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brewsci / homebrew-bio

:beer::microscope: Bioinformatics formulae for the Homebrew package manager (macOS and Linux)
http://brewsci.github.io/homebrew-bio
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Error 2... #1670

Closed brigmeyer closed 1 month ago

brigmeyer commented 2 months ago

Trying to install hh-suite on a Mac with M1 ultra, but I keep getting this mysterious "error 2" code that I can't parse further to figure out what is going on. I was considering trying Docker but figured to ask here first to see if anyone has encountered issues installing hh-suite by running brew install hh-suite. Was easily able to do this on my other laptop (Apple M2). Not very experienced with command line, so would appreciate any help!

Full output:

(base) biobooth@Mac-Studio colabfold % brew install brewsci/bio/hh-suite
==> Fetching brewsci/bio/hh-suite
==> Downloading https://github.com/soedinglab/hh-suite/archive/refs/tags/v3.3.0.
Already downloaded: /Users/biobooth/Library/Caches/Homebrew/downloads/fcc1a774c926bca93b0bb2d3aa6fc65a4b04f59c3963f716a776ffe7520690da--hh-suite-3.3.0.tar.gz
==> Installing hh-suite from brewsci/bio
==> cmake . -DCHECK_MPI=1 -DHAVE_ARM8=1 -DOpenMP_C_FLAGS=-Xpreprocessor -fopenmp
==> make install
Last 15 lines from /Users/biobooth/Library/Logs/Homebrew/hh-suite/02.make:
/usr/bin/ar qc libhhviterbialgorithm_with_celloff.a CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o
/usr/bin/ar qc libhhviterbialgorithm_and_ss.a CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o
/usr/bin/ar qc libhhviterbialgorithm_with_celloff_and_ss.a CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o
/usr/bin/ranlib libhhviterbialgorithm_with_celloff.a
/usr/bin/ranlib libhhviterbialgorithm_with_celloff_and_ss.a
/usr/bin/ranlib libhhviterbialgorithm_and_ss.a
[ 38%] Built target hhviterbialgorithm_with_celloff
[ 38%] Built target hhviterbialgorithm_with_celloff_and_ss
[ 38%] Built target hhviterbialgorithm_and_ss
cd /tmp/hh-suite-20240417-13693-g9ktsk/hh-suite-3.3.0/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /tmp/hh-suite-20240417-13693-g9ktsk/hh-suite-3.3.0/generated/context_data.lib.h > /tmp/hh-suite-20240417-13693-g9ktsk/hh-suite-3.3.0/generated/context_data.lib.h.tmp
cd /tmp/hh-suite-20240417-13693-g9ktsk/hh-suite-3.3.0/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /tmp/hh-suite-20240417-13693-g9ktsk/hh-suite-3.3.0/generated/context_data.crf.h > /tmp/hh-suite-20240417-13693-g9ktsk/hh-suite-3.3.0/generated/context_data.crf.h.tmp
cd /tmp/hh-suite-20240417-13693-g9ktsk/hh-suite-3.3.0/data && mv -f /tmp/hh-suite-20240417-13693-g9ktsk/hh-suite-3.3.0/generated/context_data.lib.h.tmp /tmp/hh-suite-20240417-13693-g9ktsk/hh-suite-3.3.0/generated/context_data.lib.h
cd /tmp/hh-suite-20240417-13693-g9ktsk/hh-suite-3.3.0/data && mv -f /tmp/hh-suite-20240417-13693-g9ktsk/hh-suite-3.3.0/generated/context_data.crf.h.tmp /tmp/hh-suite-20240417-13693-g9ktsk/hh-suite-3.3.0/generated/context_data.crf.h
[ 38%] Built target generated
make: *** [all] Error 2

If reporting this issue please do so at (not Homebrew/brew or Homebrew/homebrew-core):
  https://github.com/brewsci/homebrew-bio/issues
YoshitakaMo commented 2 months ago

Thank you for your issue report. This error is caused by a deprecated std::ptr_fun in a3m_compress.cpp. I've fixed the error now. Please try installation again!