yes
checking whether to enable maintainer-specific portions of Makefiles... no
checking build system type... arm-apple-darwin22.6.0
checking host system type... arm-apple-darwin22.6.0
checking shell variables initial values... done
checking if basename works... yes
checking if xargs works... yes
checking for cached host... none
checking enable warnings as errors... no
checking for config arm-apple-darwin22.6.0... no
checking for config arm-apple-darwin22.6.0... no
checking for config apple-darwin22.6.0... no
checking for config apple-darwin22.6.0... no
checking for config arm-darwin22.6.0... no
checking for config arm-darwin22.6.0... no
checking for config arm-apple... no
checking for config darwin22.6.0... no
checking for config darwin22.6.0... no
checking for config apple... found
compiler 'gcc-11' is GNU gcc-11.4.0
compiler 'gfortran' is GNU gfortran-14.2.0
compiler 'g++-11' is GNU g++-11.4.0
checking for config ./config/site-specific/host-sfoxliumba... no
checking for clang sanitizer checks... checking build mode... production
checking for gcc... gcc-11
checking whether the C compiler works... no
configure: error: in /Users/xliu/nanopolish/hdf5-1.13.3': configure: error: C compiler cannot create executables See config.log' for more details
make: *** [lib/libhdf5.a] Error 255

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