pip install pyhmmer fail for M1

[tmsincomb]

HMMER has a branch that can be built from source for a M1 chip https://github.com/EddyRivasLab/hmmer/tree/h3-arm, but it looks like they are holding out on merging it to main for awhile. This seems to be confirmed when they did it by accident in the closed pull request https://github.com/EddyRivasLab/hmmer/pull/232.

It looks like the pyhmmer pip install is using the main branch for hmmer that currently doesn't support M1. If there is a workaround or if this issue was fixed please let know.

Collecting pyhmmer
  Using cached pyhmmer-0.5.0.tar.gz (9.8 MB)
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Installing backend dependencies ... done
  Preparing metadata (pyproject.toml) ... done
Collecting psutil~=5.8
  Using cached psutil-5.9.0-cp310-cp310-macosx_11_0_arm64.whl
Building wheels for collected packages: pyhmmer
  Building wheel for pyhmmer (pyproject.toml) ... error
  error: subprocess-exited-with-error

  × Building wheel for pyhmmer (pyproject.toml) did not run successfully.
  │ exit code: 1
  ╰─> [794 lines of output]
      pyHMMER is not supported on CPU architecture: 'arm64'
      running bdist_wheel
      running build
      running build_py
      creating build
      creating build/lib.macosx-11.0-arm64-cpython-310
      creating build/lib.macosx-11.0-arm64-cpython-310/pyhmmer
      copying pyhmmer/hmmer.py -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer
      copying pyhmmer/__init__.py -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer
      copying pyhmmer/utils.py -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer
      running egg_info
      writing pyhmmer.egg-info/PKG-INFO
      writing dependency_links to pyhmmer.egg-info/dependency_links.txt
      writing requirements to pyhmmer.egg-info/requires.txt
      writing top-level names to pyhmmer.egg-info/top_level.txt
      reading manifest file 'pyhmmer.egg-info/SOURCES.txt'
      reading manifest template 'MANIFEST.in'
      warning: no previously-included files matching '*.ai' found under directory 'vendor/hmmer'
      warning: no previously-included files matching '*.pl' found under directory 'vendor'
      no previously-included directories found matching 'vendor/easel/demotic'
      no previously-included directories found matching 'vendor/easel/documentation'
      no previously-included directories found matching 'vendor/easel/esl_msa_testfiles'
      no previously-included directories found matching 'vendor/easel/miniapps'
      no previously-included directories found matching 'vendor/easel/testsuite'
      no previously-included directories found matching 'vendor/hmmer/autobuild'
      no previously-included directories found matching 'vendor/hmmer/documentation'
      no previously-included directories found matching 'vendor/hmmer/contrib'
      no previously-included directories found matching 'vendor/hmmer/profmark'
      no previously-included directories found matching 'vendor/hmmer/testsuite'
      no previously-included directories found matching 'vendor/hmmer/test-speed'
      no previously-included directories found matching 'vendor/hmmer/tutorial'
      adding license file 'COPYING'
      writing manifest file 'pyhmmer.egg-info/SOURCES.txt'
      copying pyhmmer/easel.pxd -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer
      copying pyhmmer/easel.pyi -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer
      copying pyhmmer/easel.pyx -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer
      copying pyhmmer/errors.pyi -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer
      copying pyhmmer/errors.pyx -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer
      copying pyhmmer/exceptions.pxi -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer
      copying pyhmmer/plan7.pxd -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer
      copying pyhmmer/plan7.pyi -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer
      copying pyhmmer/plan7.pyx -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer
      copying pyhmmer/py.typed -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer
      creating build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/fileobj
      copying pyhmmer/fileobj/bsd.pxi -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/fileobj
      copying pyhmmer/fileobj/linux.pxi -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/fileobj
      creating build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/reexports
      copying pyhmmer/reexports/__init__.pxd -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/reexports
      copying pyhmmer/reexports/esl_sqio_ascii.h -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/reexports
      copying pyhmmer/reexports/esl_sqio_ascii.pxd -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/reexports
      copying pyhmmer/reexports/p7_hmmfile.h -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/reexports
      copying pyhmmer/reexports/p7_hmmfile.pxd -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/reexports
      copying pyhmmer/reexports/p7_tophits.h -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/reexports
      copying pyhmmer/reexports/p7_tophits.pxd -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/reexports
      creating build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/tests
      copying pyhmmer/tests/__init__.py -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/tests
      copying pyhmmer/tests/requirements.txt -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/tests
      copying pyhmmer/tests/test_doctest.py -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/tests
      copying pyhmmer/tests/test_errors.py -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/tests
      copying pyhmmer/tests/test_hmmer.py -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/tests
      copying pyhmmer/tests/utils.py -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/tests
      creating build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/tests/data
      copying pyhmmer/tests/data/README.md -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/tests/data
      creating build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/tests/data/hmms
      copying pyhmmer/tests/data/hmms/make.sh -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/tests/data/hmms
      creating build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/tests/data/hmms/bin
      copying pyhmmer/tests/data/hmms/bin/PF02826.h3m -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/tests/data/hmms/bin
      copying pyhmmer/tests/data/hmms/bin/PKSI-AT.h3m -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/tests/data/hmms/bin
      copying pyhmmer/tests/data/hmms/bin/Thioesterase.h3m -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/tests/data/hmms/bin
      copying pyhmmer/tests/data/hmms/bin/t2pks.h3m -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/tests/data/hmms/bin
      creating build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/tests/data/hmms/db
      copying pyhmmer/tests/data/hmms/db/PF02826.hmm.h3f -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/tests/data/hmms/db
      copying pyhmmer/tests/data/hmms/db/PF02826.hmm.h3i -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/tests/data/hmms/db
      copying pyhmmer/tests/data/hmms/db/PF02826.hmm.h3m -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/tests/data/hmms/db
      copying pyhmmer/tests/data/hmms/db/PF02826.hmm.h3p -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/tests/data/hmms/db
      copying pyhmmer/tests/data/hmms/db/PKSI-AT.hmm.h3f -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/tests/data/hmms/db
      copying pyhmmer/tests/data/hmms/db/PKSI-AT.hmm.h3i -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/tests/data/hmms/db
      copying pyhmmer/tests/data/hmms/db/PKSI-AT.hmm.h3m -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/tests/data/hmms/db
      copying pyhmmer/tests/data/hmms/db/PKSI-AT.hmm.h3p -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/tests/data/hmms/db
      copying pyhmmer/tests/data/hmms/db/Thioesterase.hmm.h3f -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/tests/data/hmms/db
      copying pyhmmer/tests/data/hmms/db/Thioesterase.hmm.h3i -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/tests/data/hmms/db
      copying pyhmmer/tests/data/hmms/db/Thioesterase.hmm.h3m -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/tests/data/hmms/db
      copying pyhmmer/tests/data/hmms/db/Thioesterase.hmm.h3p -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/tests/data/hmms/db
      copying pyhmmer/tests/data/hmms/db/t2pks.hmm.h3f -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/tests/data/hmms/db
      copying pyhmmer/tests/data/hmms/db/t2pks.hmm.h3i -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/tests/data/hmms/db
      copying pyhmmer/tests/data/hmms/db/t2pks.hmm.h3m -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/tests/data/hmms/db
      copying pyhmmer/tests/data/hmms/db/t2pks.hmm.h3p -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/tests/data/hmms/db
      creating build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/tests/data/hmms/txt
      copying pyhmmer/tests/data/hmms/txt/LuxC.hmm -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/tests/data/hmms/txt
      copying pyhmmer/tests/data/hmms/txt/PF02826.hmm -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/tests/data/hmms/txt
      copying pyhmmer/tests/data/hmms/txt/PKSI-AT.hmm -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/tests/data/hmms/txt
      copying pyhmmer/tests/data/hmms/txt/Thioesterase.hmm -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/tests/data/hmms/txt
      copying pyhmmer/tests/data/hmms/txt/bmyD.hmm -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/tests/data/hmms/txt
      copying pyhmmer/tests/data/hmms/txt/laccase.hmm -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/tests/data/hmms/txt
      copying pyhmmer/tests/data/hmms/txt/t2pks.hmm -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/tests/data/hmms/txt
      creating build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/tests/data/hmms/txt2
      copying pyhmmer/tests/data/hmms/txt2/PF02826.hmm2 -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/tests/data/hmms/txt2
      copying pyhmmer/tests/data/hmms/txt2/PKSI-AT.hmm2 -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/tests/data/hmms/txt2
      copying pyhmmer/tests/data/hmms/txt2/Thioesterase.hmm2 -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/tests/data/hmms/txt2
      copying pyhmmer/tests/data/hmms/txt2/t2pks.hmm2 -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/tests/data/hmms/txt2
      creating build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/tests/data/msa
      copying pyhmmer/tests/data/msa/LuxC.faa -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/tests/data/msa
      copying pyhmmer/tests/data/msa/LuxC.hmmalign.sto -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/tests/data/msa
      copying pyhmmer/tests/data/msa/LuxC.sto -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/tests/data/msa
      copying pyhmmer/tests/data/msa/laccase.clw -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/tests/data/msa
      creating build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/tests/data/seqs
      copying pyhmmer/tests/data/seqs/938293.PRJEB85.HG003687.faa -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/tests/data/seqs
      copying pyhmmer/tests/data/seqs/BGC0001090.gbk -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/tests/data/seqs
      copying pyhmmer/tests/data/seqs/CP000560.2.fna -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/tests/data/seqs
      copying pyhmmer/tests/data/seqs/CP040672.1.genes_100.fna -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/tests/data/seqs
      copying pyhmmer/tests/data/seqs/LuxC.faa -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/tests/data/seqs
      copying pyhmmer/tests/data/seqs/PKSI.faa -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/tests/data/seqs
      copying pyhmmer/tests/data/seqs/bmyD.fna -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/tests/data/seqs
      creating build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/tests/data/tables
      copying pyhmmer/tests/data/tables/A0A089QRB9.domtbl -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/tests/data/tables
      copying pyhmmer/tests/data/tables/PF02826.domtbl -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/tests/data/tables
      copying pyhmmer/tests/data/tables/PF02826.tbl -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/tests/data/tables
      copying pyhmmer/tests/data/tables/bmyD1.tbl -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/tests/data/tables
      copying pyhmmer/tests/data/tables/bmyD2.tbl -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/tests/data/tables
      copying pyhmmer/tests/data/tables/bmyD3.tbl -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/tests/data/tables
      copying pyhmmer/tests/data/tables/t2pks.domtbl -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/tests/data/tables
      copying pyhmmer/tests/data/tables/t2pks.tbl -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/tests/data/tables
      creating build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/tests/test_easel
      copying pyhmmer/tests/test_easel/__init__.py -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/tests/test_easel
      copying pyhmmer/tests/test_easel/test_alphabet.py -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/tests/test_easel
      copying pyhmmer/tests/test_easel/test_bitfield.py -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/tests/test_easel
      copying pyhmmer/tests/test_easel/test_keyhash.py -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/tests/test_easel
      copying pyhmmer/tests/test_easel/test_matrix.py -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/tests/test_easel
      copying pyhmmer/tests/test_easel/test_msa.py -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/tests/test_easel
      copying pyhmmer/tests/test_easel/test_msafile.py -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/tests/test_easel
      copying pyhmmer/tests/test_easel/test_randomness.py -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/tests/test_easel
      copying pyhmmer/tests/test_easel/test_sequence.py -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/tests/test_easel
      copying pyhmmer/tests/test_easel/test_sequencefile.py -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/tests/test_easel
      copying pyhmmer/tests/test_easel/test_ssi.py -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/tests/test_easel
      copying pyhmmer/tests/test_easel/test_vector.py -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/tests/test_easel
      creating build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/tests/test_plan7
      copying pyhmmer/tests/test_plan7/__init__.py -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/tests/test_plan7
      copying pyhmmer/tests/test_plan7/test_background.py -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/tests/test_plan7
      copying pyhmmer/tests/test_plan7/test_builder.py -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/tests/test_plan7
      copying pyhmmer/tests/test_plan7/test_hmm.py -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/tests/test_plan7
      copying pyhmmer/tests/test_plan7/test_hmmfile.py -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/tests/test_plan7
      copying pyhmmer/tests/test_plan7/test_optimizedprofile.py -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/tests/test_plan7
      copying pyhmmer/tests/test_plan7/test_pipeline.py -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/tests/test_plan7
      copying pyhmmer/tests/test_plan7/test_profile.py -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/tests/test_plan7
      copying pyhmmer/tests/test_plan7/test_tophits.py -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/tests/test_plan7
      copying pyhmmer/tests/test_plan7/test_tracealigner.py -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/tests/test_plan7
      copying pyhmmer/tests/test_plan7/test_traces.py -> build/lib.macosx-11.0-arm64-cpython-310/pyhmmer/tests/test_plan7
      running build_clib
      creating build/temp.macosx-11.0-arm64-cpython-310
      generating "divsufsort.h" for divsufsort library
      copying vendor/hmmer/libdivsufsort/divsufsort.h.in -> build/temp.macosx-11.0-arm64-cpython-310/divsufsort.h
      generating "esl_config.h" for easel library
      checking whether <stdio.h> can be included... yes
      checking whether <stdlib.h> can be included... yes
      checking whether <string.h> can be included... yes
      checking whether <inttypes.h> can be included... yes
      checking whether <stdint.h> can be included... yes
      checking whether <strings.h> can be included... yes
      checking whether <sys/stat.h> can be included... yes
      checking whether <sys/types.h> can be included... yes
      checking whether <unistd.h> can be included... yes
      checking whether <endian.h> can be included... no
      checking whether <netinet/in.h> can be included... yes
      checking whether <sys/param.h> can be included... yes
      checking whether <sys/sysctl.h> can be included... yes
      checking whether function 'aligned_alloc' is available... no
      checking whether function 'erfc' is available... no
      checking whether function 'getpid' is available... no
      checking whether function '_mm_malloc' is available... no
      checking whether function 'popen' is available... no
      checking whether function 'posix_memalign' is available... no
      checking whether function 'strcasecmp' is available... no
      checking whether function 'strsep' is available... no
      checking whether function 'sysconf' is available... no
      checking whether function 'sysctl' is available... no
      checking whether function 'times' is available... no
      checking whether function 'fseeko' is available... no
      generating "p7_config.h" for hmmer library
      checking whether <endian.h> can be included... no
      checking whether <inttypes.h> can be included... yes
      checking whether <stdint.h> can be included... yes
      checking whether <unistd.h> can be included... yes
      checking whether <sys/types.h> can be included... yes
      checking whether <netinet/in.h> can be included... yes
      checking whether <sys/param.h> can be included... yes
      checking whether <sys/sysctl.h> can be included... yes
      checking whether function 'mkstemp' is available... no
      checking whether function 'popen' is available... no
      checking whether function 'putenv' is available... no
      checking whether function 'strcasecmp' is available... no
      checking whether function 'strsep' is available... no
      checking whether function 'times' is available... no
      checking whether function 'getpid' is available... no
      checking whether function 'sysctl' is available... no
      checking whether function 'sysconf' is available... no
      checking whether function 'getcwd' is available... no
      checking whether function 'chmod' is available... no
      checking whether function 'stat' is available... no
      checking whether function 'fstat' is available... no
      checking whether function 'erfc' is available... no
      generating build/temp.macosx-11.0-arm64-cpython-310/esl_sqio_ascii.c from vendor/easel/esl_sqio_ascii.c
      generating build/temp.macosx-11.0-arm64-cpython-310/p7_hmmfile.c from vendor/hmmer/src/p7_hmmfile.c
      generating build/temp.macosx-11.0-arm64-cpython-310/libdivsufsort.a from vendor/hmmer/libdivsufsort/divsufsort.c
      creating build/temp.macosx-11.0-arm64-cpython-310/vendor
      creating build/temp.macosx-11.0-arm64-cpython-310/vendor/hmmer
      creating build/temp.macosx-11.0-arm64-cpython-310/vendor/hmmer/libdivsufsort
      clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /Users/tmsincomb/miniforge3/envs/sadie/include -arch arm64 -fPIC -O2 -isystem /Users/tmsincomb/miniforge3/envs/sadie/include -arch arm64 -Ibuild/temp.macosx-11.0-arm64-cpython-310 -c vendor/hmmer/libdivsufsort/divsufsort.c -o build/temp.macosx-11.0-arm64-cpython-310/vendor/hmmer/libdivsufsort/divsufsort.o
      ar rcs build/temp.macosx-11.0-arm64-cpython-310/libdivsufsort.a build/temp.macosx-11.0-arm64-cpython-310/vendor/hmmer/libdivsufsort/divsufsort.o
      ranlib build/temp.macosx-11.0-arm64-cpython-310/libdivsufsort.a
      generating build/temp.macosx-11.0-arm64-cpython-310/libeasel.a from vendor/easel/esl_exponential.c, vendor/easel/esl_msashuffle.c, vendor/easel/esl_msafile_stockholm.c, vendor/easel/esl_msafile_a2m.c, vendor/easel/esl_ssi.c, vendor/easel/esl_subcmd.c, vendor/easel/esl_sq.c, vendor/easel/esl_matrixops.c, vendor/easel/esl_getopts.c, vendor/easel/esl_randomseq.c, vendor/easel/esl_hmm.c, vendor/easel/esl_stopwatch.c, vendor/easel/esl_neon.c, vendor/easel/esl_mpi.c, vendor/easel/esl_gencode.c, vendor/easel/esl_stats.c, vendor/easel/esl_avx512.c, vendor/easel/esl_alloc.c, vendor/easel/easel.c, vendor/easel/esl_distance.c, vendor/easel/esl_histogram.c, vendor/easel/esl_gev.c, vendor/easel/esl_paml.c, vendor/easel/esl_msafile_phylip.c, vendor/easel/esl_msa.c, vendor/easel/esl_tree.c, vendor/easel/esl_arr2.c, vendor/easel/esl_vectorops.c, vendor/easel/esl_ratematrix.c, vendor/easel/esl_msaweight.c, vendor/easel/esl_sqio_ncbi.c, vendor/easel/esl_mixgev.c, vendor/easel/esl_msafile_psiblast.c, vendor/easel/esl_minimizer.c, vendor/easel/esl_dsqdata.c, vendor/easel/esl_varint.c, vendor/easel/esl_swat.c, vendor/easel/esl_gamma.c, vendor/easel/esl_msafile_clustal.c, vendor/easel/esl_huffman.c, vendor/easel/esl_stack.c, vendor/easel/esl_msafile_afa.c, vendor/easel/esl_avx.c, vendor/easel/esl_dirichlet.c, vendor/easel/esl_regexp.c, vendor/easel/esl_stretchexp.c, vendor/easel/esl_mem.c, vendor/easel/esl_keyhash.c, vendor/easel/esl_arr3.c, vendor/easel/esl_vmx.c, vendor/easel/esl_recorder.c, vendor/easel/esl_heap.c, vendor/easel/esl_cluster.c, vendor/easel/esl_sse.c, vendor/easel/esl_random.c, vendor/easel/esl_alphabet.c, vendor/easel/esl_graph.c, vendor/easel/esl_weibull.c, vendor/easel/esl_composition.c, vendor/easel/esl_red_black.c, vendor/easel/esl_scorematrix.c, vendor/easel/interface_gsl.c, vendor/easel/esl_rand64.c, vendor/easel/esl_quicksort.c, vendor/easel/esl_sqio.c, vendor/easel/esl_fileparser.c, vendor/easel/esl_json.c, vendor/easel/esl_rootfinder.c, vendor/easel/esl_hyperexp.c, vendor/easel/esl_workqueue.c, vendor/easel/esl_msafile2.c, vendor/easel/esl_buffer.c, vendor/easel/esl_mixdchlet.c, vendor/easel/esl_dmatrix.c, vendor/easel/esl_gumbel.c, vendor/easel/esl_msafile.c, vendor/easel/esl_cpu.c, vendor/easel/interface_lapack.c, vendor/easel/esl_normal.c, vendor/easel/esl_wuss.c, vendor/easel/esl_bitfield.c, vendor/easel/esl_threads.c, vendor/easel/esl_msacluster.c, vendor/easel/esl_msafile_selex.c, build/temp.macosx-11.0-arm64-cpython-310/esl_sqio_ascii.c
      creating build/temp.macosx-11.0-arm64-cpython-310/vendor/easel
      creating build/temp.macosx-11.0-arm64-cpython-310/build
      creating build/temp.macosx-11.0-arm64-cpython-310/build/temp.macosx-11.0-arm64-cpython-310
      clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /Users/tmsincomb/miniforge3/envs/sadie/include -arch arm64 -fPIC -O2 -isystem /Users/tmsincomb/miniforge3/envs/sadie/include -arch arm64 -Ivendor/easel -Ibuild/temp.macosx-11.0-arm64-cpython-310 -c vendor/easel/esl_exponential.c -o build/temp.macosx-11.0-arm64-cpython-310/vendor/easel/esl_exponential.o
      clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /Users/tmsincomb/miniforge3/envs/sadie/include -arch arm64 -fPIC -O2 -isystem /Users/tmsincomb/miniforge3/envs/sadie/include -arch arm64 -Ivendor/easel -Ibuild/temp.macosx-11.0-arm64-cpython-310 -c vendor/easel/esl_msashuffle.c -o build/temp.macosx-11.0-arm64-cpython-310/vendor/easel/esl_msashuffle.o
      vendor/easel/esl_msashuffle.c:449:17: warning: comparison of integers of different signs: 'unsigned long' and 'int' [-Wsign-compare]
        if (strlen(y) != L) ESL_XEXCEPTION(eslEINVAL, "sequences of different lengths in qrna shuffle");
            ~~~~~~~~~ ^  ~
      1 warning generated.
      clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /Users/tmsincomb/miniforge3/envs/sadie/include -arch arm64 -fPIC -O2 -isystem /Users/tmsincomb/miniforge3/envs/sadie/include -arch arm64 -Ivendor/easel -Ibuild/temp.macosx-11.0-arm64-cpython-310 -c vendor/easel/esl_msafile_stockholm.c -o build/temp.macosx-11.0-arm64-cpython-310/vendor/easel/esl_msafile_stockholm.o
      clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /Users/tmsincomb/miniforge3/envs/sadie/include -arch arm64 -fPIC -O2 -isystem /Users/tmsincomb/miniforge3/envs/sadie/include -arch arm64 -Ivendor/easel -Ibuild/temp.macosx-11.0-arm64-cpython-310 -c vendor/easel/esl_msafile_a2m.c -o build/temp.macosx-11.0-arm64-cpython-310/vendor/easel/esl_msafile_a2m.o
      clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /Users/tmsincomb/miniforge3/envs/sadie/include -arch arm64 -fPIC -O2 -isystem /Users/tmsincomb/miniforge3/envs/sadie/include -arch arm64 -Ivendor/easel -Ibuild/temp.macosx-11.0-arm64-cpython-310 -c vendor/easel/esl_ssi.c -o build/temp.macosx-11.0-arm64-cpython-310/vendor/easel/esl_ssi.o
      vendor/easel/esl_ssi.c:261:12: warning: comparison of integers of different signs: 'int64_t' (aka 'long long') and 'uint64_t' (aka 'unsigned long long') [-Wsign-compare]
        if (nkey >= ssi->nprimary) { status = eslENOTFOUND; goto ERROR; }
            ~~~~ ^  ~~~~~~~~~~~~~
      vendor/easel/esl_ssi.c:728:13: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare]
        if ((n+1) > ns->flen) ns->flen = n+1;
             ~~~  ^ ~~~~~~~~
      vendor/easel/esl_ssi.c:862:9: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare]
        if (n > ns->plen) ns->plen = n;
            ~ ^ ~~~~~~~~
      ... 

      fatal error: too many errors emitted, stopping now [-ferror-limit=]
      20 errors generated.
      error: command '/usr/bin/clang' failed with exit code 1
      [end of output]

  note: This error originates from a subprocess, and is likely not a problem with pip.
  ERROR: Failed building wheel for pyhmmer
Failed to build pyhmmer
ERROR: Could not build wheels for pyhmmer, which is required to install pyproject.toml-based projects

[althonos]

I know about that branch, I'm the one who contributed the code :wink:

At the moment, HMMER development efforts are focusing on the next version of HMMER (v4) which will also provide an ARM NEON implementation, supporting Armv7 and Aarch64 platforms. Until either HMMER4 is released or a new HMMER3 version is released, I'm reluctant to push forward any support for Arm support in pyhmmer, because I'd have to support diverging codebases, which goes against the idea of reproducibility / providing a clearly identified version of HMMER in pyhmmer.

In the meantime, you should try to install pyhmmer via Rosetta, which should still give reasonable performances. I have no Mac to give you any help on this front, but it's been reported to work by a collaborator of mine.

[tmsincomb]

That's pretty awesome and thank you for your quick response. I'll move forward with Rosetta then and make a note for my team.

[jianshu93]

I think the develop branch of hmmer works for ARM64 (I successfully compiled and run all binaries on an arm64 iMac), which I downloaded and then put it under vendor, with easel, but I still have the compiling error:

``` pyHMMER is not supported on CPU architecture: 'arm64' running install /opt/homebrew/lib/python3.10/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools. warnings.warn( /opt/homebrew/lib/python3.10/site-packages/setuptools/command/easy_install.py:144: EasyInstallDeprecationWarning: easy_install command is deprecated. Use build and pip and other standards-based tools. warnings.warn( running bdist_egg running egg_info writing pyhmmer.egg-info/PKG-INFO writing dependency_links to pyhmmer.egg-info/dependency_links.txt writing requirements to pyhmmer.egg-info/requires.txt writing top-level names to pyhmmer.egg-info/top_level.txt reading manifest file 'pyhmmer.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'pyproject.toml' adding license file 'COPYING' writing manifest file 'pyhmmer.egg-info/SOURCES.txt' installing library code to build/bdist.macosx-12-arm64/egg running build_clib generating "divsufsort.h" for divsufsort library copying vendor/hmmer/libdivsufsort/divsufsort.h.in -> build/temp.macosx-12-arm64-cpython-310/divsufsort.h generating build/temp.macosx-12-arm64-cpython-310/esl_sqio_ascii.c from vendor/easel/esl_sqio_ascii.c generating build/temp.macosx-12-arm64-cpython-310/p7_hmmfile.c from vendor/hmmer/src/p7_hmmfile.c generating build/temp.macosx-12-arm64-cpython-310/libdivsufsort.a from vendor/hmmer/libdivsufsort/divsufsort.c generating build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/libdivsufsort/divsufsort.o from vendor/hmmer/libdivsufsort/divsufsort.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/hmmer/libdivsufsort/divsufsort.c -o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/libdivsufsort/divsufsort.o /usr/bin/xcrun ar rcs build/temp.macosx-12-arm64-cpython-310/libdivsufsort.a build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/libdivsufsort/divsufsort.o ranlib build/temp.macosx-12-arm64-cpython-310/libdivsufsort.a generating build/temp.macosx-12-arm64-cpython-310/libeasel.a from vendor/easel/esl_exponential.c, vendor/easel/esl_msashuffle.c, vendor/easel/esl_msafile_stockholm.c, vendor/easel/esl_msafile_a2m.c, vendor/easel/esl_ssi.c, vendor/easel/esl_subcmd.c, vendor/easel/esl_sq.c, vendor/easel/esl_matrixops.c, vendor/easel/esl_getopts.c, vendor/easel/esl_randomseq.c, vendor/easel/esl_hmm.c, vendor/easel/esl_stopwatch.c, vendor/easel/esl_neon.c, vendor/easel/esl_mpi.c, vendor/easel/esl_gencode.c, vendor/easel/esl_stats.c, vendor/easel/esl_avx512.c, vendor/easel/esl_alloc.c, vendor/easel/easel.c, vendor/easel/esl_distance.c, vendor/easel/esl_histogram.c, vendor/easel/esl_gev.c, vendor/easel/esl_paml.c, vendor/easel/esl_msafile_phylip.c, vendor/easel/esl_msa.c, vendor/easel/esl_tree.c, vendor/easel/esl_arr2.c, vendor/easel/esl_vectorops.c, vendor/easel/esl_ratematrix.c, vendor/easel/esl_msaweight.c, vendor/easel/esl_sqio_ncbi.c, vendor/easel/esl_mixgev.c, vendor/easel/esl_msafile_psiblast.c, vendor/easel/esl_minimizer.c, vendor/easel/esl_dsqdata.c, vendor/easel/esl_varint.c, vendor/easel/esl_swat.c, vendor/easel/esl_gamma.c, vendor/easel/esl_msafile_clustal.c, vendor/easel/esl_huffman.c, vendor/easel/esl_stack.c, vendor/easel/esl_msafile_afa.c, vendor/easel/esl_avx.c, vendor/easel/esl_dirichlet.c, vendor/easel/esl_regexp.c, vendor/easel/esl_stretchexp.c, vendor/easel/esl_mem.c, vendor/easel/esl_keyhash.c, vendor/easel/esl_arr3.c, vendor/easel/esl_vmx.c, vendor/easel/esl_recorder.c, vendor/easel/esl_heap.c, vendor/easel/esl_cluster.c, vendor/easel/esl_sse.c, vendor/easel/esl_random.c, vendor/easel/esl_alphabet.c, vendor/easel/esl_graph.c, vendor/easel/esl_weibull.c, vendor/easel/esl_composition.c, vendor/easel/esl_red_black.c, vendor/easel/esl_scorematrix.c, vendor/easel/interface_gsl.c, vendor/easel/esl_rand64.c, vendor/easel/esl_quicksort.c, vendor/easel/esl_sqio.c, vendor/easel/esl_fileparser.c, vendor/easel/esl_json.c, vendor/easel/esl_rootfinder.c, vendor/easel/esl_hyperexp.c, vendor/easel/esl_workqueue.c, vendor/easel/esl_msafile2.c, vendor/easel/esl_buffer.c, vendor/easel/esl_mixdchlet.c, vendor/easel/esl_dmatrix.c, vendor/easel/esl_gumbel.c, vendor/easel/esl_msafile.c, vendor/easel/esl_cpu.c, vendor/easel/interface_lapack.c, vendor/easel/esl_normal.c, vendor/easel/esl_wuss.c, vendor/easel/esl_bitfield.c, vendor/easel/esl_threads.c, vendor/easel/esl_msacluster.c, vendor/easel/esl_msafile_selex.c, build/temp.macosx-12-arm64-cpython-310/esl_sqio_ascii.c generating build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_exponential.o from vendor/easel/esl_exponential.c generating build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_randomseq.o from vendor/easel/esl_randomseq.c generating build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_msafile_a2m.o from vendor/easel/esl_msafile_a2m.c generating build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_sq.o from vendor/easel/esl_sq.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/easel/esl_randomseq.c -o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_randomseq.o generating build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_vectorops.o from vendor/easel/esl_vectorops.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/easel/esl_msafile_a2m.c -o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_msafile_a2m.o generating build/temp.macosx-12-arm64-cpython-310/vendor/easel/easel.o from vendor/easel/easel.c generating build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_neon.o from vendor/easel/esl_neon.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/easel/esl_vectorops.c -o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_vectorops.o generating build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_gev.o from vendor/easel/esl_gev.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/easel/easel.c -o build/temp.macosx-12-arm64-cpython-310/vendor/easel/easel.o clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/easel/esl_neon.c -o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_neon.o clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/easel/esl_sq.c -o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_sq.o clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/easel/esl_exponential.c -o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_exponential.o clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/easel/esl_gev.c -o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_gev.o generating build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_stats.o from vendor/easel/esl_stats.c generating build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_msa.o from vendor/easel/esl_msa.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/easel/esl_msa.c -o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_msa.o clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/easel/esl_stats.c -o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_stats.o vendor/easel/easel.c:80:37: warning: variable 'ap' is uninitialized when used here [-Wuninitialized] else vsyslog(LOG_ERR, format, ap); // SRE: TODO: check this. ^~ vendor/easel/easel.c:70:17: note: initialize the variable 'ap' to silence this warning va_list ap; ^ = NULL vendor/easel/easel.c:158:37: warning: variable 'argp' is uninitialized when used here [-Wuninitialized] else vsyslog(LOG_ERR, format, argp); ^~~~ vendor/easel/easel.c:132:15: note: initialize the variable 'argp' to silence this warning va_list argp; ^ = NULL vendor/easel/easel.c:309:33: warning: variable 'argp' is uninitialized when used here [-Wuninitialized] else vsyslog(LOG_ERR, format, argp); ^~~~ vendor/easel/easel.c:296:15: note: initialize the variable 'argp' to silence this warning va_list argp; ^ = NULL vendor/easel/esl_sq.c:104:22: warning: comparison of integers of different signs: 'unsigned long' and 'int64_t' (aka 'long long') [-Wsign-compare] if (strlen(ss) != n) ESL_XEXCEPTION(eslEINVAL, "ss, seq lengths mismatch"); ~~~~~~~~~~ ^ ~ vendor/easel/esl_sq.c:785:22: warning: comparison of integers of different signs: 'unsigned long' and 'int64_t' (aka 'long long') [-Wsign-compare] if (strlen(ss) != sq->n) ESL_XEXCEPTION(eslEINVAL, "ss, seq lengths mismatch"); ~~~~~~~~~~ ^ ~~~~~ vendor/easel/esl_sq.c:1636:25: warning: comparison of integers of different signs: 'uint64_t' (aka 'unsigned long long') and 'const int64_t' (aka 'const long long') [-Wsign-compare] for (pos = 0; pos < sq->n; pos++) ~~~ ^ ~~~~~ vendor/easel/esl_sq.c:1645:25: warning: comparison of integers of different signs: 'uint64_t' (aka 'unsigned long long') and 'const int64_t' (aka 'const long long') [-Wsign-compare] for (pos = 1; pos <= sq->n; pos++) ~~~ ^ ~~~~~ vendor/easel/esl_sq.c:2021:35: warning: comparison of integers of different signs: 'unsigned long' and 'int64_t' (aka 'long long') [-Wsign-compare] if (strlen(sq->ss+1) != sq->n) ESL_FAIL(eslFAIL, errmsg, "ss annotation length (for digital seq) doesn't agree with sq->n"); ~~~~~~~~~~~~~~~~ ^ ~~~~~ vendor/easel/esl_sq.c:2028:36: warning: comparison of integers of different signs: 'unsigned long' and 'int64_t' (aka 'long long') [-Wsign-compare] if (strlen(sq->seq) != sq->n) ESL_FAIL(eslFAIL, errmsg, "text seq length doesn't agree with sq->n"); ~~~~~~~~~~~~~~~ ^ ~~~~~ vendor/easel/esl_sq.c:2029:36: warning: comparison of integers of different signs: 'unsigned long' and 'int64_t' (aka 'long long') [-Wsign-compare] if (sq->ss && strlen(sq->ss) != sq->n) ESL_FAIL(eslFAIL, errmsg, "ss annotation length (for text seq) doesn't agree with sq->n"); ~~~~~~~~~~~~~~ ^ ~~~~~ generating build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_msashuffle.o from vendor/easel/esl_msashuffle.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/easel/esl_msashuffle.c -o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_msashuffle.o generating build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_paml.o from vendor/easel/esl_paml.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/easel/esl_paml.c -o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_paml.o vendor/easel/esl_msa.c:3168:31: warning: comparison of integers of different signs: 'unsigned long' and 'const int64_t' (aka 'const long long') [-Wsign-compare] if (strlen(msa->aseq[idx]) != msa->alen) ESL_FAIL(eslFAIL, errmsg, "seq %d: wrong length", idx); ~~~~~~~~~~~~~~~~~~~~~~ ^ ~~~~~~~~~ vendor/easel/esl_msa.c:3175:61: warning: comparison of integers of different signs: 'unsigned long' and 'const int64_t' (aka 'const long long') [-Wsign-compare] if (msa->ss && msa->ss[idx] && strlen(msa->ss[idx]) != msa->alen) ESL_FAIL(eslFAIL, errmsg, "seq %d: SS wrong length", idx); ~~~~~~~~~~~~~~~~~~~~ ^ ~~~~~~~~~ vendor/easel/esl_msa.c:3176:61: warning: comparison of integers of different signs: 'unsigned long' and 'const int64_t' (aka 'const long long') [-Wsign-compare] if (msa->sa && msa->sa[idx] && strlen(msa->sa[idx]) != msa->alen) ESL_FAIL(eslFAIL, errmsg, "seq %d: SA wrong length", idx); ~~~~~~~~~~~~~~~~~~~~ ^ ~~~~~~~~~ vendor/easel/esl_msa.c:3177:61: warning: comparison of integers of different signs: 'unsigned long' and 'const int64_t' (aka 'const long long') [-Wsign-compare] if (msa->pp && msa->pp[idx] && strlen(msa->pp[idx]) != msa->alen) ESL_FAIL(eslFAIL, errmsg, "seq %d: PP wrong length", idx); ~~~~~~~~~~~~~~~~~~~~ ^ ~~~~~~~~~ vendor/easel/esl_msa.c:3181:44: warning: comparison of integers of different signs: 'unsigned long' and 'const int64_t' (aka 'const long long') [-Wsign-compare] if (msa->ss_cons && strlen(msa->ss_cons) != msa->alen) ESL_FAIL(eslFAIL, errmsg, "SS_cons wrong length"); ~~~~~~~~~~~~~~~~~~~~ ^ ~~~~~~~~~ vendor/easel/esl_msa.c:3182:44: warning: comparison of integers of different signs: 'unsigned long' and 'const int64_t' (aka 'const long long') [-Wsign-compare] if (msa->sa_cons && strlen(msa->sa_cons) != msa->alen) ESL_FAIL(eslFAIL, errmsg, "SA_cons wrong length"); ~~~~~~~~~~~~~~~~~~~~ ^ ~~~~~~~~~ vendor/easel/esl_msa.c:3183:44: warning: comparison of integers of different signs: 'unsigned long' and 'const int64_t' (aka 'const long long') [-Wsign-compare] if (msa->pp_cons && strlen(msa->pp_cons) != msa->alen) ESL_FAIL(eslFAIL, errmsg, "PP_cons wrong length"); ~~~~~~~~~~~~~~~~~~~~ ^ ~~~~~~~~~ vendor/easel/esl_msa.c:3184:44: warning: comparison of integers of different signs: 'unsigned long' and 'const int64_t' (aka 'const long long') [-Wsign-compare] if (msa->rf && strlen(msa->rf) != msa->alen) ESL_FAIL(eslFAIL, errmsg, "RF wrong length"); ~~~~~~~~~~~~~~~ ^ ~~~~~~~~~ vendor/easel/esl_msa.c:3185:44: warning: comparison of integers of different signs: 'unsigned long' and 'const int64_t' (aka 'const long long') [-Wsign-compare] if (msa->mm && strlen(msa->mm ) != msa->alen) ESL_FAIL(eslFAIL, errmsg, "MM wrong length"); ~~~~~~~~~~~~~~~~~~ ^ ~~~~~~~~~ generating build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_mpi.o from vendor/easel/esl_mpi.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/easel/esl_mpi.c -o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_mpi.o vendor/easel/esl_msashuffle.c:449:17: warning: comparison of integers of different signs: 'unsigned long' and 'int' [-Wsign-compare] if (strlen(y) != L) ESL_XEXCEPTION(eslEINVAL, "sequences of different lengths in qrna shuffle"); ~~~~~~~~~ ^ ~ generating build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_avx512.o from vendor/easel/esl_avx512.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/easel/esl_avx512.c -o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_avx512.o generating build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_msafile_phylip.o from vendor/easel/esl_msafile_phylip.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/easel/esl_msafile_phylip.c -o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_msafile_phylip.o 3 warnings generated. generating build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_alloc.o from vendor/easel/esl_alloc.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/easel/esl_alloc.c -o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_alloc.o generating build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_distance.o from vendor/easel/esl_distance.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/easel/esl_distance.c -o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_distance.o generating build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_gencode.o from vendor/easel/esl_gencode.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/easel/esl_gencode.c -o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_gencode.o generating build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_ssi.o from vendor/easel/esl_ssi.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/easel/esl_ssi.c -o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_ssi.o 1 warning generated. generating build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_msafile_stockholm.o from vendor/easel/esl_msafile_stockholm.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/easel/esl_msafile_stockholm.c -o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_msafile_stockholm.o vendor/easel/esl_alloc.c:147:3: warning: misleading indentation; statement is not part of the previous 'if' [-Wmisleading-indentation] return p; ^ vendor/easel/esl_alloc.c:145:3: note: previous statement is here if (p == NULL) ^ 1 warning generated. generating build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_sqio_ncbi.o from vendor/easel/esl_sqio_ncbi.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/easel/esl_sqio_ncbi.c -o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_sqio_ncbi.o vendor/easel/esl_ssi.c:261:12: warning: comparison of integers of different signs: 'int64_t' (aka 'long long') and 'uint64_t' (aka 'unsigned long long') [-Wsign-compare] if (nkey >= ssi->nprimary) { status = eslENOTFOUND; goto ERROR; } ~~~~ ^ ~~~~~~~~~~~~~ generating build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_hmm.o from vendor/easel/esl_hmm.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/easel/esl_hmm.c -o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_hmm.o vendor/easel/esl_ssi.c:728:13: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare] if ((n+1) > ns->flen) ns->flen = n+1; ~~~ ^ ~~~~~~~~ vendor/easel/esl_ssi.c:862:9: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare] if (n > ns->plen) ns->plen = n; ~ ^ ~~~~~~~~ vendor/easel/esl_ssi.c:893:27: warning: comparison of integers of different signs: 'int' and 'unsigned long long' [-Wsign-compare] for (i = ns->nprimary; i < ns->nprimary + eslSSI_KCHUNK; i++) ~ ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ vendor/easel/esl_ssi.c:941:9: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare] if (n > ns->slen) ns->slen = n; ~ ^ ~~~~~~~~ vendor/easel/esl_ssi.c:957:29: warning: comparison of integers of different signs: 'int' and 'unsigned long long' [-Wsign-compare] for (i = ns->nsecondary; i < ns->nsecondary+eslSSI_KCHUNK; i++) { ~ ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ vendor/easel/esl_ssi.c:1149:21: warning: comparison of integers of different signs: 'int' and 'uint64_t' (aka 'unsigned long long') [-Wsign-compare] for (i = 0; i < ns->nprimary; i++) ~ ^ ~~~~~~~~~~~~ vendor/easel/esl_ssi.c:1167:21: warning: comparison of integers of different signs: 'int' and 'uint64_t' (aka 'unsigned long long') [-Wsign-compare] for (i = 0; i < ns->nprimary; i++) ~ ^ ~~~~~~~~~~~~ vendor/easel/esl_ssi.c:1187:21: warning: comparison of integers of different signs: 'int' and 'uint64_t' (aka 'unsigned long long') [-Wsign-compare] for (i = 0; i < ns->nsecondary; i++) ~ ^ ~~~~~~~~~~~~~~ vendor/easel/esl_ssi.c:1204:21: warning: comparison of integers of different signs: 'int' and 'uint64_t' (aka 'unsigned long long') [-Wsign-compare] for (i = 0; i < ns->nsecondary; i++) ~ ^ ~~~~~~~~~~~~~~ vendor/easel/esl_ssi.c:1253:18: warning: comparison of integers of different signs: 'int' and 'uint64_t' (aka 'unsigned long long') [-Wsign-compare] for (i = 0; i < ns->nprimary; i++) ~ ^ ~~~~~~~~~~~~ vendor/easel/esl_ssi.c:1259:18: warning: comparison of integers of different signs: 'int' and 'uint64_t' (aka 'unsigned long long') [-Wsign-compare] for (i = 0; i < ns->nsecondary; i++) ~ ^ ~~~~~~~~~~~~~~ vendor/easel/esl_ssi.c:1351:17: warning: comparison of integers of different signs: 'int' and 'uint64_t' (aka 'unsigned long long') [-Wsign-compare] for (i = 0; i < ns->nprimary; i++) { ~ ^ ~~~~~~~~~~~~ vendor/easel/esl_ssi.c:1370:17: warning: comparison of integers of different signs: 'int' and 'uint64_t' (aka 'unsigned long long') [-Wsign-compare] for (i = 0; i < ns->nsecondary; i++) ~ ^ ~~~~~~~~~~~~~~ vendor/easel/esl_ssi.c:1376:17: warning: comparison of integers of different signs: 'int' and 'uint64_t' (aka 'unsigned long long') [-Wsign-compare] for (i = 0; i < ns->nprimary; i++) free(ns->pkeys[i].key); ~ ^ ~~~~~~~~~~~~ vendor/easel/esl_ssi.c:1377:17: warning: comparison of integers of different signs: 'int' and 'uint64_t' (aka 'unsigned long long') [-Wsign-compare] for (i = 0; i < ns->nsecondary; i++) free(ns->skeys[i].key); ~ ^ ~~~~~~~~~~~~~~ vendor/easel/esl_ssi.c:1378:17: warning: comparison of integers of different signs: 'int' and 'uint64_t' (aka 'unsigned long long') [-Wsign-compare] for (i = 0; i < ns->nsecondary; i++) free(ns->skeys[i].pkey); ~ ^ ~~~~~~~~~~~~~~ vendor/easel/esl_sqio_ncbi.c:216:24: warning: comparison of integers of different signs: 'unsigned int' and 'int' [-Wsign-compare] if (htobe32(info[1]) != dbtype) status = eslEUNIMPLEMENTED; ~~~~~~~~~~~~~~~~ ^ ~~~~~~ vendor/easel/esl_sqio_ncbi.c:226:58: warning: comparison of integers of different signs: 'unsigned long' and 'int' [-Wsign-compare] if (fread(ncbi->title, sizeof(char), len, ncbi->fppin) != len) { status = eslFAIL; goto ERROR; } ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ ~~~ vendor/easel/esl_sqio_ncbi.c:233:62: warning: comparison of integers of different signs: 'unsigned long' and 'int' [-Wsign-compare] if (fread(ncbi->timestamp, sizeof(char), len, ncbi->fppin) != len) { status = eslFAIL; goto ERROR; } ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ ~~~ vendor/easel/esl_sqio_ncbi.c:758:19: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare] if (ncbi->index >= ncbi->num_seq) return eslEOF; ~~~~~~~~~~~ ^ ~~~~~~~~~~~~~ vendor/easel/esl_sqio_ncbi.c:809:19: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare] if (ncbi->index >= ncbi->num_seq) return eslEOF; ~~~~~~~~~~~ ^ ~~~~~~~~~~~~~ vendor/easel/esl_sqio_ncbi.c:860:19: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare] if (ncbi->index >= ncbi->num_seq) return eslEOF; ~~~~~~~~~~~ ^ ~~~~~~~~~~~~~ vendor/easel/esl_sqio_ncbi.c:1036:33: warning: comparison of integers of different signs: 'uint64_t' (aka 'unsigned long long') and 'int' [-Wsign-compare] if (status != eslOK || nres != W) { ~~~~ ^ ~ vendor/easel/esl_sqio_ncbi.c:1059:23: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare] if (ncbi->index >= ncbi->num_seq) return eslEOF; ~~~~~~~~~~~ ^ ~~~~~~~~~~~~~ vendor/easel/esl_sqio_ncbi.c:1421:28: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare] if (volume < 0 || volume > ncbi->volumes) return eslEINVAL; ~~~~~~ ^ ~~~~~~~~~~~~~ vendor/easel/esl_sqio_ncbi.c:1458:24: warning: comparison of integers of different signs: 'unsigned int' and 'int' [-Wsign-compare] if (htobe32(info[1]) != dbtype) status = eslEFORMAT; ~~~~~~~~~~~~~~~~ ^ ~~~~~~ vendor/easel/esl_sqio_ncbi.c:1513:22: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare] if (inx < 0 || inx > ncbi->num_seq) return eslEINVAL; ~~~ ^ ~~~~~~~~~~~~~ vendor/easel/esl_sqio_ncbi.c:1519:53: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare] if (ncbi->index_start == -1 || inx < start || inx > end) { ~~~ ^ ~~~ vendor/easel/esl_sqio_ncbi.c:1519:38: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare] if (ncbi->index_start == -1 || inx < start || inx > end) { ~~~ ^ ~~~~~ vendor/easel/esl_sqio_ncbi.c:1519:25: warning: comparison of integers of different signs: 'uint32_t' (aka 'unsigned int') and 'int' [-Wsign-compare] if (ncbi->index_start == -1 || inx < start || inx > end) { ~~~~~~~~~~~~~~~~~ ^ ~~ vendor/easel/esl_sqio_ncbi.c:1524:42: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare] if (inx < volume->start_seq || inx > volume->end_seq) { ~~~ ^ ~~~~~~~~~~~~~~~ vendor/easel/esl_sqio_ncbi.c:1524:15: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare] if (inx < volume->start_seq || inx > volume->end_seq) { ~~~ ^ ~~~~~~~~~~~~~~~~~ vendor/easel/esl_sqio_ncbi.c:1526:20: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare] for (cnt = 0; cnt < ncbi->volumes; ++cnt) { ~~~ ^ ~~~~~~~~~~~~~ vendor/easel/esl_sqio_ncbi.c:1527:12: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare] if (inx < volume->end_seq) break; ~~~ ^ ~~~~~~~~~~~~~~~ vendor/easel/esl_sqio_ncbi.c:1532:10: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare] if (cnt >= ncbi->volumes) return eslFAIL; ~~~ ^ ~~~~~~~~~~~~~ vendor/easel/esl_sqio_ncbi.c:1539:40: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare] if (ncbi->index_start == -1 || inx > end) { ~~~ ^ ~~~ vendor/easel/esl_sqio_ncbi.c:1539:27: warning: comparison of integers of different signs: 'uint32_t' (aka 'unsigned int') and 'int' [-Wsign-compare] if (ncbi->index_start == -1 || inx > end) { ~~~~~~~~~~~~~~~~~ ^ ~~ vendor/easel/esl_sqio_ncbi.c:1564:70: warning: comparison of integers of different signs: 'unsigned long' and 'int' [-Wsign-compare] if (fread(ncbi->hdr_indexes, sizeof(uint32_t), cnt, ncbi->fppin) != cnt) { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ ~~~ vendor/easel/esl_sqio_ncbi.c:1572:70: warning: comparison of integers of different signs: 'unsigned long' and 'int' [-Wsign-compare] if (fread(ncbi->seq_indexes, sizeof(uint32_t), cnt, ncbi->fppin) != cnt) { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ ~~~ vendor/easel/esl_sqio_ncbi.c:1581:72: warning: comparison of integers of different signs: 'unsigned long' and 'int' [-Wsign-compare] if (fread(ncbi->amb_indexes, sizeof(uint32_t), cnt, ncbi->fppin) != cnt) { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ ~~~ vendor/easel/esl_sqio_ncbi.c:1623:19: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare] if (ncbi->index >= ncbi->num_seq) return eslEOF; ~~~~~~~~~~~ ^ ~~~~~~~~~~~~~ vendor/easel/esl_sqio_ncbi.c:1633:53: warning: comparison of integers of different signs: 'unsigned long' and 'int' [-Wsign-compare] if (fread(ptr, sizeof(char), size, ncbi->fppsq) != size) return eslEFORMAT; ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ ~~~~ vendor/easel/esl_sqio_ncbi.c:1641:53: warning: comparison of integers of different signs: 'unsigned long' and 'int' [-Wsign-compare] if (fread(ptr, sizeof(char), size, ncbi->fppsq) != size) return eslEFORMAT; ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ ~~~~ vendor/easel/esl_sqio_ncbi.c:1690:19: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare] if (ncbi->index >= ncbi->num_seq) return eslEOF; ~~~~~~~~~~~ ^ ~~~~~~~~~~~~~ vendor/easel/esl_sqio_ncbi.c:1701:61: warning: comparison of integers of different signs: 'unsigned long' and 'int' [-Wsign-compare] if (fread(ncbi->hdr_buf, sizeof(char), size, ncbi->fppsq) != size) return eslEFORMAT; ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ ~~~~ vendor/easel/esl_sqio_ncbi.c:1831:19: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare] if (ncbi->index >= ncbi->num_seq) return eslEOF; ~~~~~~~~~~~ ^ ~~~~~~~~~~~~~ vendor/easel/esl_sqio_ncbi.c:1856:51: warning: comparison of integers of different signs: 'unsigned long' and 'int' [-Wsign-compare] if (fread(ptr, sizeof(char), size, ncbi->fppsq) != size) return eslEFORMAT; ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ ~~~~ vendor/easel/esl_sqio_ncbi.c:1924:65: warning: comparison of integers of different signs: 'unsigned long' and 'int64_t' (aka 'long long') [-Wsign-compare] if (fread(ncbi->hdr_buf, sizeof(char), size, ncbi->fppsq) != size) return eslEFORMAT; ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ ~~~~ vendor/easel/esl_sqio_ncbi.c:2005:19: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare] if (ncbi->index >= ncbi->num_seq) return eslEOF; ~~~~~~~~~~~ ^ ~~~~~~~~~~~~~ vendor/easel/esl_sqio_ncbi.c:2047:62: warning: comparison of integers of different signs: 'unsigned long' and 'int' [-Wsign-compare] if (fread(ncbi->hdr_buf, sizeof(char), ssize, ncbi->fppsq) != ssize) return eslEFORMAT; ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ ~~~~~ vendor/easel/esl_sqio_ncbi.c:2178:17: warning: comparison of integers of different signs: 'int' and 'unsigned long' [-Wsign-compare] for (x = 0; x < strlen(ncbisym); ++x) { ~ ^ ~~~~~~~~~~~~~~~ vendor/easel/esl_sqio_ncbi.c:2179:19: warning: comparison of integers of different signs: 'int' and 'unsigned long' [-Wsign-compare] for (y = 0; y < strlen(abc->sym); ++y) { ~ ^ ~~~~~~~~~~~~~~~~ vendor/easel/esl_sqio_ncbi.c:2187:11: warning: comparison of integers of different signs: 'int' and 'unsigned long' [-Wsign-compare] if (y >= strlen(abc->sym)) return eslEFORMAT; ~ ^ ~~~~~~~~~~~~~~~~ vendor/easel/esl_sqio_ncbi.c:2226:17: warning: comparison of integers of different signs: 'int' and 'unsigned long' [-Wsign-compare] for (x = 0; x < strlen(ncbisym); ++x) { ~ ^ ~~~~~~~~~~~~~~~ vendor/easel/esl_sqio_ncbi.c:2227:19: warning: comparison of integers of different signs: 'int' and 'unsigned long' [-Wsign-compare] for (y = 0; y < strlen(abc->sym); ++y) { ~ ^ ~~~~~~~~~~~~~~~~ vendor/easel/esl_sqio_ncbi.c:2235:11: warning: comparison of integers of different signs: 'int' and 'unsigned long' [-Wsign-compare] if (y >= strlen(abc->sym)) return eslEFORMAT; ~ ^ ~~~~~~~~~~~~~~~~ vendor/easel/esl_sqio_ncbi.c:2463:61: warning: comparison of integers of different signs: 'unsigned long' and 'int' [-Wsign-compare] if (fread(ncbi->hdr_buf, sizeof(char), size, ncbi->fpphr) != size) return eslEFORMAT; ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ ~~~~ 7 warnings generated. vendor/easel/esl_hmm.c:265:20: warning: comparison of integers of different signs: 'unsigned long long' and 'int' [-Wsign-compare] mx->validR = ESL_MIN(mx->ncells / mx->allocM, mx->allocR); ^ ~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~ vendor/easel/easel.h:416:36: note: expanded from macro 'ESL_MIN' #define ESL_MIN(a,b) (((a)<(b))?(a):(b)) ~ ^ ~ generating build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_matrixops.o from vendor/easel/esl_matrixops.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/easel/esl_matrixops.c -o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_matrixops.o generating build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_histogram.o from vendor/easel/esl_histogram.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/easel/esl_histogram.c -o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_histogram.o generating build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_minimizer.o from vendor/easel/esl_minimizer.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/easel/esl_minimizer.c -o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_minimizer.o vendor/easel/esl_histogram.c:541:12: warning: comparison of integers of different signs: 'int' and 'uint64_t' (aka 'unsigned long long') [-Wsign-compare] if (rank > h->n) ~~~~ ^ ~~~~ generating build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_swat.o from vendor/easel/esl_swat.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/easel/esl_swat.c -o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_swat.o generating build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_ratematrix.o from vendor/easel/esl_ratematrix.c generating build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_getopts.o from vendor/easel/esl_getopts.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/easel/esl_ratematrix.c -o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_ratematrix.o 17 warnings generated. clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/easel/esl_getopts.c -o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_getopts.o generating build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_subcmd.o from vendor/easel/esl_subcmd.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/easel/esl_subcmd.c -o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_subcmd.o 1 warning generated. generating build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_stopwatch.o from vendor/easel/esl_stopwatch.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/easel/esl_stopwatch.c -o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_stopwatch.o generating build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_gamma.o from vendor/easel/esl_gamma.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/easel/esl_gamma.c -o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_gamma.o generating build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_huffman.o from vendor/easel/esl_huffman.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/easel/esl_huffman.c -o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_huffman.o vendor/easel/esl_getopts.c:1308:8: warning: comparison of integers of different signs: 'int' and 'unsigned long' [-Wsign-compare] if (n == strlen(g->opt[i].name)) { nexact++; break; } /* an exact match; can stop now (xref bug #e4) */ ~ ^ ~~~~~~~~~~~~~~~~~~~~~~ generating build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_dsqdata.o from vendor/easel/esl_dsqdata.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/easel/esl_dsqdata.c -o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_dsqdata.o vendor/easel/esl_dsqdata.c:253:21: warning: comparison of integers of different signs: 'uint32_t' (aka 'unsigned int') and 'int' [-Wsign-compare] if (alphatype != dd->abc_r->type) ~~~~~~~~~ ^ ~~~~~~~~~~~~~~~ 9 warnings generated. vendor/easel/esl_dsqdata.c:614:17: warning: comparison of integers of different signs: 'int64_t' (aka 'long long') and 'uint64_t' (aka 'unsigned long long') [-Wsign-compare] if (sq->n > max_seqlen) max_seqlen = sq->n; ~~~~~ ^ ~~~~~~~~~~ vendor/easel/esl_dsqdata.c:615:35: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare] n = strlen(sq->name); if (n > max_namelen) max_namelen = n; ~ ^ ~~~~~~~~~~~ vendor/easel/esl_dsqdata.c:616:35: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare] n = strlen(sq->acc); if (n > max_acclen) max_acclen = n; ~ ^ ~~~~~~~~~~ vendor/easel/esl_dsqdata.c:617:35: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare] n = strlen(sq->desc); if (n > max_desclen) max_desclen = n; ~ ^ ~~~~~~~~~~~ vendor/easel/esl_dsqdata.c:676:53: warning: comparison of integers of different signs: 'unsigned long' and 'int' [-Wsign-compare] if ( fwrite(psq, sizeof(uint32_t), plen, sfp) != plen) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ ~~~~ vendor/easel/esl_dsqdata.c:682:53: warning: comparison of integers of different signs: 'unsigned long' and 'int' [-Wsign-compare] if ( fwrite(sq->name, sizeof(char), n+1, mfp) != n+1) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ ~~~ vendor/easel/esl_dsqdata.c:687:53: warning: comparison of integers of different signs: 'unsigned long' and 'int' [-Wsign-compare] if ( fwrite(sq->acc, sizeof(char), n+1, mfp) != n+1) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ ~~~ vendor/easel/esl_dsqdata.c:692:53: warning: comparison of integers of different signs: 'unsigned long' and 'int' [-Wsign-compare] if ( fwrite(sq->desc, sizeof(char), n+1, mfp) != n+1) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ ~~~ generating build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_tree.o from vendor/easel/esl_tree.c generating build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_avx.o from vendor/easel/esl_avx.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/easel/esl_tree.c -o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_tree.o clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/easel/esl_avx.c -o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_avx.o generating build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_stretchexp.o from vendor/easel/esl_stretchexp.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/easel/esl_stretchexp.c -o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_stretchexp.o generating build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_msafile_clustal.o from vendor/easel/esl_msafile_clustal.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/easel/esl_msafile_clustal.c -o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_msafile_clustal.o 1 warning generated. generating build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_arr3.o from vendor/easel/esl_arr3.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/easel/esl_arr3.c -o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_arr3.o generating build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_msaweight.o from vendor/easel/esl_msaweight.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/easel/esl_msaweight.c -o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_msaweight.o generating build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_dirichlet.o from vendor/easel/esl_dirichlet.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/easel/esl_dirichlet.c -o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_dirichlet.o generating build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_stack.o from vendor/easel/esl_stack.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/easel/esl_stack.c -o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_stack.o generating build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_vmx.o from vendor/easel/esl_vmx.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/easel/esl_vmx.c -o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_vmx.o generating build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_mem.o from vendor/easel/esl_mem.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/easel/esl_mem.c -o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_mem.o 1 warning generated. generating build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_heap.o from vendor/easel/esl_heap.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/easel/esl_heap.c -o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_heap.o generating build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_regexp.o from vendor/easel/esl_regexp.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/easel/esl_regexp.c -o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_regexp.o generating build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_recorder.o from vendor/easel/esl_recorder.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/easel/esl_recorder.c -o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_recorder.o 41 warnings generated. generating build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_mixgev.o from vendor/easel/esl_mixgev.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/easel/esl_mixgev.c -o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_mixgev.o generating build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_random.o from vendor/easel/esl_random.c generating build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_msafile_afa.o from vendor/easel/esl_msafile_afa.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/easel/esl_random.c -o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_random.o clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/easel/esl_msafile_afa.c -o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_msafile_afa.o generating build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_cluster.o from vendor/easel/esl_cluster.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/easel/esl_cluster.c -o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_cluster.o 9 warnings generated. generating build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_varint.o from vendor/easel/esl_varint.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/easel/esl_varint.c -o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_varint.o vendor/easel/esl_cluster.c:151:18: warning: comparison of integers of different signs: 'int' and 'size_t' (aka 'unsigned long') [-Wsign-compare] for (v = 0; v < n; v++) a[v] = n-v-1; /* initialize by pushing all vertices onto available list (backwards) */ ~ ^ ~ vendor/easel/esl_random.c:652:17: warning: comparison of integers of different signs: 'int' and 'unsigned int' [-Wsign-compare] for (i = 0; i < a; i++) ~ ^ ~ generating build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_weibull.o from vendor/easel/esl_weibull.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/easel/esl_weibull.c -o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_weibull.o generating build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_keyhash.o from vendor/easel/esl_keyhash.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/easel/esl_keyhash.c -o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_keyhash.o vendor/easel/esl_varint.c:339:13: warning: variable 'v' set but not used [-Wunused-but-set-variable] int a,b,n,v, status; ^ 1 warning generated. generating build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_sse.o from vendor/easel/esl_sse.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/easel/esl_sse.c -o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_sse.o generating build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_scorematrix.o from vendor/easel/esl_scorematrix.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/easel/esl_scorematrix.c -o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_scorematrix.o generating build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_quicksort.o from vendor/easel/esl_quicksort.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/easel/esl_quicksort.c -o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_quicksort.o generating build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_msafile_psiblast.o from vendor/easel/esl_msafile_psiblast.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/easel/esl_msafile_psiblast.c -o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_msafile_psiblast.o 1 warning generated. generating build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_json.o from vendor/easel/esl_json.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/easel/esl_json.c -o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_json.o generating build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_workqueue.o from vendor/easel/esl_workqueue.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/easel/esl_workqueue.c -o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_workqueue.o vendor/easel/esl_keyhash.c:94:17: warning: comparison of integers of different signs: 'int' and 'const uint32_t' (aka 'const unsigned int') [-Wsign-compare] for (h = 0; h < kh->hashsize; h++) ~ ^ ~~~~~~~~~~~~ vendor/easel/esl_keyhash.c:171:17: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare] for (i = 0; i < kh->hashsize; i++) kh->hashtable[i] = -1; ~ ^ ~~~~~~~~~~~~ vendor/easel/esl_keyhash.c:215:17: warning: comparison of integers of different signs: 'int' and 'const uint32_t' (aka 'const unsigned int') [-Wsign-compare] for (h = 0; h < kh->hashsize; h++) ~ ^ ~~~~~~~~~~~~ vendor/easel/esl_keyhash.c:310:17: warning: comparison of integers of different signs: 'int' and 'unsigned int' [-Wsign-compare] if (kh->nkeys > 3*kh->hashsize) ~~~~~~~~~ ^ ~~~~~~~~~~~~~~ vendor/easel/esl_keyhash.c:401:17: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare] for (i = 0; i < kh->hashsize; i++) kh->hashtable[i] = -1; ~ ^ ~~~~~~~~~~~~ vendor/easel/esl_keyhash.c:491:17: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare] for (i = 0; i < kh->hashsize; i++) kh->hashtable[i] = -1; ~ ^ ~~~~~~~~~~~~ generating build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_composition.o from vendor/easel/esl_composition.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/easel/esl_composition.c -o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_composition.o generating build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_sqio.o from vendor/easel/esl_sqio.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/easel/esl_sqio.c -o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_sqio.o generating build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_arr2.o from vendor/easel/esl_arr2.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/easel/esl_arr2.c -o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_arr2.o 6 warnings generated. generating build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_mixdchlet.o from vendor/easel/esl_mixdchlet.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/easel/esl_mixdchlet.c -o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_mixdchlet.o generating build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_red_black.o from vendor/easel/esl_red_black.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/easel/esl_red_black.c -o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_red_black.o generating build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_msafile2.o from vendor/easel/esl_msafile2.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/easel/esl_msafile2.c -o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_msafile2.o 1 warning generated. generating build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_alphabet.o from vendor/easel/esl_alphabet.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/easel/esl_alphabet.c -o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_alphabet.o generating build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_msafile.o from vendor/easel/esl_msafile.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/easel/esl_msafile.c -o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_msafile.o generating build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_normal.o from vendor/easel/esl_normal.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/easel/esl_normal.c -o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_normal.o vendor/easel/esl_msafile2.c:630:43: warning: comparison of integers of different signs: 'int' and 'unsigned long' [-Wsign-compare] for(i = 0; i < msa->ngc; i++) maxgc = ESL_MAX(maxgc, strlen(msa->gc_tag[i])); ^ ~~~~~ ~~~~~~~~~~~~~~~~~~~~~~ vendor/easel/easel.h:417:36: note: expanded from macro 'ESL_MAX' #define ESL_MAX(a,b) (((a)>(b))?(a):(b)) ~ ^ ~ vendor/easel/esl_msafile2.c:639:43: warning: comparison of integers of different signs: 'int' and 'unsigned long' [-Wsign-compare] for(i = 0; i < msa->ngf; i++) maxgf = ESL_MAX(maxgf, strlen(msa->gf_tag[i])); ^ ~~~~~ ~~~~~~~~~~~~~~~~~~~~~~ vendor/easel/easel.h:417:36: note: expanded from macro 'ESL_MAX' #define ESL_MAX(a,b) (((a)>(b))?(a):(b)) ~ ^ ~ vendor/easel/esl_alphabet.c:107:24: warning: comparison of integers of different signs: 'unsigned long' and 'int' [-Wsign-compare] if (strlen(alphabet) != Kp) ESL_XEXCEPTION(eslEINVAL, "alphabet length != Kp"); ~~~~~~~~~~~~~~~~ ^ ~~ generating build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_threads.o from vendor/easel/esl_threads.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/easel/esl_threads.c -o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_threads.o generating build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_wuss.o from vendor/easel/esl_wuss.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/easel/esl_wuss.c -o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_wuss.o generating build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_fileparser.o from vendor/easel/esl_fileparser.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/easel/esl_fileparser.c -o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_fileparser.o generating build/temp.macosx-12-arm64-cpython-310/build/temp.macosx-12-arm64-cpython-310/esl_sqio_ascii.o from build/temp.macosx-12-arm64-cpython-310/esl_sqio_ascii.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ibuild/temp.macosx-12-arm64-cpython-310 -c build/temp.macosx-12-arm64-cpython-310/esl_sqio_ascii.c -o build/temp.macosx-12-arm64-cpython-310/build/temp.macosx-12-arm64-cpython-310/esl_sqio_ascii.o generating build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_msacluster.o from vendor/easel/esl_msacluster.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/easel/esl_msacluster.c -o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_msacluster.o generating build/temp.macosx-12-arm64-cpython-310/vendor/easel/interface_gsl.o from vendor/easel/interface_gsl.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/easel/interface_gsl.c -o build/temp.macosx-12-arm64-cpython-310/vendor/easel/interface_gsl.o generating build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_cpu.o from vendor/easel/esl_cpu.c generating build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_dmatrix.o from vendor/easel/esl_dmatrix.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/easel/esl_dmatrix.c -o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_dmatrix.o clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/easel/esl_cpu.c -o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_cpu.o generating build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_rootfinder.o from vendor/easel/esl_rootfinder.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/easel/esl_rootfinder.c -o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_rootfinder.o In file included from build/temp.macosx-12-arm64-cpython-310/esl_sqio_ascii.c:30: In file included from vendor/easel/easel.h:19: vendor/easel/esl_config.h:19:9: warning: 'EASEL_COPYRIGHT' macro redefined [-Wmacro-redefined] #define EASEL_COPYRIGHT "Copyright (C) 2020 Howard Hughes Medical Institute." ^ build/temp.macosx-12-arm64-cpython-310/esl_config.h:4:9: note: previous definition is here #define EASEL_COPYRIGHT "Copyright (C) 2020 Howard Hughes Medical Institute" ^ generating build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_rand64.o from vendor/easel/esl_rand64.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/easel/esl_rand64.c -o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_rand64.o generating build/temp.macosx-12-arm64-cpython-310/vendor/easel/interface_lapack.o from vendor/easel/interface_lapack.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/easel/interface_lapack.c -o build/temp.macosx-12-arm64-cpython-310/vendor/easel/interface_lapack.o build/temp.macosx-12-arm64-cpython-310/esl_sqio_ascii.c:1669:60: warning: comparison of integers of different signs: 'unsigned long' and 'int' [-Wsign-compare] if (fwrite(ascii->buf, sizeof(char), ascii->nc, ofp) != ascii->nc) ESL_EXCEPTION(eslESYS, "fwrite() failed"); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ ~~~~~~~~~ generating build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_msafile_selex.o from vendor/easel/esl_msafile_selex.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/easel/esl_msafile_selex.c -o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_msafile_selex.o generating build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_bitfield.o from vendor/easel/esl_bitfield.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/easel/esl_bitfield.c -o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_bitfield.o generating build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_hyperexp.o from vendor/easel/esl_hyperexp.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/easel/esl_hyperexp.c -o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_hyperexp.o 1 warning generated. generating build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_graph.o from vendor/easel/esl_graph.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/easel/esl_graph.c -o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_graph.o 2 warnings generated. generating build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_buffer.o from vendor/easel/esl_buffer.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/easel/esl_buffer.c -o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_buffer.o vendor/easel/esl_buffer.c:1494:23: warning: comparison of integers of different signs: 'long long' and 'size_t' (aka 'unsigned long') [-Wsign-compare] if (bf->n - bf->pos < nbytes) ~~~~~~~~~~~~~~~ ^ ~~~~~~ vendor/easel/esl_buffer.c:1499:31: warning: comparison of integers of different signs: 'long long' and 'size_t' (aka 'unsigned long') [-Wsign-compare] else if (bf->n-bf->pos < nbytes) return eslEOF; ~~~~~~~~~~~~~ ^ ~~~~~~ generating build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_gumbel.o from vendor/easel/esl_gumbel.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/easel/esl_gumbel.c -o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_gumbel.o 2 warnings generated. 2 warnings generated. /usr/bin/xcrun ar rcs build/temp.macosx-12-arm64-cpython-310/libeasel.a build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_exponential.o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_msashuffle.o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_msafile_stockholm.o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_msafile_a2m.o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_ssi.o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_subcmd.o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_sq.o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_matrixops.o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_getopts.o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_randomseq.o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_hmm.o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_stopwatch.o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_neon.o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_mpi.o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_gencode.o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_stats.o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_avx512.o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_alloc.o build/temp.macosx-12-arm64-cpython-310/vendor/easel/easel.o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_distance.o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_histogram.o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_gev.o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_paml.o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_msafile_phylip.o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_msa.o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_tree.o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_arr2.o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_vectorops.o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_ratematrix.o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_msaweight.o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_sqio_ncbi.o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_mixgev.o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_msafile_psiblast.o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_minimizer.o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_dsqdata.o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_varint.o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_swat.o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_gamma.o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_msafile_clustal.o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_huffman.o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_stack.o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_msafile_afa.o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_avx.o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_dirichlet.o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_regexp.o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_stretchexp.o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_mem.o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_keyhash.o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_arr3.o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_vmx.o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_recorder.o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_heap.o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_cluster.o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_sse.o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_random.o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_alphabet.o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_graph.o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_weibull.o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_composition.o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_red_black.o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_scorematrix.o build/temp.macosx-12-arm64-cpython-310/vendor/easel/interface_gsl.o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_rand64.o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_quicksort.o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_sqio.o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_fileparser.o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_json.o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_rootfinder.o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_hyperexp.o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_workqueue.o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_msafile2.o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_buffer.o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_mixdchlet.o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_dmatrix.o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_gumbel.o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_msafile.o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_cpu.o build/temp.macosx-12-arm64-cpython-310/vendor/easel/interface_lapack.o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_normal.o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_wuss.o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_bitfield.o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_threads.o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_msacluster.o build/temp.macosx-12-arm64-cpython-310/vendor/easel/esl_msafile_selex.o build/temp.macosx-12-arm64-cpython-310/build/temp.macosx-12-arm64-cpython-310/esl_sqio_ascii.o ranlib build/temp.macosx-12-arm64-cpython-310/libeasel.a generating build/temp.macosx-12-arm64-cpython-310/libhmmer.a from vendor/hmmer/src/build.c, vendor/hmmer/src/cachedb.c, vendor/hmmer/src/cachedb_shard.c, vendor/hmmer/src/emit.c, vendor/hmmer/src/errors.c, vendor/hmmer/src/evalues.c, vendor/hmmer/src/eweight.c, vendor/hmmer/src/generic_decoding.c, vendor/hmmer/src/generic_fwdback.c, vendor/hmmer/src/generic_fwdback_chk.c, vendor/hmmer/src/generic_fwdback_banded.c, vendor/hmmer/src/generic_null2.c, vendor/hmmer/src/generic_msv.c, vendor/hmmer/src/generic_optacc.c, vendor/hmmer/src/generic_stotrace.c, vendor/hmmer/src/generic_viterbi.c, vendor/hmmer/src/generic_vtrace.c, vendor/hmmer/src/h2_io.c, vendor/hmmer/src/heatmap.c, vendor/hmmer/src/hmmlogo.c, vendor/hmmer/src/hmmdmstr.c, vendor/hmmer/src/hmmdmstr_shard.c, vendor/hmmer/src/hmmd_search_status.c, vendor/hmmer/src/hmmdwrkr.c, vendor/hmmer/src/hmmdwrkr_shard.c, vendor/hmmer/src/hmmdutils.c, vendor/hmmer/src/hmmer.c, vendor/hmmer/src/logsum.c, vendor/hmmer/src/modelconfig.c, vendor/hmmer/src/modelstats.c, vendor/hmmer/src/mpisupport.c, vendor/hmmer/src/seqmodel.c, vendor/hmmer/src/tracealign.c, vendor/hmmer/src/p7_alidisplay.c, vendor/hmmer/src/p7_bg.c, vendor/hmmer/src/p7_builder.c, vendor/hmmer/src/p7_domain.c, vendor/hmmer/src/p7_domaindef.c, vendor/hmmer/src/p7_gbands.c, vendor/hmmer/src/p7_gmx.c, vendor/hmmer/src/p7_gmxb.c, vendor/hmmer/src/p7_gmxchk.c, vendor/hmmer/src/p7_hit.c, vendor/hmmer/src/p7_hmm.c, vendor/hmmer/src/p7_hmmcache.c, vendor/hmmer/src/p7_hmmd_search_stats.c, vendor/hmmer/src/p7_hmmwindow.c, vendor/hmmer/src/p7_pipeline.c, vendor/hmmer/src/p7_prior.c, vendor/hmmer/src/p7_profile.c, vendor/hmmer/src/p7_spensemble.c, vendor/hmmer/src/p7_tophits.c, vendor/hmmer/src/p7_trace.c, vendor/hmmer/src/p7_scoredata.c, vendor/hmmer/src/hmmpgmd2msa.c, vendor/hmmer/src/fm_alphabet.c, vendor/hmmer/src/fm_general.c, vendor/hmmer/src/fm_sse.c, vendor/hmmer/src/fm_ssv.c, build/temp.macosx-12-arm64-cpython-310/p7_hmmfile.c generating build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/build.o from vendor/hmmer/src/build.c generating build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/cachedb_shard.o from vendor/hmmer/src/cachedb_shard.c generating build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/generic_fwdback_banded.o from vendor/hmmer/src/generic_fwdback_banded.c generating build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/errors.o from vendor/hmmer/src/errors.c generating build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/generic_msv.o from vendor/hmmer/src/generic_msv.c generating build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/generic_vtrace.o from vendor/hmmer/src/generic_vtrace.c generating build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/eweight.o from vendor/hmmer/src/eweight.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/hmmer/src/generic_fwdback_banded.c -o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/generic_fwdback_banded.o clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/hmmer/src/build.c -o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/build.o generating build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/generic_fwdback.o from vendor/hmmer/src/generic_fwdback.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/hmmer/src/errors.c -o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/errors.o clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/hmmer/src/eweight.c -o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/eweight.o generating build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/generic_stotrace.o from vendor/hmmer/src/generic_stotrace.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/hmmer/src/generic_vtrace.c -o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/generic_vtrace.o clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/hmmer/src/cachedb_shard.c -o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/cachedb_shard.o clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/hmmer/src/generic_msv.c -o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/generic_msv.o clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/hmmer/src/generic_fwdback.c -o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/generic_fwdback.o clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/hmmer/src/generic_stotrace.c -o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/generic_stotrace.o generating build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/heatmap.o from vendor/hmmer/src/heatmap.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/hmmer/src/heatmap.c -o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/heatmap.o generating build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/hmmlogo.o from vendor/hmmer/src/hmmlogo.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/hmmer/src/hmmlogo.c -o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/hmmlogo.o vendor/hmmer/src/cachedb_shard.c:117:17: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare] for (i = 0; i < db_cnt; ++i) { ~ ^ ~~~~~~ vendor/hmmer/src/cachedb_shard.c:159:17: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare] for (i = 0; i < db_cnt; ++i) db_inx[i] = 0; ~ ^ ~~~~~~ vendor/hmmer/src/cachedb_shard.c:167:13: warning: comparison of integers of different signs: 'int' and 'uint64_t' (aka 'unsigned long long') [-Wsign-compare] if (inx >= seq_cnt) { printf("inx: %d\n", inx); return eslEFORMAT; } ~~~ ^ ~~~~~~~ vendor/hmmer/src/cachedb_shard.c:225:11: warning: comparison of integers of different signs: 'int' and 'uint64_t' (aka 'unsigned long long') [-Wsign-compare] if (inx != seq_cnt) { printf("inx:: %d %" PRIu64 "\n", inx, seq_cnt); return eslEFORMAT; } ~~~ ^ ~~~~~~~ vendor/hmmer/src/cachedb_shard.c:235:18: warning: comparison of integers of different signs: 'int' and 'uint64_t' (aka 'unsigned long long') [-Wsign-compare] for (i = 0 ; i < seq_cnt; ++i) { ~ ^ ~~~~~~~ vendor/hmmer/src/cachedb_shard.c:243:18: warning: comparison of integers of different signs: 'int' and 'uint64_t' (aka 'unsigned long long') [-Wsign-compare] for (i = 0 ; i < seq_cnt; ++i) { ~ ^ ~~~~~~~ vendor/hmmer/src/cachedb_shard.c:259:17: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare] for (i = 0; i < cache->db_cnt; ++i) { ~ ^ ~~~~~~~~~~~~~ vendor/hmmer/src/cachedb_shard.c:282:17: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare] for (i = 0; i < db_cnt; ++i) { ~ ^ ~~~~~~ generating build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/generic_decoding.o from vendor/hmmer/src/generic_decoding.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/hmmer/src/generic_decoding.c -o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/generic_decoding.o generating build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/evalues.o from vendor/hmmer/src/evalues.c vendor/hmmer/src/cachedb_shard.c:297:21: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare] for (i = 0; i < cache->db_cnt; ++i) { ~ ^ ~~~~~~~~~~~~~ vendor/hmmer/src/cachedb_shard.c:388:17: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare] for (i = 0; i < db_cnt; ++i) { ~ ^ ~~~~~~ vendor/hmmer/src/cachedb_shard.c:398:17: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare] for (i = 0; i < db_cnt; i++){ ~ ^ ~~~~~~ vendor/hmmer/src/cachedb_shard.c:434:17: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare] for (i = 0; i < db_cnt; ++i) db_inx[i] = 0; ~ ^ ~~~~~~ vendor/hmmer/src/cachedb_shard.c:445:13: warning: comparison of integers of different signs: 'int' and 'uint64_t' (aka 'unsigned long long') [-Wsign-compare] if (inx >= seq_cnt) { printf("inx: %d\n", inx); rclang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/hmmer/src/evalues.c -o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/evalues.o eturn eslEFORMAT; } ~~~ ^ ~~~~~~~ vendor/hmmer/src/cachedb_shard.c:446:19: warning: comparison of integers of different signs: 'long long' and 'uint64_t' (aka 'unsigned long long') [-Wsign-compare] if (sq->n + 1 > res_size) { printf("inx: %d size %d %d\n", inx, (int)sq->n + 1, (int)res_size); return eslEFORMAT; } ~~~~~~~~~ ^ ~~~~~~~~ vendor/hmmer/src/cachedb_shard.c:463:41: warning: comparison of integers of different signs: 'unsigned long long' and 'int' [-Wsign-compare] if(db_seq_count[i] % num_shards == my_shard){ //this sequence is part of database i and belongs to this node's shard ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ ~~~~~~~~ vendor/hmmer/src/cachedb_shard.c:544:16: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare] for(i = 0; i < db_cnt; i++){ ~ ^ ~~~~~~ vendor/hmmer/src/cachedb_shard.c:560:18: warning: comparison of integers of different signs: 'int' and 'uint64_t' (aka 'unsigned long long') [-Wsign-compare] for (i = 0 ; i < seq_cnt; ++i) { ~ ^ ~~~~~~~ vendor/hmmer/src/cachedb_shard.c:568:18: warning: comparison of integers of different signs: 'int' and 'uint64_t' (aka 'unsigned long long') [-Wsign-compare] for (i = 0 ; i < seq_cnt; ++i) { ~ ^ ~~~~~~~ vendor/hmmer/src/cachedb_shard.c:585:17: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare] for (i = 0; i < cache->db_cnt; ++i) { ~ ^ ~~~~~~~~~~~~~ vendor/hmmer/src/cachedb_shard.c:615:17: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare] for (i = 0; i < db_cnt; ++i) { ~ ^ ~~~~~~ generating build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/generic_viterbi.o from vendor/hmmer/src/generic_viterbi.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/hmmer/src/generic_viterbi.c -o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/generic_viterbi.o generating build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/generic_null2.o from vendor/hmmer/src/generic_null2.c generating build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/generic_optacc.o from vendor/hmmer/src/generic_optacc.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/hmmer/src/generic_optacc.c -o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/generic_optacc.o clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/hmmer/src/generic_null2.c -o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/generic_null2.o generating build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/h2_io.o from vendor/hmmer/src/h2_io.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/hmmer/src/h2_io.c -o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/h2_io.o generating build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/cachedb.o from vendor/hmmer/src/cachedb.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/hmmer/src/cachedb.c -o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/cachedb.o generating build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/generic_fwdback_chk.o from vendor/hmmer/src/generic_fwdback_chk.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/hmmer/src/generic_fwdback_chk.c -o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/generic_fwdback_chk.o generating build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/hmmdmstr.o from vendor/hmmer/src/hmmdmstr.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/hmmer/src/hmmdmstr.c -o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/hmmdmstr.o generating build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/hmmd_search_status.o from vendor/hmmer/src/hmmd_search_status.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/hmmer/src/hmmd_search_status.c -o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/hmmd_search_status.o 20 warnings generated. generating build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/emit.o from vendor/hmmer/src/emit.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/hmmer/src/emit.c -o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/emit.o generating build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/hmmdwrkr_shard.o from vendor/hmmer/src/hmmdwrkr_shard.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/hmmer/src/hmmdwrkr_shard.c -o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/hmmdwrkr_shard.o vendor/hmmer/src/h2_io.c:213:40: warning: comparison of integers of different signs: 'unsigned long' and 'int' [-Wsign-compare] if (fwrite(sptr, sizeof(char), n, fp) != n) ESL_EXCEPTION_SYS(eslEWRITE, "h2 profile write failed"); /* using fwrite lets us write fixed # of chars */ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ ~ vendor/hmmer/src/cachedb.c:95:14: warning: comparison of integers of different signs: 'int32_t' (aka 'int') and 'unsigned long' [-Wsign-compare] if (db_cnt > (sizeof(db_inx)/sizeof(db_inx[0]))) return eslEFORMAT; ~~~~~~ ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ vendor/hmmer/src/cachedb.c:157:13: warning: comparison of integers of different signs: 'int' and 'uint64_t' (aka 'unsigned long long') [-Wsign-compare] if (inx >= seq_cnt) { printf("inx: %d\n", inx); return eslEFORMAT; } ~~~ ^ ~~~~~~~ vendor/hmmer/src/cachedb.c:158:19: warning: comparison of integers of different signs: 'long long' and 'uint64_t' (aka 'unsigned long long') [-Wsign-compare] if (sq->n + 1 > res_size) { printf("inx: %d size %d %d\n", inx, (int)sq->n + 1, (int)res_size); return eslEFORMAT; } ~~~~~~~~~ ^ ~~~~~~~~ vendor/hmmer/src/cachedb.c:212:11: warning: comparison of integers of different signs: 'int' and 'uint64_t' (aka 'unsigned long long') [-Wsign-compare] if (inx != seq_cnt) { printf("inx:: %d %" PRIu64 "\n", inx, seq_cnt); return eslEFORMAT; } ~~~ ^ ~~~~~~~ vendor/hmmer/src/cachedb.c:222:18: warning: comparison of integers of different signs: 'int' and 'uint64_t' (aka 'unsigned long long') [-Wsign-compare] for (i = 0 ; i < seq_cnt; ++i) { ~ ^ ~~~~~~~ vendor/hmmer/src/cachedb.c:230:18: warning: comparison of integers of different signs: 'int' and 'uint64_t' (aka 'unsigned long long') [-Wsign-compare] for (i = 0 ; i < seq_cnt; ++i) { ~ ^ ~~~~~~~ vendor/hmmer/src/cachedb.c:236:25: warning: comparison of integers of different signs: 'int32_t' (aka 'int') and 'uint32_t' (aka 'unsigned int') [-Wsign-compare] if (db_inx[inx] >= db->count) { printf("sort:: %d %d\n", db_inx[inx], db->count); return eslEFORMAT; } ~~~~~~~~~~~ ^ ~~~~~~~~~ vendor/hmmer/src/cachedb.c:246:17: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare] for (i = 0; i < cache->db_cnt; ++i) { ~ ^ ~~~~~~~~~~~~~ generating build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/hmmer.o from vendor/hmmer/src/hmmer.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/hmmer/src/hmmer.c -o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/hmmer.o vendor/hmmer/src/cachedb.c:284:21: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare] for (i = 0; i < cache->db_cnt; ++i) { ~ ^ ~~~~~~~~~~~~~ 1 warning generated. generating build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/modelconfig.o from vendor/hmmer/src/modelconfig.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/hmmer/src/modelconfig.c -o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/modelconfig.o generating build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/mpisupport.o from vendor/hmmer/src/mpisupport.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/hmmer/src/mpisupport.c -o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/mpisupport.o generating build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/tracealign.o from vendor/hmmer/src/tracealign.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/hmmer/src/tracealign.c -o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/tracealign.o 9 warnings generated. generating build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/p7_bg.o from vendor/hmmer/src/p7_bg.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/hmmer/src/p7_bg.c -o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/p7_bg.o vendor/hmmer/src/hmmdmstr.c:192:16: warning: variable 'tail' set but not used [-Wunused-but-set-variable] WORKER_DATA *tail = NULL; ^ generating build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/seqmodel.o from vendor/hmmer/src/seqmodel.c vendor/hmmer/src/hmmdmstr.c:311:73: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare] if((args->seq_db == NULL)||(args->seq_db->db == NULL)|| (query->dbx >= args->seq_db->db_cnt) || (query->dbx < 0)){ ~~~~~~~~~~ ^ ~~~~~~~~~~~~~~~~~~~~ clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/hmmer/src/seqmodel.c -o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/seqmodel.o vendor/hmmer/src/hmmdmstr.c:735:48: warning: comparison of integers of different signs: 'int' and 'uint64_t' (aka 'unsigned long long') [-Wsign-compare] for(int i0 = 0, i1 = previous_hits; i1 < results->stats.nhits; i0++, i1++){ ~~ ^ ~~~~~~~~~~~~~~~~~~~~ vendor/hmmer/src/hmmdmstr.c:852:18: warning: comparison of integers of different signs: 'int' and 'uint64_t' (aka 'unsigned long long') [-Wsign-compare] for(int i =0; i< results->stats.nhits; i++){ ~^ ~~~~~~~~~~~~~~~~~~~~ vendor/hmmer/src/hmmdmstr.c:885:31: warning: comparison of integers of different signs: 'size_t' (aka 'unsigned long') and 'int' [-Wsign-compare] if (writen(fd, buf3_ptr, n) != n) { ~~~~~~~~~~~~~~~~~~~~~~~ ^ ~ vendor/hmmer/src/hmmdmstr.c:893:31: warning: comparison of integers of different signs: 'size_t' (aka 'unsigned long') and 'int' [-Wsign-compare] if (writen(fd, buf2_ptr, n) != n) { ~~~~~~~~~~~~~~~~~~~~~~~ ^ ~ vendor/hmmer/src/hmmdmstr.c:901:30: warning: comparison of integers of different signs: 'size_t' (aka 'unsigned long') and 'int' [-Wsign-compare] if (writen(fd, buf_ptr, n) != n) { ~~~~~~~~~~~~~~~~~~~~~~ ^ ~ vendor/hmmer/src/hmmdmstr.c:911:20: warning: comparison of integers of different signs: 'int' and 'uint64_t' (aka 'unsigned long long') [-Wsign-compare] for(int i = 0; i < results->stats.nhits; i++){ ~ ^ ~~~~~~~~~~~~~~~~~~~~ vendor/hmmer/src/hmmdmstr.c:943:24: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare] for(int i = 0; i < worker->allocated_hits; i++){ ~ ^ ~~~~~~~~~~~~~~~~~~~~~~ vendor/hmmer/src/hmmdmstr.c:970:23: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare] for(int i =0; i < worker->allocated_hits; i++){ ~ ^ ~~~~~~~~~~~~~~~~~~~~~~ vendor/hmmer/src/hmmdmstr.c:1424:3: warning: code will never be executed [-Wunreachable-code] pthread_exit(NULL); ^~~~~~~~~~~~ vendor/hmmer/src/hmmdmstr.c:1502:51: warning: comparison of integers of different signs: 'size_t' (aka 'unsigned long') and 'int' [-Wsign-compare] if (writen(worker->sock_fd, worker->cmd, n) != n) { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ ~ vendor/hmmer/src/hmmdmstr.c:1542:42: warning: comparison of integers of different signs: 'size_t' (aka 'unsigned long') and 'int' [-Wsign-compare] if (writen(worker->sock_fd, &cmd, n) != n) { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ ~ vendor/hmmer/src/hmmdmstr.c:1551:41: warning: comparison of integers of different signs: 'size_t' (aka 'unsigned long') and 'int' [-Wsign-compare] if (writen(worker->sock_fd, ptr, n) != n) { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ ~ vendor/hmmer/src/hmmdmstr.c:1612:26: warning: comparison of integers of different signs: 'int' and 'uint64_t' (aka 'unsigned long long') [-Wsign-compare] for(int i = 0; i < stats->nhits; i++){ ~ ^ ~~~~~~~~~~~~ vendor/hmmer/src/hmmdmstr.c:1723:41: warning: comparison of integers of different signs: 'size_t' (aka 'unsigned long') and 'int' [-Wsign-compare] if (writen(worker->sock_fd, cmd, n) != n) { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ ~ vendor/hmmer/src/hmmdmstr.c:1729:51: warning: comparison of integers of different signs: 'size_t' (aka 'unsigned long') and 'int' [-Wsign-compare] if (readn(worker->sock_fd, &hdr, sizeof(hdr)) == -1) { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ ~~ vendor/hmmer/src/hmmdmstr.c:1745:58: warning: comparison of integers of different signs: 'size_t' (aka 'unsigned long') and 'int' [-Wsign-compare] if (readn(worker->sock_fd, &(cmd->init), hdr.length) == -1) { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ ~~ vendor/hmmer/src/hmmdmstr.c:1856:3: warning: code will never be executed [-Wunreachable-code] pthread_exit(NULL); ^~~~~~~~~~~~ vendor/hmmer/src/hmmdmstr.c:184:1: warning: unused function 'validate_workers' [-Wunused-function] validate_workers(WORKERSIDE_ARGS *args) ^ vendor/hmmer/src/hmmdwrkr_shard.c:137:41: warning: comparison of integers of different signs: 'size_t' (aka 'unsigned long') and 'int' [-Wsign-compare] if (readn(env->fd, &hdr, sizeof(hdr)) == -1) { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ ~~ vendor/hmmer/src/hmmdwrkr_shard.c:149:48: warning: comparison of integers of different signs: 'size_t' (aka 'unsigned long') and 'int' [-Wsign-compare] if (readn(env->fd, &cmd->init, hdr.length) == -1) { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ ~~ generating build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/hmmdwrkr.o from vendor/hmmer/src/hmmdwrkr.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/hmmer/src/hmmdwrkr.c -o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/hmmdwrkr.o vendor/hmmer/src/hmmdwrkr_shard.c:480:31: warning: comparison of integers of different signs: 'size_t' (aka 'unsigned long') and 'int' [-Wsign-compare] if (writen(env->fd, cmd, n) != n) { ~~~~~~~~~~~~~~~~~~~~~~~ ^ ~ vendor/hmmer/src/hmmdwrkr_shard.c:565:31: warning: comparison of integers of different signs: 'size_t' (aka 'unsigned long') and 'int' [-Wsign-compare] if (writen(env->fd, cmd, n) != n) { ~~~~~~~~~~~~~~~~~~~~~~~ ^ ~ vendor/hmmer/src/hmmdwrkr_shard.c:852:18: warning: comparison of integers of different signs: 'int' and 'uint64_t' (aka 'unsigned long long') [-Wsign-compare] for(int i =0; i< stats.nhits; i++){ ~^ ~~~~~~~~~~~ generating build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/p7_gbands.o from vendor/hmmer/src/p7_gbands.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/hmmer/src/p7_gbands.c -o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/p7_gbands.o generating build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/p7_domain.o from vendor/hmmer/src/p7_domain.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/hmmer/src/p7_domain.c -o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/p7_domain.o generating build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/logsum.o from vendor/hmmer/src/logsum.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/hmmer/src/logsum.c -o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/logsum.o generating build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/p7_gmx.o from vendor/hmmer/src/p7_gmx.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/hmmer/src/p7_gmx.c -o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/p7_gmx.o generating build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/modelstats.o from vendor/hmmer/src/modelstats.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/hmmer/src/modelstats.c -o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/modelstats.o generating build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/p7_gmxb.o from vendor/hmmer/src/p7_gmxb.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/hmmer/src/p7_gmxb.c -o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/p7_gmxb.o generating build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/p7_builder.o from vendor/hmmer/src/p7_builder.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/hmmer/src/p7_builder.c -o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/p7_builder.o 5 warnings generated. generating build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/hmmdutils.o from vendor/hmmer/src/hmmdutils.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/hmmer/src/hmmdutils.c -o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/hmmdutils.o vendor/hmmer/src/hmmdwrkr.c:120:41: warning: comparison of integers of different signs: 'size_t' (aka 'unsigned long') and 'int' [-Wsign-compare] if (readn(env->fd, &hdr, sizeof(hdr)) == -1) { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ ~~ vendor/hmmer/src/hmmdwrkr.c:132:48: warning: comparison of integers of different signs: 'size_t' (aka 'unsigned long') and 'int' [-Wsign-compare] if (readn(env->fd, &cmd->init, hdr.length) == -1) { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ ~~ vendor/hmmer/src/hmmdwrkr.c:453:31: warning: comparison of integers of different signs: 'size_t' (aka 'unsigned long') and 'int' [-Wsign-compare] if (writen(env->fd, cmd, n) != n) { ~~~~~~~~~~~~~~~~~~~~~~~ ^ ~ vendor/hmmer/src/hmmdwrkr.c:536:31: warning: comparison of integers of different signs: 'size_t' (aka 'unsigned long') and 'int' [-Wsign-compare] if (writen(env->fd, cmd, n) != n) { ~~~~~~~~~~~~~~~~~~~~~~~ ^ ~ vendor/hmmer/src/hmmdwrkr.c:816:18: warning: comparison of integers of different signs: 'int' and 'uint64_t' (aka 'unsigned long long') [-Wsign-compare] for(int i =0; i< stats.nhits; i++){ ~^ ~~~~~~~~~~~ generating build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/p7_hit.o from vendor/hmmer/src/p7_hit.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/hmmer/src/p7_hit.c -o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/p7_hit.o generating build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/p7_domaindef.o from vendor/hmmer/src/p7_domaindef.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/hmmer/src/p7_domaindef.c -o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/p7_domaindef.o vendor/hmmer/src/p7_gmx.c:144:20: warning: comparison of integers of different signs: 'unsigned long long' and 'int' [-Wsign-compare] gx->validR = ESL_MIN(gx->ncells / gx->allocW, gx->allocR); ^ ~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~ vendor/easel/easel.h:416:36: note: expanded from macro 'ESL_MIN' #define ESL_MIN(a,b) (((a)<(b))?(a):(b)) ~ ^ ~ 20 warnings generated. generating build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/hmmdmstr_shard.o from vendor/hmmer/src/hmmdmstr_shard.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/hmmer/src/hmmdmstr_shard.c -o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/hmmdmstr_shard.o generating build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/p7_alidisplay.o from vendor/hmmer/src/p7_alidisplay.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/hmmer/src/p7_alidisplay.c -o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/p7_alidisplay.o 5 warnings generated. generating build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/p7_hmmcache.o from vendor/hmmer/src/p7_hmmcache.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/hmmer/src/p7_hmmcache.c -o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/p7_hmmcache.o 1 warning generated. generating build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/p7_hmmwindow.o from vendor/hmmer/src/p7_hmmwindow.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/hmmer/src/p7_hmmwindow.c -o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/p7_hmmwindow.o generating build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/p7_gmxchk.o from vendor/hmmer/src/p7_gmxchk.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/hmmer/src/p7_gmxchk.c -o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/p7_gmxchk.o generating build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/p7_prior.o from vendor/hmmer/src/p7_prior.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/hmmer/src/p7_prior.c -o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/p7_prior.o generating build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/p7_spensemble.o from vendor/hmmer/src/p7_spensemble.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/hmmer/src/p7_spensemble.c -o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/p7_spensemble.o generating build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/p7_hmm.o from vendor/hmmer/src/p7_hmm.c vendor/hmmer/src/hmmdmstr_shard.c:212:16: warning: variable 'tail' set but not used [-Wunused-but-set-variable] WORKER_DATA *tail = NULL; ^ clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/hmmer/src/p7_hmm.c -o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/p7_hmm.o vendor/hmmer/src/hmmdmstr_shard.c:330:73: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare] if((args->seq_db == NULL)||(args->seq_db->db == NULL)|| (query->dbx >= args->seq_db->db_cnt) || (query->dbx < 0)){ ~~~~~~~~~~ ^ ~~~~~~~~~~~~~~~~~~~~ vendor/hmmer/src/hmmdmstr_shard.c:377:21: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare] if (args->ready == args->num_shards) { ~~~~~~~~~~~ ^ ~~~~~~~~~~~~~~~~ vendor/hmmer/src/hmmdmstr_shard.c:464:19: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare] if (args->ready != args->num_shards) { ~~~~~~~~~~~ ^ ~~~~~~~~~~~~~~~~ vendor/hmmer/src/hmmdmstr_shard.c:616:16: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare] for(i = 0; i < worker_comm.num_shards; i++){ ~ ^ ~~~~~~~~~~~~~~~~~~~~~~ vendor/hmmer/src/hmmdmstr_shard.c:772:48: warning: comparison of integers of different signs: 'int' and 'uint64_t' (aka 'unsigned long long') [-Wsign-compare] for(int i0 = 0, i1 = previous_hits; i1 < results->stats.nhits; i0++, i1++){ ~~ ^ ~~~~~~~~~~~~~~~~~~~~ vendor/hmmer/src/hmmdmstr_shard.c:891:18: warning: comparison of integers of different signs: 'int' and 'uint64_t' (aka 'unsigned long long') [-Wsign-compare] for(int i =0; i< results->stats.nhits; i++){ ~^ ~~~~~~~~~~~~~~~~~~~~ vendor/hmmer/src/hmmdmstr_shard.c:924:31: warning: comparison of integers of different signs: 'size_t' (aka 'unsigned long') and 'int' [-Wsign-compare] if (writen(fd, buf3_ptr, n) != n) { ~~~~~~~~~~~~~~~~~~~~~~~ ^ ~ vendor/hmmer/src/hmmdmstr_shard.c:932:31: warning: comparison of integers of different signs: 'size_t' (aka 'unsigned long') and 'int' [-Wsign-compare] if (writen(fd, buf2_ptr, n) != n) { ~~~~~~~~~~~~~~~~~~~~~~~ ^ ~ vendor/hmmer/src/hmmdmstr_shard.c:940:30: warning: comparison of integers of different signs: 'size_t' (aka 'unsigned long') and 'int' [-Wsign-compare] if (writen(fd, buf_ptr, n) != n) { ~~~~~~~~~~~~~~~~~~~~~~ ^ ~ vendor/hmmer/src/hmmdmstr_shard.c:950:20: warning: comparison of integers of different signs: 'int' and 'uint64_t' (aka 'unsigned long long') [-Wsign-compare] for(int i = 0; i < results->stats.nhits; i++){ ~ ^ ~~~~~~~~~~~~~~~~~~~~ vendor/hmmer/src/hmmdmstr_shard.c:982:24: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare] for(int i = 0; i < worker->allocated_hits; i++){ ~ ^ ~~~~~~~~~~~~~~~~~~~~~~ vendor/hmmer/src/hmmdmstr_shard.c:1009:23: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare] for(int i =0; i < worker->allocated_hits; i++){ ~ ^ ~~~~~~~~~~~~~~~~~~~~~~ vendor/hmmer/src/hmmdmstr_shard.c:1463:3: warning: code will never be executed [-Wunreachable-code] pthread_exit(NULL); ^~~~~~~~~~~~ vendor/hmmer/src/hmmdmstr_shard.c:1542:51: warning: comparison of integers of different signs: 'size_t' (aka 'unsigned long') and 'int' [-Wsign-compare] if (writen(worker->sock_fd, worker->cmd, n) != n) { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ ~ vendor/hmmer/src/hmmdmstr_shard.c:1582:42: warning: comparison of integers of different signs: 'size_t' (aka 'unsigned long') and 'int' [-Wsign-compare] if (writen(worker->sock_fd, &cmd, n) != n) { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ ~ vendor/hmmer/src/hmmdmstr_shard.c:1591:41: warning: comparison of integers of different signs: 'size_t' (aka 'unsigned long') and 'int' [-Wsign-compare] if (writen(worker->sock_fd, ptr, n) != n) { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ ~ vendor/hmmer/src/hmmdmstr_shard.c:1652:26: warning: comparison of integers of different signs: 'int' and 'uint64_t' (aka 'unsigned long long') [-Wsign-compare] for(int i = 0; i < stats->nhits; i++){ ~ ^ ~~~~~~~~~~~~ vendor/hmmer/src/hmmdmstr_shard.c:1765:41: warning: comparison of integers of different signs: 'size_t' (aka 'unsigned long') and 'int' [-Wsign-compare] if (writen(worker->sock_fd, cmd, n) != n) { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ ~ vendor/hmmer/src/hmmdmstr_shard.c:1771:51: warning: comparison of integers of different signs: 'size_t' (aka 'unsigned long') and 'int' [-Wsign-compare] if (readn(worker->sock_fd, &hdr, sizeof(hdr)) == -1) { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ ~~ vendor/hmmer/src/hmmdmstr_shard.c:1787:58: warning: comparison of integers of different signs: 'size_t' (aka 'unsigned long') and 'int' [-Wsign-compare] if (readn(worker->sock_fd, &(cmd->init), hdr.length) == -1) { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ ~~ vendor/hmmer/src/hmmdmstr_shard.c:1893:18: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare] for(i = 0; i < data->num_shards; i++){ ~ ^ ~~~~~~~~~~~~~~~~ vendor/hmmer/src/hmmdmstr_shard.c:1916:3: warning: code will never be executed [-Wunreachable-code] pthread_exit(NULL); ^~~~~~~~~~~~ vendor/hmmer/src/hmmdmstr_shard.c:204:1: warning: unused function 'validate_workers' [-Wunused-function] validate_workers(WORKERSIDE_ARGS *args) ^ vendor/hmmer/src/p7_alidisplay.c:725:23: warning: comparison of integers of different signs: 'int' and 'unsigned long' [-Wsign-compare] if(ret_obj->memsize < (obj_size - SER_BASE_SIZE)){ // ret_obj doesn't have enough space for this P7_ALIDISPLAY ~~~~~~~~~~~~~~~~ ^ ~~~~~~~~~~~~~~~~~~~~~~~~ vendor/hmmer/src/p7_hmmcache.c:110:17: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare] for (i = 0; i < cache->n; i++) ~ ^ ~~~~~~~~ vendor/hmmer/src/p7_hmmcache.c:138:17: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare] for (i = 0; i < cache->n; i++) ~ ^ ~~~~~~~~ vendor/hmmer/src/p7_hmmcache.c:161:21: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare] for (i = 0; i < cache->n; i++) ~ ^ ~~~~~~~~ generating build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/p7_trace.o from vendor/hmmer/src/p7_trace.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/hmmer/src/p7_trace.c -o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/p7_trace.o generating build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/p7_pipeline.o from vendor/hmmer/src/p7_pipeline.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/hmmer/src/p7_pipeline.c -o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/p7_pipeline.o 3 warnings generated. generating build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/p7_hmmd_search_stats.o from vendor/hmmer/src/p7_hmmd_search_stats.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/hmmer/src/p7_hmmd_search_stats.c -o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/p7_hmmd_search_stats.o generating build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/hmmpgmd2msa.o from vendor/hmmer/src/hmmpgmd2msa.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/hmmer/src/hmmpgmd2msa.c -o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/hmmpgmd2msa.o generating build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/p7_profile.o from vendor/hmmer/src/p7_profile.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/hmmer/src/p7_profile.c -o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/p7_profile.o generating build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/fm_general.o from vendor/hmmer/src/fm_general.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/hmmer/src/fm_general.c -o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/fm_general.o generating build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/p7_tophits.o from vendor/hmmer/src/p7_tophits.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/hmmer/src/p7_tophits.c -o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/p7_tophits.o vendor/hmmer/src/p7_hmm.c:1282:85: warning: comparison of integers of different signs: 'unsigned long' and 'int' [-Wsign-compare] if (hmm->flags & p7H_RF) { if (hmm->rf == NULL || strlen(hmm->rf) != hmm->M+1) ESL_XFAIL(eslFAIL, errbuf, "p7H_RF flag up, but rf string is invalid"); } ~~~~~~~~~~~~~~~ ^ ~~~~~~~~ vendor/hmmer/src/p7_hmm.c:1285:86: warning: comparison of integers of different signs: 'unsigned long' and 'int' [-Wsign-compare] if (hmm->flags & p7H_MMASK) { if (hmm->mm == NULL || strlen(hmm->mm) != hmm->M+1) ESL_XFAIL(eslFAIL, errbuf, "p7H_MMASK flag up, but mm string is invalid"); } ~~~~~~~~~~~~~~~ ^ ~~~~~~~~ vendor/hmmer/src/p7_hmm.c:1288:85: warning: comparison of integers of different signs: 'unsigned long' and 'int' [-Wsign-compare] if (hmm->flags & p7H_CONS) { if (hmm->consensus == NULL || strlen(hmm->consensus) != hmm->M+1) ESL_XFAIL(eslFAIL, errbuf, "p7H_CONS flag up, but consensus string is invalid"); } ~~~~~~~~~~~~~~~~~~~~~~ ^ ~~~~~~~~ vendor/hmmer/src/p7_hmm.c:1291:85: warning: comparison of integers of different signs: 'unsigned long' and 'int' [-Wsign-compare] if (hmm->flags & p7H_CS) { if (hmm->cs == NULL || strlen(hmm->cs) != hmm->M+1) ESL_XFAIL(eslFAIL, errbuf, "p7H_CS flag up, but cs string is invalid"); } ~~~~~~~~~~~~~~~ ^ ~~~~~~~~ vendor/hmmer/src/p7_hmm.c:1294:85: warning: comparison of integers of different signs: 'unsigned long' and 'int' [-Wsign-compare] if (hmm->flags & p7H_CA) { if (hmm->ca == NULL || strlen(hmm->ca) != hmm->M+1) ESL_XFAIL(eslFAIL, errbuf, "p7H_CA flag up, but ca string is invalid"); } ~~~~~~~~~~~~~~~ ^ ~~~~~~~~ vendor/hmmer/src/p7_hmmd_search_stats.c:204:22: warning: comparison of integers of different signs: 'int' and 'const uint64_t' (aka 'const unsigned long long') [-Wsign-compare] for(int i = 0; i < obj->nhits; i++){ ~ ^ ~~~~~~~~~~ vendor/hmmer/src/p7_hmmd_search_stats.c:377:22: warning: comparison of integers of different signs: 'int' and 'uint64_t' (aka 'unsigned long long') [-Wsign-compare] for(int i = 1; i < ret_obj->nhits; i++){ ~ ^ ~~~~~~~~~~~~~~ vendor/hmmer/src/p7_pipeline.c:1391:61: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare] p7_hmmwindow_new(vit_windowlist, 0, new_n, 0, 0, ESL_MIN(max_window_len,new_len), 0.0, p7_NOCOMPLEMENT, new_len ); ^ ~~~~~~~~~~~~~~ ~~~~~~~ vendor/easel/easel.h:416:36: note: expanded from macro 'ESL_MIN' #define ESL_MIN(a,b) (((a)<(b))?(a):(b)) ~ ^ ~ vendor/hmmer/src/p7_pipeline.c:1392:27: warning: comparison of integers of different signs: 'uint32_t' (aka 'unsigned int') and 'int' [-Wsign-compare] } while (new_len > max_window_len); ~~~~~~~ ^ ~~~~~~~~~~~~~~ vendor/hmmer/src/hmmpgmd2msa.c:135:17: warning: comparison of integers of different signs: 'int' and 'uint64_t' (aka 'unsigned long long') [-Wsign-compare] for (i = 0; i < stats->nhits; ++i) { ~ ^ ~~~~~~~~~~~~ vendor/hmmer/src/hmmpgmd2msa.c:149:14: warning: comparison of integers of different signs: 'int' and 'uint64_t' (aka 'unsigned long long') [-Wsign-compare] for (i=0; inhits; i++) { ~^~~~~~~~~~~~~ vendor/hmmer/src/hmmpgmd2msa.c:168:19: warning: comparison of integers of different signs: 'int' and 'uint64_t' (aka 'unsigned long long') [-Wsign-compare] for (i = 0; i < th.N; i++) { ~ ^ ~~~~ vendor/hmmer/src/hmmpgmd2msa.c:177:17: warning: comparison of integers of different signs: 'int' and 'uint64_t' (aka 'unsigned long long') [-Wsign-compare] for (i = 0; i < th.N; i++) { ~ ^ ~~~~ vendor/hmmer/src/hmmpgmd2msa.c:210:17: warning: comparison of integers of different signs: 'int' and 'uint64_t' (aka 'unsigned long long') [-Wsign-compare] for (i = 0; i < th.N; i++) { ~ ^ ~~~~ vendor/hmmer/src/hmmpgmd2msa.c:226:17: warning: comparison of integers of different signs: 'int' and 'uint64_t' (aka 'unsigned long long') [-Wsign-compare] for (i = 0; i < th.N; i++) { ~ ^ ~~~~ vendor/hmmer/src/hmmpgmd2msa.c:332:14: warning: comparison of integers of different signs: 'int' and 'uint64_t' (aka 'unsigned long long') [-Wsign-compare] for (i=0; inhits; i++) { ~^~~~~~~~~~~~~ vendor/hmmer/src/hmmpgmd2msa.c:348:17: warning: comparison of integers of different signs: 'int' and 'uint64_t' (aka 'unsigned long long') [-Wsign-compare] for (i = 0; i < th.N; i++) ~ ^ ~~~~ vendor/hmmer/src/hmmpgmd2msa.c:471:17: warning: comparison of integers of different signs: 'int' and 'uint64_t' (aka 'unsigned long long') [-Wsign-compare] for (i = 0; i < th.N; i++) { ~ ^ ~~~~ vendor/hmmer/src/hmmpgmd2msa.c:494:17: warning: comparison of integers of different signs: 'int' and 'uint64_t' (aka 'unsigned long long') [-Wsign-compare] for (i = 0; i < th.N; i++) { ~ ^ ~~~~ 2 warnings generated. vendor/hmmer/src/fm_general.c:292:24: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare] if (ranges[lo].lower > end) return -1; ~~~~~~~~~~~~~~~~ ^ ~~~ vendor/hmmer/src/fm_general.c:293:24: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare] if (ranges[hi].upper < start) return -1; ~~~~~~~~~~~~~~~~ ^ ~~~~~ vendor/hmmer/src/fm_general.c:297:34: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare] if (ranges[mid].lower < start) lo = mid + 1; // too far left ~~~~~~~~~~~~~~~~~ ^ ~~~~~ vendor/hmmer/src/fm_general.c:302:73: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare] if (lo>0 && ranges[lo-1].upper >= start && ranges[lo-1].lower <= end) return lo-1; ~~~~~~~~~~~~~~~~~~ ^ ~~~ vendor/hmmer/src/fm_general.c:302:42: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare] if (lo>0 && ranges[lo-1].upper >= start && ranges[lo-1].lower <= end) return lo-1; ~~~~~~~~~~~~~~~~~~ ^ ~~~~~ vendor/hmmer/src/fm_general.c:303:73: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare] else if ( ranges[lo].upper >= start && ranges[lo].lower <= end) return lo; ~~~~~~~~~~~~~~~~ ^ ~~~ vendor/hmmer/src/fm_general.c:303:42: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare] else if ( ranges[lo].upper >= start && ranges[lo].lower <= end) return lo; ~~~~~~~~~~~~~~~~ ^ ~~~~~ vendor/hmmer/src/fm_general.c:350:98: warning: comparison of integers of different signs: 'int' and 'unsigned long long' [-Wsign-compare] while (pos <= fm->ambig_offset + fm->ambig_cnt -1 && meta->ambig_list->ranges[pos].lower <= first+length-1) { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ ~~~~~~~~~~~~~~ vendor/hmmer/src/fm_general.c:350:20: warning: comparison of integers of different signs: 'int32_t' (aka 'int') and 'unsigned int' [-Wsign-compare] while (pos <= fm->ambig_offset + fm->ambig_cnt -1 && meta->ambig_list->ranges[pos].lower <= first+length-1) { ~~~ ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ vendor/hmmer/src/fm_general.c:351:23: warning: comparison of integers of different signs: 'uint64_t' (aka 'unsigned long long') and 'int' [-Wsign-compare] int start = ESL_MAX(first, meta->ambig_list->ranges[pos].lower); ^ ~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ vendor/easel/easel.h:417:36: note: expanded from macro 'ESL_MAX' #define ESL_MAX(a,b) (((a)>(b))?(a):(b)) ~ ^ ~ vendor/hmmer/src/fm_general.c:352:23: warning: comparison of integers of different signs: 'unsigned long long' and 'int' [-Wsign-compare] int end = ESL_MIN(first+length-1, meta->ambig_list->ranges[pos].upper); ^ ~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ vendor/easel/easel.h:416:36: note: expanded from macro 'ESL_MIN' #define ESL_MIN(a,b) (((a)<(b))?(a):(b)) ~ ^ ~ vendor/hmmer/src/fm_general.c:353:27: warning: comparison of integers of different signs: 'uint64_t' (aka 'unsigned long long') and 'int' [-Wsign-compare] for (j= start; j<=end; j++) ~^ ~~~ generating build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/fm_ssv.o from vendor/hmmer/src/fm_ssv.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/hmmer/src/fm_ssv.c -o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/fm_ssv.o vendor/hmmer/src/fm_general.c:538:68: warning: comparison of integers of different signs: 'unsigned long' and 'int32_t' (aka 'int') [-Wsign-compare] (fread(fm->BWT, sizeof(uint8_t), compressed_bytes, meta->fp) != compressed_bytes) || ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ ~~~~~~~~~~~~~~~~ vendor/hmmer/src/fm_general.c:537:75: warning: comparison of integers of different signs: 'unsigned long' and 'int32_t' (aka 'int') [-Wsign-compare] (getAll && fread(fm->T, sizeof(uint8_t), compressed_bytes, meta->fp) != compressed_bytes) || ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ ~~~~~~~~~~~~~~~~ vendor/hmmer/src/fm_general.c:620:14: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare] for (i=0; iseq_count; i++) { ~^~~~~~~~~~~~~~~~ vendor/hmmer/src/fm_general.c:651:14: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare] for (i=0; iambig_list->count; i++) { ~^~~~~~~~~~~~~~~~~~~~~~~~ vendor/hmmer/src/fm_general.c:663:16: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare] for (i=0; iseq_count; i++) ~^~~~~~~~~~~~~~~~ vendor/hmmer/src/fm_general.c:727:16: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare] for (i=0; iseq_count; i++) { ~^~~~~~~~~~~~~~~~ vendor/hmmer/src/p7_tophits.c:89:21: warning: comparison of integers of different signs: 'int' and 'uint64_t' (aka 'unsigned long long') [-Wsign-compare] for (i = 0; i < h->N; i++) ~ ^ ~~~~ vendor/hmmer/src/p7_tophits.c:344:17: warning: comparison of integers of different signs: 'int' and 'uint64_t' (aka 'unsigned long long') [-Wsign-compare] for (i = 0; i < h->N; i++) h->hit[i] = h->unsrt + i; ~ ^ ~~~~ vendor/hmmer/src/p7_tophits.c:377:17: warning: comparison of integers of different signs: 'int' and 'uint64_t' (aka 'unsigned long long') [-Wsign-compare] for (i = 0; i < h->N; i++) h->hit[i] = h->unsrt + i; ~ ^ ~~~~ vendor/hmmer/src/p7_tophits.c:398:17: warning: comparison of integers of different signs: 'int' and 'uint64_t' (aka 'unsigned long long') [-Wsign-compare] for (i = 0; i < h->N; i++) h->hit[i] = h->unsrt + i; ~ ^ ~~~~ vendor/hmmer/src/p7_tophits.c:442:17: warning: comparison of integers of different signs: 'int' and 'uint64_t' (aka 'unsigned long long') [-Wsign-compare] for (i = 0; i < h1->N; i++) ~ ^ ~~~~~ vendor/hmmer/src/p7_tophits.c:450:36: warning: comparison of integers of different signs: 'int' and 'uint64_t' (aka 'unsigned long long') [-Wsign-compare] for (i=0,j=0,k=0; i < h1->N && j < h2->N ; k++) ~ ^ ~~~~~ vendor/hmmer/src/p7_tophits.c:450:23: warning: comparison of integers of different signs: 'int' and 'uint64_t' (aka 'unsigned long long') [-Wsign-compare] for (i=0,j=0,k=0; i < h1->N && j < h2->N ; k++) ~ ^ ~~~~~ vendor/hmmer/src/p7_tophits.c:452:12: warning: comparison of integers of different signs: 'int' and 'uint64_t' (aka 'unsigned long long') [-Wsign-compare] while (i < h1->N) new_hit[k++] = h1->hit[i++]; ~ ^ ~~~~~ vendor/hmmer/src/p7_tophits.c:453:12: warning: comparison of integers of different signs: 'int' and 'uint64_t' (aka 'unsigned long long') [-Wsign-compare] while (j < h2->N) new_hit[k++] = new2 + (h2->hit[j++] - h2->unsrt); ~ ^ ~~~~~ vendor/hmmer/src/p7_tophits.c:457:17: warning: comparison of integers of different signs: 'int' and 'uint64_t' (aka 'unsigned long long') [-Wsign-compare] for (i = 0; i < h2->N; i++) ~ ^ ~~~~~ vendor/hmmer/src/p7_tophits.c:505:17: warning: comparison of integers of different signs: 'int64_t' (aka 'long long') and 'uint64_t' (aka 'unsigned long long') [-Wsign-compare] for (i = 0; i < h->N; i++) { ~ ^ ~~~~ vendor/hmmer/src/p7_tophits.c:535:26: warning: comparison of integers of different signs: 'int' and 'uint64_t' (aka 'unsigned long long') [-Wsign-compare] for (max = 0, i = 0; i < h->N; i++) ~ ^ ~~~~ vendor/hmmer/src/p7_tophits.c:554:26: warning: comparison of integers of different signs: 'int' and 'uint64_t' (aka 'unsigned long long') [-Wsign-compare] for (max = 0, i = 0; i < h->N; i++) ~ ^ ~~~~ vendor/hmmer/src/p7_tophits.c:576:26: warning: comparison of integers of different signs: 'int' and 'uint64_t' (aka 'unsigned long long') [-Wsign-compare] for (max = 0, i = 0; i < h->N; i++) ~ ^ ~~~~ vendor/hmmer/src/p7_tophits.c:609:19: warning: comparison of integers of different signs: 'int' and 'uint64_t' (aka 'unsigned long long') [-Wsign-compare] for (i = 0; i < h->N; i++) ~ ^ ~~~~ vendor/hmmer/src/p7_tophits.c:639:19: warning: comparison of integers of different signs: 'int' and 'uint64_t' (aka 'unsigned long long') [-Wsign-compare] for (i = 0; i < h->N; i++) ~ ^ ~~~~ vendor/hmmer/src/p7_tophits.c:708:17: warning: comparison of integers of different signs: 'int' and 'uint64_t' (aka 'unsigned long long') [-Wsign-compare] for (h = 0; h < th->N; h++) ~ ^ ~~~~~ vendor/hmmer/src/p7_tophits.c:745:17: warning: comparison of integers of different signs: 'int' and 'uint64_t' (aka 'unsigned long long') [-Wsign-compare] for (i = 0; i < th->N ; i++) ~ ^ ~~~~~ vendor/hmmer/src/p7_tophits.c:781:17: warning: comparison of integers of different signs: 'int' and 'uint64_t' (aka 'unsigned long long') [-Wsign-compare] for (i = 1; i < th->N; i++) ~ ^ ~~~~~ vendor/hmmer/src/p7_tophits.c:880:19: warning: comparison of integers of different signs: 'int' and 'uint64_t' (aka 'unsigned long long') [-Wsign-compare] for (h = 0; h < th->N; h++) ~ ^ ~~~~~ vendor/hmmer/src/p7_tophits.c:901:17: warning: comparison of integers of different signs: 'int' and 'uint64_t' (aka 'unsigned long long') [-Wsign-compare] for (h = 0; h < th->N; h++) ~ ^ ~~~~~ vendor/hmmer/src/p7_tophits.c:919:19: warning: comparison of integers of different signs: 'int' and 'uint64_t' (aka 'unsigned long long') [-Wsign-compare] for (h = 0; h < th->N; h++) ~ ^ ~~~~~ vendor/hmmer/src/p7_tophits.c:936:17: warning: comparison of integers of different signs: 'int' and 'uint64_t' (aka 'unsigned long long') [-Wsign-compare] for (h = 0; h < th->N; h++) ~ ^ ~~~~~ vendor/hmmer/src/p7_tophits.c:1011:17: warning: comparison of integers of different signs: 'int' and 'uint64_t' (aka 'unsigned long long') [-Wsign-compare] for (h = 0; h < th->N; h++) ~ ^ ~~~~~ vendor/hmmer/src/p7_tophits.c:1027:17: warning: comparison of integers of different signs: 'int' and 'uint64_t' (aka 'unsigned long long') [-Wsign-compare] for (h = 0; h < th->N; h++) ~ ^ ~~~~~ vendor/hmmer/src/p7_tophits.c:1115:17: warning: comparison of integers of different signs: 'int' and 'uint64_t' (aka 'unsigned long long') [-Wsign-compare] for (h = 0; h < th->N; h++) ~ ^ ~~~~~ vendor/hmmer/src/p7_tophits.c:1231:17: warning: comparison of integers of different signs: 'int' and 'uint64_t' (aka 'unsigned long long') [-Wsign-compare] for (h = 0; h < th->N; h++) ~ ^ ~~~~~ vendor/hmmer/src/p7_tophits.c:1470:17: warning: comparison of integers of different signs: 'int' and 'const uint64_t' (aka 'const unsigned long long') [-Wsign-compare] for (h = 0; h < th->N; h++) ~ ^ ~~~~~ vendor/hmmer/src/p7_tophits.c:1496:17: warning: comparison of integers of different signs: 'int' and 'const uint64_t' (aka 'const unsigned long long') [-Wsign-compare] for (h = 0; h < th->N; h++) ~ ^ ~~~~~ vendor/hmmer/src/p7_tophits.c:1585:17: warning: comparison of integers of different signs: 'int' and 'uint64_t' (aka 'unsigned long long') [-Wsign-compare] for (h = 0; h < th->N; h++) ~ ^ ~~~~~ vendor/hmmer/src/p7_tophits.c:1678:17: warning: comparison of integers of different signs: 'int' and 'uint64_t' (aka 'unsigned long long') [-Wsign-compare] for (h = 0; h < th->N; h++) ~ ^ ~~~~~ vendor/hmmer/src/p7_tophits.c:1781:19: warning: comparison of integers of different signs: 'int' and 'uint64_t' (aka 'unsigned long long') [-Wsign-compare] for (h = 0; h < th->N; h++) ~ ^ ~~~~~ vendor/hmmer/src/p7_tophits.c:1815:21: warning: comparison of integers of different signs: 'int' and 'uint64_t' (aka 'unsigned long long') [-Wsign-compare] for (h = 0; h < th->N; h++) ~ ^ ~~~~~ vendor/hmmer/src/p7_tophits.c:1840:21: warning: comparison of integers of different signs: 'int' and 'uint64_t' (aka 'unsigned long long') [-Wsign-compare] for (h = 0; h < th->N; h++) ~ ^ ~~~~~ vendor/hmmer/src/p7_tophits.c:1874:21: warning: comparison of integers of different signs: 'int' and 'uint64_t' (aka 'unsigned long long') [-Wsign-compare] for (h = 0; h < domHitlist->N; h++) ~ ^ ~~~~~~~~~~~~~ vendor/hmmer/src/p7_tophits.c:1927:17: warning: comparison of integers of different signs: 'int' and 'uint64_t' (aka 'unsigned long long') [-Wsign-compare] for (h = 0; h < th->N; h++) { ~ ^ ~~~~~ 24 warnings generated. 1 warning generated. 5 warnings generated. 10 warnings generated. generating build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/fm_alphabet.o from vendor/hmmer/src/fm_alphabet.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/hmmer/src/fm_alphabet.c -o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/fm_alphabet.o 18 warnings generated. generating build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/fm_sse.o from vendor/hmmer/src/fm_sse.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/hmmer/src/fm_sse.c -o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/fm_sse.o vendor/hmmer/src/fm_ssv.c:71:35: warning: comparison of integers of different signs: 'unsigned long long' and 'int' [-Wsign-compare] && next.n + next.length < curr_n + curr_len + ssv_length //overlapping, or close to it ~~~~~~~~~~~~~~~~~~~~ ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ vendor/hmmer/src/fm_ssv.c:70:33: warning: comparison of integers of different signs: 'unsigned long long' and 'int' [-Wsign-compare] && ( next.n - next.k) == curr_diagval //overlapping diagonals will share the same value of (n - k) ~~~~~~~~~~~~~~~ ^ ~~~~~~~~~~~~ vendor/hmmer/src/fm_ssv.c:134:13: warning: comparison of integers of different signs: 'int' and 'const uint32_t' (aka 'const unsigned int') [-Wsign-compare] while ( j != fmf->term_loc && (j % fm_cfg->meta->freq_SA)) { //go until we hit a position in the full SA that was sampled during FM index construction ~ ^ ~~~~~~~~~~~~~ vendor/hmmer/src/fm_ssv.c:141:18: warning: comparison of integers of different signs: 'int' and 'const uint32_t' (aka 'const unsigned int') [-Wsign-compare] return len + (j==fmf->term_loc ? 0 : fmf->SA[ j / fm_cfg->meta->freq_SA ]) ; // len is how many backward steps we had to take to find a sampled SA position ~^ ~~~~~~~~~~~~~ vendor/hmmer/src/fm_ssv.c:665:18: warning: comparison of integers of different signs: 'int64_t' (aka 'long long') and 'unsigned long long' [-Wsign-compare] if (target_end > fm->N-2) { ~~~~~~~~~~ ^ ~~~~~~~ vendor/hmmer/src/fm_ssv.c:679:14: warning: comparison of integers of different signs: 'uint64_t' (aka 'unsigned long long') and 'int32_t' (aka 'int') [-Wsign-compare] for ( ; k <= model_end; k++, n++) { ~ ^ ~~~~~~~~~ generating build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/p7_scoredata.o from vendor/hmmer/src/p7_scoredata.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.macosx-12-arm64-cpython-310 -c vendor/hmmer/src/p7_scoredata.c -o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/p7_scoredata.o vendor/hmmer/src/fm_sse.c:201:16: warning: comparison of integers of different signs: 'int' and 'const uint64_t' (aka 'const unsigned long long') [-Wsign-compare] if (landmark >= fm->N) { // special case: for a count in the final block, just count from the bottom ~~~~~~~~ ^ ~~~~~ vendor/hmmer/src/fm_sse.c:389:16: warning: comparison of integers of different signs: 'int' and 'const uint64_t' (aka 'const unsigned long long') [-Wsign-compare] if (landmark >= fm->N) { // special case: for a count in the final block, just count from the bottom ~~~~~~~~ ^ ~~~~~ vendor/hmmer/src/fm_sse.c:404:21: warning: comparison of integers of different signs: 'const int' and 'unsigned int' [-Wsign-compare] } else if ( b_pos != sb_pos * (meta->freq_cnt_sb / meta->freq_cnt_b)) { ~~~~~ ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2 warnings generated. 6 warnings generated. generating build/temp.macosx-12-arm64-cpython-310/build/temp.macosx-12-arm64-cpython-310/p7_hmmfile.o from build/temp.macosx-12-arm64-cpython-310/p7_hmmfile.c clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/openblas/include -Ivendor/easel -Ivendor/hmmer/src -Ivendor/hmmer/libdivsufsort -Ibuild/temp.macosx-12-arm64-cpython-310 -c build/temp.macosx-12-arm64-cpython-310/p7_hmmfile.c -o build/temp.macosx-12-arm64-cpython-310/build/temp.macosx-12-arm64-cpython-310/p7_hmmfile.o 3 warnings generated. 36 warnings generated. build/temp.macosx-12-arm64-cpython-310/p7_hmmfile.c:1074:70: warning: comparison of integers of different signs: 'unsigned long' and 'const int' [-Wsign-compare] if (fwrite((char *) hmm->mat[k], sizeof(float), hmm->abc->K, fp) != hmm->abc->K) ESL_EXCEPTION_SYS(eslEWRITE, "hmm binary write failed"); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ ~~~~~~~~~~~ build/temp.macosx-12-arm64-cpython-310/p7_hmmfile.c:1076:70: warning: comparison of integers of different signs: 'unsigned long' and 'const int' [-Wsign-compare] if (fwrite((char *) hmm->ins[k], sizeof(float), hmm->abc->K, fp) != hmm->abc->K) ESL_EXCEPTION_SYS(eslEWRITE, "hmm binary write failed"); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ ~~~~~~~~~~~ build/temp.macosx-12-arm64-cpython-310/p7_hmmfile.c:1085:95: warning: comparison of integers of different signs: 'unsigned long' and 'int' [-Wsign-compare] if ((hmm->flags & p7H_RF) && (fwrite((char *) hmm->rf, sizeof(char), hmm->M+2, fp) != hmm->M+2)) ESL_EXCEPTION_SYS(eslEWRITE, "hmm binary write failed"); /* +2: 1..M and trailing \0 */ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ ~~~~~~~~ build/temp.macosx-12-arm64-cpython-310/p7_hmmfile.c:1086:95: warning: comparison of integers of different signs: 'unsigned long' and 'int' [-Wsign-compare] if ((hmm->flags & p7H_MMASK)&& (fwrite((char *) hmm->mm, sizeof(char), hmm->M+2, fp) != hmm->M+2)) ESL_EXCEPTION_SYS(eslEWRITE, "hmm binary write failed"); /* +2: 1..M and trailing \0 */ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ ~~~~~~~~ build/temp.macosx-12-arm64-cpython-310/p7_hmmfile.c:1087:95: warning: comparison of integers of different signs: 'unsigned long' and 'int' [-Wsign-compare] if ((hmm->flags & p7H_CONS) && (fwrite((char *) hmm->consensus, sizeof(char), hmm->M+2, fp) != hmm->M+2)) ESL_EXCEPTION_SYS(eslEWRITE, "hmm binary write failed"); /* don't need to test for >=3e format; p7H_CONS flag suffices (didn't exist pre-3e) */ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ ~~~~~~~~ build/temp.macosx-12-arm64-cpython-310/p7_hmmfile.c:1088:95: warning: comparison of integers of different signs: 'unsigned long' and 'int' [-Wsign-compare] if ((hmm->flags & p7H_CS) && (fwrite((char *) hmm->cs, sizeof(char), hmm->M+2, fp) != hmm->M+2)) ESL_EXCEPTION_SYS(eslEWRITE, "hmm binary write failed"); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ ~~~~~~~~ build/temp.macosx-12-arm64-cpython-310/p7_hmmfile.c:1089:95: warning: comparison of integers of different signs: 'unsigned long' and 'int' [-Wsign-compare] if ((hmm->flags & p7H_CA) && (fwrite((char *) hmm->ca, sizeof(char), hmm->M+2, fp) != hmm->M+2)) ESL_EXCEPTION_SYS(eslEWRITE, "hmm binary write failed"); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ ~~~~~~~~ build/temp.macosx-12-arm64-cpython-310/p7_hmmfile.c:1095:95: warning: comparison of integers of different signs: 'unsigned long' and 'int' [-Wsign-compare] if ((hmm->flags & p7H_MAP) && (fwrite((char *) hmm->map, sizeof(int), hmm->M+1, fp) != hmm->M+1)) ESL_EXCEPTION_SYS(eslEWRITE, "hmm binary write failed"); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ ~~~~~~~~ build/temp.macosx-12-arm64-cpython-310/p7_hmmfile.c:1112:96: warning: comparison of integers of different signs: 'unsigned long' and 'const int' [-Wsign-compare] if ((hmm->flags & p7H_COMPO) && (fwrite((char *) hmm->compo, sizeof(float), hmm->abc->K, fp) != hmm->abc->K)) ESL_EXCEPTION_SYS(eslEWRITE, "hmm binary write failed"); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ ~~~~~~~~~~~ build/temp.macosx-12-arm64-cpython-310/p7_hmmfile.c:2067:44: warning: comparison of integers of different signs: 'unsigned long' and 'int' [-Wsign-compare] if (fwrite(sptr, sizeof(char), n, fp) != n) ESL_EXCEPTION_SYS(eslEWRITE, "hmm write failed"); /* using fwrite lets us write fixed # of chars */ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ ~ build/temp.macosx-12-arm64-cpython-310/p7_hmmfile.c:2189:56: warning: comparison of integers of different signs: 'unsigned long' and 'int' [-Wsign-compare] if (fwrite((char *) s, sizeof(char), len, fp) != len) ESL_EXCEPTION_SYS(eslEWRITE, "hmm binary write failed"); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ ~~~ 11 warnings generated. /usr/bin/xcrun ar rcs build/temp.macosx-12-arm64-cpython-310/libhmmer.a build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/build.o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/cachedb.o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/cachedb_shard.o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/emit.o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/errors.o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/evalues.o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/eweight.o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/generic_decoding.o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/generic_fwdback.o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/generic_fwdback_chk.o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/generic_fwdback_banded.o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/generic_null2.o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/generic_msv.o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/generic_optacc.o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/generic_stotrace.o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/generic_viterbi.o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/generic_vtrace.o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/h2_io.o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/heatmap.o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/hmmlogo.o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/hmmdmstr.o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/hmmdmstr_shard.o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/hmmd_search_status.o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/hmmdwrkr.o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/hmmdwrkr_shard.o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/hmmdutils.o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/hmmer.o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/logsum.o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/modelconfig.o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/modelstats.o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/mpisupport.o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/seqmodel.o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/tracealign.o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/p7_alidisplay.o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/p7_bg.o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/p7_builder.o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/p7_domain.o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/p7_domaindef.o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/p7_gbands.o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/p7_gmx.o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/p7_gmxb.o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/p7_gmxchk.o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/p7_hit.o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/p7_hmm.o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/p7_hmmcache.o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/p7_hmmd_search_stats.o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/p7_hmmwindow.o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/p7_pipeline.o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/p7_prior.o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/p7_profile.o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/p7_spensemble.o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/p7_tophits.o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/p7_trace.o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/p7_scoredata.o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/hmmpgmd2msa.o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/fm_alphabet.o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/fm_general.o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/fm_sse.o build/temp.macosx-12-arm64-cpython-310/vendor/hmmer/src/fm_ssv.o build/temp.macosx-12-arm64-cpython-310/build/temp.macosx-12-arm64-cpython-310/p7_hmmfile.o ranlib build/temp.macosx-12-arm64-cpython-310/libhmmer.a running install_lib running build_py /opt/homebrew/lib/python3.10/site-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: Installing 'pyhmmer.fileobj' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'pyhmmer.fileobj' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'pyhmmer.fileobj' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'pyhmmer.fileobj' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /opt/homebrew/lib/python3.10/site-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: Installing 'pyhmmer.reexports' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'pyhmmer.reexports' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'pyhmmer.reexports' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'pyhmmer.reexports' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /opt/homebrew/lib/python3.10/site-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: Installing 'pyhmmer.tests' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'pyhmmer.tests' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'pyhmmer.tests' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'pyhmmer.tests' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /opt/homebrew/lib/python3.10/site-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: Installing 'pyhmmer.tests.data' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'pyhmmer.tests.data' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'pyhmmer.tests.data' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'pyhmmer.tests.data' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /opt/homebrew/lib/python3.10/site-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: Installing 'pyhmmer.tests.data.hmms' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'pyhmmer.tests.data.hmms' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'pyhmmer.tests.data.hmms' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'pyhmmer.tests.data.hmms' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /opt/homebrew/lib/python3.10/site-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: Installing 'pyhmmer.tests.data.hmms.bin' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'pyhmmer.tests.data.hmms.bin' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'pyhmmer.tests.data.hmms.bin' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'pyhmmer.tests.data.hmms.bin' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /opt/homebrew/lib/python3.10/site-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: Installing 'pyhmmer.tests.data.hmms.db' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'pyhmmer.tests.data.hmms.db' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'pyhmmer.tests.data.hmms.db' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'pyhmmer.tests.data.hmms.db' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /opt/homebrew/lib/python3.10/site-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: Installing 'pyhmmer.tests.data.hmms.txt' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'pyhmmer.tests.data.hmms.txt' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'pyhmmer.tests.data.hmms.txt' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'pyhmmer.tests.data.hmms.txt' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /opt/homebrew/lib/python3.10/site-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: Installing 'pyhmmer.tests.data.hmms.txt2' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'pyhmmer.tests.data.hmms.txt2' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'pyhmmer.tests.data.hmms.txt2' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'pyhmmer.tests.data.hmms.txt2' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /opt/homebrew/lib/python3.10/site-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: Installing 'pyhmmer.tests.data.jackhmmer' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'pyhmmer.tests.data.jackhmmer' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'pyhmmer.tests.data.jackhmmer' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'pyhmmer.tests.data.jackhmmer' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /opt/homebrew/lib/python3.10/site-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: Installing 'pyhmmer.tests.data.msa' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'pyhmmer.tests.data.msa' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'pyhmmer.tests.data.msa' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'pyhmmer.tests.data.msa' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /opt/homebrew/lib/python3.10/site-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: Installing 'pyhmmer.tests.data.seqs' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'pyhmmer.tests.data.seqs' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'pyhmmer.tests.data.seqs' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'pyhmmer.tests.data.seqs' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /opt/homebrew/lib/python3.10/site-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: Installing 'pyhmmer.tests.data.tables' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'pyhmmer.tests.data.tables' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'pyhmmer.tests.data.tables' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'pyhmmer.tests.data.tables' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /opt/homebrew/lib/python3.10/site-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: Installing 'pyhmmer.tests.test_easel' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'pyhmmer.tests.test_easel' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'pyhmmer.tests.test_easel' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'pyhmmer.tests.test_easel' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /opt/homebrew/lib/python3.10/site-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: Installing 'pyhmmer.tests.test_plan7' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'pyhmmer.tests.test_plan7' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'pyhmmer.tests.test_plan7' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'pyhmmer.tests.test_plan7' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) running build_ext Traceback (most recent call last): File "/Users/jianshuzhao/Github/pyhmmer/setup.py", line 696, in setuptools.setup( File "/opt/homebrew/lib/python3.10/site-packages/setuptools/__init__.py", line 87, in setup return distutils.core.setup(**attrs) File "/opt/homebrew/lib/python3.10/site-packages/setuptools/_distutils/core.py", line 185, in setup return run_commands(dist) File "/opt/homebrew/lib/python3.10/site-packages/setuptools/_distutils/core.py", line 201, in run_commands dist.run_commands() File "/opt/homebrew/lib/python3.10/site-packages/setuptools/_distutils/dist.py", line 973, in run_commands self.run_command(cmd) File "/opt/homebrew/lib/python3.10/site-packages/setuptools/dist.py", line 1217, in run_command super().run_command(command) File "/opt/homebrew/lib/python3.10/site-packages/setuptools/_distutils/dist.py", line 992, in run_command cmd_obj.run() File "/opt/homebrew/lib/python3.10/site-packages/setuptools/command/install.py", line 74, in run self.do_egg_install() File "/opt/homebrew/lib/python3.10/site-packages/setuptools/command/install.py", line 123, in do_egg_install self.run_command('bdist_egg') File "/opt/homebrew/lib/python3.10/site-packages/setuptools/_distutils/cmd.py", line 319, in run_command self.distribution.run_command(command) File "/opt/homebrew/lib/python3.10/site-packages/setuptools/dist.py", line 1217, in run_command super().run_command(command) File "/opt/homebrew/lib/python3.10/site-packages/setuptools/_distutils/dist.py", line 992, in run_command cmd_obj.run() File "/opt/homebrew/lib/python3.10/site-packages/setuptools/command/bdist_egg.py", line 165, in run cmd = self.call_command('install_lib', warn_dir=0) File "/opt/homebrew/lib/python3.10/site-packages/setuptools/command/bdist_egg.py", line 151, in call_command self.run_command(cmdname) File "/opt/homebrew/lib/python3.10/site-packages/setuptools/_distutils/cmd.py", line 319, in run_command self.distribution.run_command(command) File "/opt/homebrew/lib/python3.10/site-packages/setuptools/dist.py", line 1217, in run_command super().run_command(command) File "/opt/homebrew/lib/python3.10/site-packages/setuptools/_distutils/dist.py", line 992, in run_command cmd_obj.run() File "/opt/homebrew/lib/python3.10/site-packages/setuptools/command/install_lib.py", line 11, in run self.build() File "/opt/homebrew/lib/python3.10/site-packages/setuptools/_distutils/command/install_lib.py", line 112, in build self.run_command('build_ext') File "/opt/homebrew/lib/python3.10/site-packages/setuptools/_distutils/cmd.py", line 319, in run_command self.distribution.run_command(command) File "/opt/homebrew/lib/python3.10/site-packages/setuptools/dist.py", line 1217, in run_command super().run_command(command) File "/opt/homebrew/lib/python3.10/site-packages/setuptools/_distutils/dist.py", line 992, in run_command cmd_obj.run() File "/Users/jianshuzhao/Github/pyhmmer/setup.py", line 93, in run raise RuntimeError('Could not select implementation for CPU architecture: "{}"'.format(machine)) RuntimeError: Could not select implementation for CPU architecture: "arm64" ```

Is there technique issue for the Cython to support AMR64?

Thanks,

Jianshu

[althonos]

@jianshu93 : the NEON branch definitely works, yes, but it still hasn't been released in a public version by the HMMER team. For reproducibility sake I want to have PyHMMER compile versioned releases only. They are actively working on it at the moment so I'm hoping a new release is due soon.

[tmsincomb]

Hi @althonos! It looks like they merged your updates to main and was able to be installed for ARM using a collaborators pip install hmmer. I wanted to get it working and submit a pull request, but I needed help with replacing #include <emmintrin.h> found https://github.com/althonos/pyhmmer/blob/master/setup.py#L299. I didn't want to start pulling in more overhead with sse2neon.h so I was hoping if you already new the equivalents for these helpers on ARM from your previous work.

[althonos]

Hi @tmsincomb !

I'm still reluctant to merge the ARM code in a non-development version because I would like to keep in sync with stable HMMER releases. Nevertheless, I'm adding a new branch so that pyhmmer can be compiled for Arm as well, and once that's done I'll maybe publish some pre-releases specifically for Arm.

[althonos]

You can try to install from the neon-supportbranch now, with:

$ python3 -m pip install -U git+https://github.com/althonos/pyhmmer@neon-support

This will hopefully work on a M1 MAC, it works on a Raspberry Pi 4. You'll get a big warning when importing though :yum:

[tmsincomb]

Awesome! Our Sadie package passed all tests on ARM thanks to your neon-support branch! This is what we needed, I can't thank you enough 🙂

[althonos]

Cool! I hope HMMER makes an official Arm release at some point, I'd then be happy to officially support Arm as a platform and provide pre-built wheels in PyPI as well...

[althonos]

HMMER was updated to v3.4 in v0.10.0, meaning that there's now an official Arm release and pre-built wheels for MacOS and Linux on PyPI.

[tmsincomb]

This is wonderful news, thank you so much for all your hard work!