Mock Version: 5.5 Mock Version: 5.5 Mock Version: 5.5 ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --noclean --target aarch64 --nodeps /builddir/build/SPECS/python-pysam.spec'], chrootPath='/var/lib/mock/f41-build-50506752-6046589/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'C.UTF-8'}shell=Falselogger=timeout=201600uid=1000gid=425user='mockbuild'nspawn_args=['--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.tqh4msxi:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11']unshare_net=TrueprintOutput=False) Using nspawn with args ['--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.tqh4msxi:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11'] Executing command: ['/usr/bin/systemd-nspawn', '-q', '-M', '3b3fd1af1eef4fc0a0e0935526c3477a', '-D', '/var/lib/mock/f41-build-50506752-6046589/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.tqh4msxi:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11', '--console=pipe', '--setenv=TERM=vt100', '--setenv=SHELL=/bin/bash', '--setenv=HOME=/builddir', '--setenv=HOSTNAME=mock', '--setenv=PATH=/usr/bin:/bin:/usr/sbin:/sbin', '--setenv=PROMPT_COMMAND=printf "\\033]0;\\007"', '--setenv=PS1= \\s-\\v\\$ ', '--setenv=LANG=C.UTF-8', '--resolv-conf=off', 'bash', '--login', '-c', '/usr/bin/rpmbuild -bs --noclean --target aarch64 --nodeps /builddir/build/SPECS/python-pysam.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'C.UTF-8', 'SYSTEMD_NSPAWN_TMPFS_TMP': '0', 'SYSTEMD_SECCOMP': '0'} and shell False Building target platforms: aarch64 Building for target aarch64 setting SOURCE_DATE_EPOCH=1706227200 Wrote: /builddir/build/SRPMS/python-pysam-0.22.0-4.fc41.src.rpm Child return code was: 0 ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --noclean --target aarch64 --nodeps /builddir/build/SPECS/python-pysam.spec'], chrootPath='/var/lib/mock/f41-build-50506752-6046589/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'C.UTF-8'}shell=Falselogger=timeout=201600uid=1000gid=425user='mockbuild'nspawn_args=['--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.tqh4msxi:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11']unshare_net=TrueprintOutput=False) Using nspawn with args ['--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.tqh4msxi:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11'] Executing command: ['/usr/bin/systemd-nspawn', '-q', '-M', 'bd4e8de842f24b469a08655639971fac', '-D', '/var/lib/mock/f41-build-50506752-6046589/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.tqh4msxi:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11', '--console=pipe', '--setenv=TERM=vt100', '--setenv=SHELL=/bin/bash', '--setenv=HOME=/builddir', '--setenv=HOSTNAME=mock', '--setenv=PATH=/usr/bin:/bin:/usr/sbin:/sbin', '--setenv=PROMPT_COMMAND=printf "\\033]0;\\007"', '--setenv=PS1= \\s-\\v\\$ ', '--setenv=LANG=C.UTF-8', '--resolv-conf=off', 'bash', '--login', '-c', '/usr/bin/rpmbuild -bb --noclean --target aarch64 --nodeps /builddir/build/SPECS/python-pysam.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'C.UTF-8', 'SYSTEMD_NSPAWN_TMPFS_TMP': '0', 'SYSTEMD_SECCOMP': '0'} and shell False Building target platforms: aarch64 Building for target aarch64 setting SOURCE_DATE_EPOCH=1706227200 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.mRi7O5 + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf pysam-0.22.0 + /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/pysam-0.22.0.tar.gz + STATUS=0 + '[' 0 -ne 0 ']' + cd pysam-0.22.0 + rm -rf /builddir/build/BUILD/pysam-0.22.0-SPECPARTS + /usr/bin/mkdir -p /builddir/build/BUILD/pysam-0.22.0-SPECPARTS + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + /usr/lib/rpm/rpmuncompress /builddir/build/SOURCES/python-pysam-configure-c99.patch + /usr/bin/patch -p1 -s --fuzz=0 --no-backup-if-mismatch -f + rm -rf pysam.egg-info ++ grep -rl '/\* Generated by Cython' + rm pysam/libcalignedsegment.c pysam/libcalignmentfile.c pysam/libcbcf.c pysam/libcbcftools.c pysam/libcbgzf.c pysam/libcfaidx.c pysam/libchtslib.c pysam/libcsamfile.c pysam/libcsamtools.c pysam/libctabix.c pysam/libctabixproxies.c pysam/libcutils.c pysam/libcvcf.c + RPM_EC=0 ++ jobs -p + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.u9g9KD + umask 022 + cd /builddir/build/BUILD + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd pysam-0.22.0 + FORCE_CYTHON=1 + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + /usr/bin/python3 setup.py build '--executable=/usr/bin/python3 -sP' # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is shared # pysam: HTSLIB_CONFIGURE_OPTIONS=None # pysam: (env) CC=gcc # pysam: (env) CFLAGS=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC # pysam: (env) LDFLAGS=-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for ranlib... ranlib checking for grep that handles long lines and -e... /usr/bin/grep checking for C compiler warning flags... -Wall checking how to run the C preprocessor... gcc -E checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking whether _XOPEN_SOURCE is declared... no checking C compiler flags needed for ssse3... none checking C compiler flags needed for popcnt... none checking C compiler flags needed for sse4.1... none checking C compiler flags needed for avx2... none checking C compiler flags needed for avx512f... none checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking shared library type for unknown-Linux... plain .so checking whether the linker supports versioned symbols... no checking whether the compiler accepts -fvisibility=hidden... yes checking for stdlib.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/param.h... yes checking for getpagesize... yes checking for working mmap... yes checking for gmtime_r... yes checking for fsync... yes checking for drand48... yes checking for srand48_deterministic... no checking whether fdatasync is declared... yes checking for fdatasync... yes checking for library containing log... -lm checking for zlib.h... yes checking for inflate in -lz... yes checking for library containing recv... none required checking for bzlib.h... yes checking for BZ2_bzBuffToBuffCompress in -lbz2... yes checking for lzma.h... yes checking for lzma_easy_buffer_encode in -llzma... yes checking whether htscodecs files are present... yes checking for libdeflate.h... no checking for libdeflate_deflate_compress in -ldeflate... no checking for curl/curl.h... no checking for curl_easy_pause in -lcurl... no checking for curl_easy_init in -lcurl... no configure: error: libcurl library not found Support for HTTPS and other SSL-based URLs requires routines from the libcurl library . Building HTSlib with libcurl enabled requires libcurl development files to be installed on the build machine; you may need to ensure a package such as libcurl4-{gnutls,nss,openssl}-dev (on Debian or Ubuntu Linux) or libcurl-devel (on RPM-based Linux distributions or Cygwin) is installed. Either configure with --disable-libcurl or resolve this error to build HTSlib. checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for ranlib... ranlib checking for grep that handles long lines and -e... /usr/bin/grep checking for C compiler warning flags... -Wall checking how to run the C preprocessor... gcc -E checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking whether _XOPEN_SOURCE is declared... no checking C compiler flags needed for ssse3... none checking C compiler flags needed for popcnt... none checking C compiler flags needed for sse4.1... none checking C compiler flags needed for avx2... none checking C compiler flags needed for avx512f... none checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking shared library type for unknown-Linux... plain .so checking whether the linker supports versioned symbols... no checking whether the compiler accepts -fvisibility=hidden... yes checking for stdlib.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/param.h... yes checking for getpagesize... yes checking for working mmap... yes checking for gmtime_r... yes checking for fsync... yes checking for drand48... yes checking for srand48_deterministic... no checking whether fdatasync is declared... yes checking for fdatasync... yes checking for library containing log... -lm checking for zlib.h... yes checking for inflate in -lz... yes checking for library containing recv... none required checking for bzlib.h... yes checking for BZ2_bzBuffToBuffCompress in -lbz2... yes checking for lzma.h... yes checking for lzma_easy_buffer_encode in -llzma... yes checking whether htscodecs files are present... yes checking for libdeflate.h... no checking for libdeflate_deflate_compress in -ldeflate... no configure: WARNING: GCS support not enabled: requires libcurl support configure: WARNING: S3 support not enabled: requires libcurl support checking for library containing regcomp... none required configure: creating ./config.status config.status: creating config.mk config.status: creating htslib.pc.tmp config.status: creating config.h config.status: linking htscodecs_bundled.mk to htscodecs.mk # pysam: htslib configure options: --disable-libcurl # pysam: htslib_config HTS_CFLAGS_AVX2= # pysam: htslib_config HTS_CFLAGS_AVX512= # pysam: htslib_config HTS_CFLAGS_SSE4= # pysam: htslib_config LIBHTS_OBJS=kfunc.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o header.o hfile.o hts.o hts_expr.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o region.o sam.o sam_mods.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_stats.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/string_alloc.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/utils.o # pysam: htslib_config LIBS=-llzma -lbz2 -lz -lm # pysam: htslib_config PLATFORM=default # pysam: config_option: ENABLE_GCS=0 # pysam: config_option: ENABLE_PLUGINS=0 # pysam: config_option: ENABLE_S3=0 # pysam: config_option: HAVE_COMMONCRYPTO=0 # pysam: config_option: HAVE_HMAC=0 # pysam: config_option: HAVE_LIBBZ2=1 # pysam: config_option: HAVE_LIBCURL=0 # pysam: config_option: HAVE_LIBDEFLATE=0 # pysam: config_option: HAVE_LIBLZMA=1 # pysam: config_option: HAVE_MMAP=1 running build running build_py creating build creating build/lib.linux-aarch64-cpython-312 creating build/lib.linux-aarch64-cpython-312/pysam copying pysam/Pileup.py -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/__init__.py -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/bcftools.py -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/samtools.py -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/utils.py -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/version.py -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/config.py -> build/lib.linux-aarch64-cpython-312/pysam creating build/lib.linux-aarch64-cpython-312/pysam/include copying pysam/include/__init__.py -> build/lib.linux-aarch64-cpython-312/pysam/include running egg_info creating pysam.egg-info writing pysam.egg-info/PKG-INFO writing dependency_links to pysam.egg-info/dependency_links.txt writing top-level names to pysam.egg-info/top_level.txt writing manifest file 'pysam.egg-info/SOURCES.txt' reading manifest file 'pysam.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'KNOWN_BUGS' warning: no files found matching 'THANKS' warning: no files found matching 'pysam/libc*.c' no previously-included directories found matching 'tests/' adding license file 'COPYING' adding license file 'AUTHORS' writing manifest file 'pysam.egg-info/SOURCES.txt' /usr/lib/python3.12/site-packages/setuptools/command/build_py.py:207: _Warning: Package 'pysam.include.htslib.cram' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'pysam.include.htslib.cram' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'pysam.include.htslib.cram' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'pysam.include.htslib.cram' to be distributed and are already explicitly excluding 'pysam.include.htslib.cram' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3.12/site-packages/setuptools/command/build_py.py:207: _Warning: Package 'pysam.include.htslib.htscodecs.htscodecs' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'pysam.include.htslib.htscodecs.htscodecs' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'pysam.include.htslib.htscodecs.htscodecs' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'pysam.include.htslib.htscodecs.htscodecs' to be distributed and are already explicitly excluding 'pysam.include.htslib.htscodecs.htscodecs' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3.12/site-packages/setuptools/command/build_py.py:207: _Warning: Package 'pysam.include.htslib.m4' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'pysam.include.htslib.m4' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'pysam.include.htslib.m4' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'pysam.include.htslib.m4' to be distributed and are already explicitly excluding 'pysam.include.htslib.m4' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3.12/site-packages/setuptools/command/build_py.py:207: _Warning: Package 'pysam.include.htslib.os' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'pysam.include.htslib.os' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'pysam.include.htslib.os' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'pysam.include.htslib.os' to be distributed and are already explicitly excluding 'pysam.include.htslib.os' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3.12/site-packages/setuptools/command/build_py.py:207: _Warning: Package 'pysam.include.samtools.lz4' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'pysam.include.samtools.lz4' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'pysam.include.samtools.lz4' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'pysam.include.samtools.lz4' to be distributed and are already explicitly excluding 'pysam.include.samtools.lz4' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) copying pysam/cbcftools_util.h -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/csamtools_util.h -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/htslib_util.c -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/htslib_util.h -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/libcalignedsegment.pxd -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/libcalignedsegment.pyi -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/libcalignedsegment.pyx -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/libcalignmentfile.pxd -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/libcalignmentfile.pyi -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/libcalignmentfile.pyx -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/libcbcf.pxd -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/libcbcf.pyi -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/libcbcf.pyx -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/libcbcftools.pxd -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/libcbcftools.pyi -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/libcbcftools.pyx -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/libcbgzf.pyi -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/libcbgzf.pyx -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/libcfaidx.pxd -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/libcfaidx.pyi -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/libcfaidx.pyx -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/libchtslib.pxd -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/libchtslib.pyi -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/libchtslib.pyx -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/libcsamfile.pxd -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/libcsamfile.pyi -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/libcsamfile.pyx -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/libcsamtools.pxd -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/libcsamtools.pyi -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/libcsamtools.pyx -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/libctabix.pxd -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/libctabix.pyi -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/libctabix.pyx -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/libctabixproxies.pxd -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/libctabixproxies.pyi -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/libctabixproxies.pyx -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/libcutils.pxd -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/libcutils.pyi -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/libcutils.pyx -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/libcvcf.pxd -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/libcvcf.pyi -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/libcvcf.pyx -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/py.typed -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/pysam_stream.h -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/pysam_util.c -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/pysam_util.h -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/version.h -> build/lib.linux-aarch64-cpython-312/pysam copying pysam/version.pyi -> build/lib.linux-aarch64-cpython-312/pysam creating build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/LICENSE -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/README -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/amplicon_stats.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/amplicon_stats.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam.h -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam2depth.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam2depth.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_addrprg.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_addrprg.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_ampliconclip.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_ampliconclip.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_ampliconclip.h -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_aux.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_aux.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_cat.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_cat.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_color.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_color.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_consensus.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_consensus.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_fastq.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_fastq.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_flags.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_flags.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_import.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_import.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_index.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_index.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_lpileup.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_lpileup.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_lpileup.h -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_markdup.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_markdup.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_mate.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_mate.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_md.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_md.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_plbuf.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_plbuf.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_plbuf.h -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_plcmd.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_plcmd.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_quickcheck.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_quickcheck.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_reheader.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_reheader.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_rmdup.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_rmdup.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_rmdupse.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_rmdupse.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_samples.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_samples.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_sort.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_sort.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_split.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_split.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_stat.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bam_stat.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bamshuf.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bamshuf.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bamtk.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bamtk.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bedcov.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bedcov.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bedidx.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bedidx.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/bedidx.h -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/consensus_pileup.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/consensus_pileup.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/consensus_pileup.h -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/coverage.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/coverage.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/cram_size.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/cram_size.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/cut_target.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/cut_target.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/dict.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/dict.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/faidx.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/faidx.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/padding.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/padding.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/phase.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/phase.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/reference.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/reference.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/reset.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/reset.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/sam_opts.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/sam_opts.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/sam_opts.h -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/sam_utils.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/sam_utils.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/sam_utils.h -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/sam_view.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/sam_view.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/sample.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/sample.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/sample.h -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/samtools.h -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/samtools.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/samtools.pysam.h -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/splaysort.h -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/stats.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/stats.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/stats_isize.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/stats_isize.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/stats_isize.h -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/tmp_file.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/tmp_file.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/tmp_file.h -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools copying samtools/version.sh -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools creating build/lib.linux-aarch64-cpython-312/pysam/include/samtools/lz4 copying samtools/lz4/LICENSE -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools/lz4 copying samtools/lz4/lz4.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools/lz4 copying samtools/lz4/lz4.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools/lz4 copying samtools/lz4/lz4.h -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools/lz4 copying samtools/config.h -> build/lib.linux-aarch64-cpython-312/pysam/include/samtools creating build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/HMM.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/HMM.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/HMM.h -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/LICENSE -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/README -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/abuf.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/abuf.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/abuf.h -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/bam2bcf.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/bam2bcf.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/bam2bcf.h -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/bam2bcf_iaux.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/bam2bcf_iaux.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/bam2bcf_indel.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/bam2bcf_indel.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/bam_sample.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/bam_sample.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/bam_sample.h -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/bcftools.h -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/bcftools.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/bcftools.pysam.h -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/bin.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/bin.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/bin.h -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/call.h -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/ccall.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/ccall.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/cigar_state.h -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/cols.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/cols.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/cols.h -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/consensus.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/consensus.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/convert.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/convert.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/convert.h -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/csq.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/csq.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/dbuf.h -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/dist.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/dist.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/dist.h -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/em.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/em.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/extsort.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/extsort.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/extsort.h -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/filter.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/filter.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/filter.h -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/gff.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/gff.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/gff.h -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/gvcf.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/gvcf.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/gvcf.h -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/hclust.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/hclust.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/hclust.h -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/hex.h -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/khash_str2str.h -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/kheap.h -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/kmin.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/kmin.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/kmin.h -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/main.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/main.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/mcall.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/mcall.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/mpileup.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/mpileup.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/mw.h -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/ploidy.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/ploidy.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/ploidy.h -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/prob1.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/prob1.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/prob1.h -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/rbuf.h -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/read_consensus.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/read_consensus.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/read_consensus.h -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/regidx.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/regidx.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/regidx.h -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/reheader.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/reheader.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/smpl_ilist.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/smpl_ilist.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/smpl_ilist.h -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/str_finder.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/str_finder.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/str_finder.h -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/tabix.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/tabix.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/tsv2vcf.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/tsv2vcf.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/tsv2vcf.h -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/utlist.h -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/variantkey.h -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/vcfannotate.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/vcfannotate.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/vcfbuf.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/vcfbuf.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/vcfbuf.h -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/vcfcall.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/vcfcall.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/vcfcnv.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/vcfcnv.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/vcfconcat.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/vcfconcat.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/vcfconvert.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/vcfconvert.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/vcffilter.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/vcffilter.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/vcfgtcheck.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/vcfgtcheck.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/vcfhead.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/vcfhead.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/vcfindex.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/vcfindex.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/vcfisec.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/vcfisec.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/vcfmerge.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/vcfmerge.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/vcfnorm.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/vcfnorm.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/vcfplugin.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/vcfplugin.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/vcfquery.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/vcfquery.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/vcfroh.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/vcfroh.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/vcfsom.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/vcfsom.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/vcfsort.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/vcfsort.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/vcfstats.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/vcfstats.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/vcfview.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/vcfview.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/vcmp.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/vcmp.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/vcmp.h -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/version.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/version.c.pysam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/version.sh -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools copying bcftools/config.h -> build/lib.linux-aarch64-cpython-312/pysam/include/bcftools creating build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/LICENSE -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/Makefile -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/README -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/bcf_sr_sort.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/bcf_sr_sort.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/bgzf.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/bgzip.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/builddir_vars.mk.in -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/config.h.in -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/config.mk.in -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/configure -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/configure.ac -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/errmod.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/faidx.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/header.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/header.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/hfile.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/hfile_gcs.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/hfile_internal.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/hfile_libcurl.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/hfile_s3.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/hfile_s3_write.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/hts.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/hts_expr.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/hts_internal.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/hts_os.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/hts_time_funcs.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/htscodecs_bundled.mk -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/htscodecs_external.mk -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/htsfile.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/htslib.mk -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/htslib.pc.in -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/htslib_vars.mk -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/kfunc.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/kstring.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/md5.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/multipart.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/plugin.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/probaln.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/realn.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/regidx.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/region.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/sam.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/sam_internal.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/sam_mods.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/synced_bcf_reader.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/tabix.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/tbx.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/textutils.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/textutils_internal.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/thread_pool.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/thread_pool_internal.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/vcf.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/vcf_sweep.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/vcfutils.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib copying htslib/version.sh -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib creating build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram copying htslib/cram/cram.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram copying htslib/cram/cram_codecs.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram copying htslib/cram/cram_codecs.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram copying htslib/cram/cram_decode.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram copying htslib/cram/cram_decode.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram copying htslib/cram/cram_encode.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram copying htslib/cram/cram_encode.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram copying htslib/cram/cram_external.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram copying htslib/cram/cram_index.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram copying htslib/cram/cram_index.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram copying htslib/cram/cram_io.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram copying htslib/cram/cram_io.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram copying htslib/cram/cram_samtools.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram copying htslib/cram/cram_stats.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram copying htslib/cram/cram_stats.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram copying htslib/cram/cram_structs.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram copying htslib/cram/mFILE.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram copying htslib/cram/mFILE.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram copying htslib/cram/misc.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram copying htslib/cram/open_trace_file.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram copying htslib/cram/open_trace_file.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram copying htslib/cram/os.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram copying htslib/cram/pooled_alloc.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram copying htslib/cram/pooled_alloc.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram copying htslib/cram/string_alloc.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram copying htslib/cram/string_alloc.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram creating build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs creating build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/arith_dynamic.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/arith_dynamic.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/c_range_coder.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/c_simple_model.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/fqzcomp_qual.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/fqzcomp_qual.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/htscodecs.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/htscodecs.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/htscodecs_endian.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/pack.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/pack.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/permute.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/pooled_alloc.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_byte.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_static.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_static.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_static16_int.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_static32x16pr.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_static32x16pr.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_static32x16pr_avx2.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_static32x16pr_avx512.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_static32x16pr_neon.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_static32x16pr_sse4.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_static4x16.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_static4x16pr.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_word.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rle.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rle.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/tokenise_name3.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/tokenise_name3.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/utils.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/utils.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/varint.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/varint2.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/version.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs creating build/lib.linux-aarch64-cpython-312/pysam/include/htslib/m4 copying htslib/m4/hts_check_compile_flags_needed.m4 -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/m4 copying htslib/m4/hts_hide_dynamic_syms.m4 -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/m4 copying htslib/m4/hts_prog_cc_warnings.m4 -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/m4 copying htslib/m4/pkg.m4 -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/m4 creating build/lib.linux-aarch64-cpython-312/pysam/include/htslib/os copying htslib/os/lzma_stub.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/os copying htslib/os/rand.c -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/os copying htslib/config.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib creating build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/bgzf.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/cram.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/faidx.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/hfile.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/hts.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/hts_defs.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/hts_endian.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/hts_expr.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/hts_log.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/hts_os.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/kbitset.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/kfunc.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/khash.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/khash_str2int.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/klist.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/knetfile.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/kroundup.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/kseq.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/ksort.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/kstring.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/regidx.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/sam.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/synced_bcf_reader.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/tbx.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/thread_pool.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/vcf.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/vcf_sweep.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/vcfutils.h -> build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib running build_ext creating htslib/config_vars.h for 'pysam.libchtslib' extension building 'libhts.a' gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o kfunc.o kfunc.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o kstring.o kstring.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o bcf_sr_sort.o bcf_sr_sort.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o bgzf.o bgzf.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o errmod.o errmod.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o faidx.o faidx.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o header.o header.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o hfile.o hfile.c echo '#define HTS_VERSION_TEXT "1.18"' > version.h gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o hts.o hts.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o hts_expr.o hts_expr.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o hts_os.o hts_os.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o md5.o md5.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o multipart.o multipart.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o probaln.o probaln.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o realn.o realn.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o regidx.o regidx.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o region.o region.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o sam.o sam.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o sam_mods.o sam_mods.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o synced_bcf_reader.o synced_bcf_reader.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o vcf_sweep.o vcf_sweep.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o tbx.o tbx.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o textutils.o textutils.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o thread_pool.o thread_pool.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o vcf.o vcf.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o vcfutils.o vcfutils.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o cram/cram_codecs.o cram/cram_codecs.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o cram/cram_decode.o cram/cram_decode.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o cram/cram_encode.o cram/cram_encode.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o cram/cram_external.o cram/cram_external.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o cram/cram_index.o cram/cram_index.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o cram/cram_io.o cram/cram_io.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o cram/cram_stats.o cram/cram_stats.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o cram/mFILE.o cram/mFILE.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o cram/open_trace_file.o cram/open_trace_file.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o cram/pooled_alloc.o cram/pooled_alloc.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o cram/string_alloc.o cram/string_alloc.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/arith_dynamic.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/fqzcomp_qual.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/htscodecs.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o htscodecs/htscodecs/pack.o htscodecs/htscodecs/pack.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static4x16pr.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx2.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_avx512.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_sse4.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr_neon.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static32x16pr.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rANS_static.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o htscodecs/htscodecs/rle.o htscodecs/htscodecs/rle.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/tokenise_name3.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o htscodecs/htscodecs/utils.o htscodecs/htscodecs/utils.c ar -rc libhts.a kfunc.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o header.o hfile.o hts.o hts_expr.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o region.o sam.o sam_mods.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_stats.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/string_alloc.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/utils.o ranlib libhts.a Compiling pysam/libchtslib.pyx because it changed. [1/1] Cythonizing pysam/libchtslib.pyx building 'pysam.libchtslib' extension creating build/temp.linux-aarch64-cpython-312 creating build/temp.linux-aarch64-cpython-312/pysam gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c pysam/htslib_util.c -o build/temp.linux-aarch64-cpython-312/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c pysam/libchtslib.c -o build/temp.linux-aarch64-cpython-312/pysam/libchtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC build/temp.linux-aarch64-cpython-312/pysam/htslib_util.o build/temp.linux-aarch64-cpython-312/pysam/libchtslib.o htslib/kfunc.o htslib/kstring.o htslib/bcf_sr_sort.o htslib/bgzf.o htslib/errmod.o htslib/faidx.o htslib/header.o htslib/hfile.o htslib/hts.o htslib/hts_expr.o htslib/hts_os.o htslib/md5.o htslib/multipart.o htslib/probaln.o htslib/realn.o htslib/regidx.o htslib/region.o htslib/sam.o htslib/sam_mods.o htslib/synced_bcf_reader.o htslib/vcf_sweep.o htslib/tbx.o htslib/textutils.o htslib/thread_pool.o htslib/vcf.o htslib/vcfutils.o htslib/cram/cram_codecs.o htslib/cram/cram_decode.o htslib/cram/cram_encode.o htslib/cram/cram_external.o htslib/cram/cram_index.o htslib/cram/cram_io.o htslib/cram/cram_stats.o htslib/cram/mFILE.o htslib/cram/open_trace_file.o htslib/cram/pooled_alloc.o htslib/cram/string_alloc.o htslib/htscodecs/htscodecs/arith_dynamic.o htslib/htscodecs/htscodecs/fqzcomp_qual.o htslib/htscodecs/htscodecs/htscodecs.o htslib/htscodecs/htscodecs/pack.o htslib/htscodecs/htscodecs/rANS_static4x16pr.o htslib/htscodecs/htscodecs/rANS_static32x16pr_avx2.o htslib/htscodecs/htscodecs/rANS_static32x16pr_avx512.o htslib/htscodecs/htscodecs/rANS_static32x16pr_sse4.o htslib/htscodecs/htscodecs/rANS_static32x16pr_neon.o htslib/htscodecs/htscodecs/rANS_static32x16pr.o htslib/htscodecs/htscodecs/rANS_static.o htslib/htscodecs/htscodecs/rle.o htslib/htscodecs/htscodecs/tokenise_name3.o htslib/htscodecs/htscodecs/utils.o -L/builddir/build/BUILD/pysam-0.22.0/pysam -L/builddir/build/BUILD/pysam-0.22.0 -Lbuild/lib.linux-aarch64-cpython-312/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -o build/lib.linux-aarch64-cpython-312/pysam/libchtslib.cpython-312-aarch64-linux-gnu.so -Wl,-rpath,$ORIGIN creating samtools/samtools_config_vars.h for 'pysam.libcsamtools' extension Compiling pysam/libcsamtools.pyx because it changed. [1/1] Cythonizing pysam/libcsamtools.pyx building 'pysam.libcsamtools' extension creating build/temp.linux-aarch64-cpython-312/samtools creating build/temp.linux-aarch64-cpython-312/samtools/lz4 gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c pysam/libcsamtools.c -o build/temp.linux-aarch64-cpython-312/pysam/libcsamtools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c samtools/amplicon_stats.c.pysam.c -o build/temp.linux-aarch64-cpython-312/samtools/amplicon_stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c samtools/bam.c.pysam.c -o build/temp.linux-aarch64-cpython-312/samtools/bam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c samtools/bam2depth.c.pysam.c -o build/temp.linux-aarch64-cpython-312/samtools/bam2depth.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c samtools/bam_addrprg.c.pysam.c -o build/temp.linux-aarch64-cpython-312/samtools/bam_addrprg.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c samtools/bam_ampliconclip.c.pysam.c -o build/temp.linux-aarch64-cpython-312/samtools/bam_ampliconclip.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c samtools/bam_aux.c.pysam.c -o build/temp.linux-aarch64-cpython-312/samtools/bam_aux.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c samtools/bam_cat.c.pysam.c -o build/temp.linux-aarch64-cpython-312/samtools/bam_cat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c samtools/bam_color.c.pysam.c -o build/temp.linux-aarch64-cpython-312/samtools/bam_color.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c samtools/bam_consensus.c.pysam.c -o build/temp.linux-aarch64-cpython-312/samtools/bam_consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c samtools/bam_fastq.c.pysam.c -o build/temp.linux-aarch64-cpython-312/samtools/bam_fastq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c samtools/bam_flags.c.pysam.c -o build/temp.linux-aarch64-cpython-312/samtools/bam_flags.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c samtools/bam_import.c.pysam.c -o build/temp.linux-aarch64-cpython-312/samtools/bam_import.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c samtools/bam_index.c.pysam.c -o build/temp.linux-aarch64-cpython-312/samtools/bam_index.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c samtools/bam_lpileup.c.pysam.c -o build/temp.linux-aarch64-cpython-312/samtools/bam_lpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c samtools/bam_markdup.c.pysam.c -o build/temp.linux-aarch64-cpython-312/samtools/bam_markdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c samtools/bam_mate.c.pysam.c -o build/temp.linux-aarch64-cpython-312/samtools/bam_mate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c samtools/bam_md.c.pysam.c -o build/temp.linux-aarch64-cpython-312/samtools/bam_md.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c samtools/bam_plbuf.c.pysam.c -o build/temp.linux-aarch64-cpython-312/samtools/bam_plbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c samtools/bam_plcmd.c.pysam.c -o build/temp.linux-aarch64-cpython-312/samtools/bam_plcmd.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c samtools/bam_quickcheck.c.pysam.c -o build/temp.linux-aarch64-cpython-312/samtools/bam_quickcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c samtools/bam_reheader.c.pysam.c -o build/temp.linux-aarch64-cpython-312/samtools/bam_reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c samtools/bam_rmdup.c.pysam.c -o build/temp.linux-aarch64-cpython-312/samtools/bam_rmdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c samtools/bam_rmdupse.c.pysam.c -o build/temp.linux-aarch64-cpython-312/samtools/bam_rmdupse.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c samtools/bam_samples.c.pysam.c -o build/temp.linux-aarch64-cpython-312/samtools/bam_samples.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c samtools/bam_sort.c.pysam.c -o build/temp.linux-aarch64-cpython-312/samtools/bam_sort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement samtools/bam_sort.c.pysam.c: In function ‘reverse_complement.isra.0’: samtools/bam_sort.c.pysam.c:2986:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 2986 | seq[j] = comp[tmp]; | ~~~~~~~^~~~~~~~~~~ samtools/bam_sort.c.pysam.c:2973:10: note: at offset 2147483647 into destination object ‘seq_’ of size 10000 2973 | char seq_[10000], *seq = seq_; | ^~~~ gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c samtools/bam_split.c.pysam.c -o build/temp.linux-aarch64-cpython-312/samtools/bam_split.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c samtools/bam_stat.c.pysam.c -o build/temp.linux-aarch64-cpython-312/samtools/bam_stat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c samtools/bamshuf.c.pysam.c -o build/temp.linux-aarch64-cpython-312/samtools/bamshuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c samtools/bamtk.c.pysam.c -o build/temp.linux-aarch64-cpython-312/samtools/bamtk.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c samtools/bedcov.c.pysam.c -o build/temp.linux-aarch64-cpython-312/samtools/bedcov.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c samtools/bedidx.c.pysam.c -o build/temp.linux-aarch64-cpython-312/samtools/bedidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c samtools/consensus_pileup.c.pysam.c -o build/temp.linux-aarch64-cpython-312/samtools/consensus_pileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c samtools/coverage.c.pysam.c -o build/temp.linux-aarch64-cpython-312/samtools/coverage.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c samtools/cram_size.c.pysam.c -o build/temp.linux-aarch64-cpython-312/samtools/cram_size.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c samtools/cut_target.c.pysam.c -o build/temp.linux-aarch64-cpython-312/samtools/cut_target.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c samtools/dict.c.pysam.c -o build/temp.linux-aarch64-cpython-312/samtools/dict.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c samtools/faidx.c.pysam.c -o build/temp.linux-aarch64-cpython-312/samtools/faidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c samtools/lz4/lz4.c -o build/temp.linux-aarch64-cpython-312/samtools/lz4/lz4.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c samtools/padding.c.pysam.c -o build/temp.linux-aarch64-cpython-312/samtools/padding.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c samtools/phase.c.pysam.c -o build/temp.linux-aarch64-cpython-312/samtools/phase.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c samtools/reference.c.pysam.c -o build/temp.linux-aarch64-cpython-312/samtools/reference.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c samtools/reset.c.pysam.c -o build/temp.linux-aarch64-cpython-312/samtools/reset.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c samtools/sam_opts.c.pysam.c -o build/temp.linux-aarch64-cpython-312/samtools/sam_opts.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c samtools/sam_utils.c.pysam.c -o build/temp.linux-aarch64-cpython-312/samtools/sam_utils.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c samtools/sam_view.c.pysam.c -o build/temp.linux-aarch64-cpython-312/samtools/sam_view.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c samtools/sample.c.pysam.c -o build/temp.linux-aarch64-cpython-312/samtools/sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c samtools/samtools.pysam.c -o build/temp.linux-aarch64-cpython-312/samtools/samtools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c samtools/stats.c.pysam.c -o build/temp.linux-aarch64-cpython-312/samtools/stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c samtools/stats_isize.c.pysam.c -o build/temp.linux-aarch64-cpython-312/samtools/stats_isize.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c samtools/tmp_file.c.pysam.c -o build/temp.linux-aarch64-cpython-312/samtools/tmp_file.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC build/temp.linux-aarch64-cpython-312/pysam/libcsamtools.o build/temp.linux-aarch64-cpython-312/samtools/amplicon_stats.c.pysam.o build/temp.linux-aarch64-cpython-312/samtools/bam.c.pysam.o build/temp.linux-aarch64-cpython-312/samtools/bam2depth.c.pysam.o build/temp.linux-aarch64-cpython-312/samtools/bam_addrprg.c.pysam.o build/temp.linux-aarch64-cpython-312/samtools/bam_ampliconclip.c.pysam.o build/temp.linux-aarch64-cpython-312/samtools/bam_aux.c.pysam.o build/temp.linux-aarch64-cpython-312/samtools/bam_cat.c.pysam.o build/temp.linux-aarch64-cpython-312/samtools/bam_color.c.pysam.o build/temp.linux-aarch64-cpython-312/samtools/bam_consensus.c.pysam.o build/temp.linux-aarch64-cpython-312/samtools/bam_fastq.c.pysam.o build/temp.linux-aarch64-cpython-312/samtools/bam_flags.c.pysam.o build/temp.linux-aarch64-cpython-312/samtools/bam_import.c.pysam.o build/temp.linux-aarch64-cpython-312/samtools/bam_index.c.pysam.o build/temp.linux-aarch64-cpython-312/samtools/bam_lpileup.c.pysam.o build/temp.linux-aarch64-cpython-312/samtools/bam_markdup.c.pysam.o build/temp.linux-aarch64-cpython-312/samtools/bam_mate.c.pysam.o build/temp.linux-aarch64-cpython-312/samtools/bam_md.c.pysam.o build/temp.linux-aarch64-cpython-312/samtools/bam_plbuf.c.pysam.o build/temp.linux-aarch64-cpython-312/samtools/bam_plcmd.c.pysam.o build/temp.linux-aarch64-cpython-312/samtools/bam_quickcheck.c.pysam.o build/temp.linux-aarch64-cpython-312/samtools/bam_reheader.c.pysam.o build/temp.linux-aarch64-cpython-312/samtools/bam_rmdup.c.pysam.o build/temp.linux-aarch64-cpython-312/samtools/bam_rmdupse.c.pysam.o build/temp.linux-aarch64-cpython-312/samtools/bam_samples.c.pysam.o build/temp.linux-aarch64-cpython-312/samtools/bam_sort.c.pysam.o build/temp.linux-aarch64-cpython-312/samtools/bam_split.c.pysam.o build/temp.linux-aarch64-cpython-312/samtools/bam_stat.c.pysam.o build/temp.linux-aarch64-cpython-312/samtools/bamshuf.c.pysam.o build/temp.linux-aarch64-cpython-312/samtools/bamtk.c.pysam.o build/temp.linux-aarch64-cpython-312/samtools/bedcov.c.pysam.o build/temp.linux-aarch64-cpython-312/samtools/bedidx.c.pysam.o build/temp.linux-aarch64-cpython-312/samtools/consensus_pileup.c.pysam.o build/temp.linux-aarch64-cpython-312/samtools/coverage.c.pysam.o build/temp.linux-aarch64-cpython-312/samtools/cram_size.c.pysam.o build/temp.linux-aarch64-cpython-312/samtools/cut_target.c.pysam.o build/temp.linux-aarch64-cpython-312/samtools/dict.c.pysam.o build/temp.linux-aarch64-cpython-312/samtools/faidx.c.pysam.o build/temp.linux-aarch64-cpython-312/samtools/lz4/lz4.o build/temp.linux-aarch64-cpython-312/samtools/padding.c.pysam.o build/temp.linux-aarch64-cpython-312/samtools/phase.c.pysam.o build/temp.linux-aarch64-cpython-312/samtools/reference.c.pysam.o build/temp.linux-aarch64-cpython-312/samtools/reset.c.pysam.o build/temp.linux-aarch64-cpython-312/samtools/sam_opts.c.pysam.o build/temp.linux-aarch64-cpython-312/samtools/sam_utils.c.pysam.o build/temp.linux-aarch64-cpython-312/samtools/sam_view.c.pysam.o build/temp.linux-aarch64-cpython-312/samtools/sample.c.pysam.o build/temp.linux-aarch64-cpython-312/samtools/samtools.pysam.o build/temp.linux-aarch64-cpython-312/samtools/stats.c.pysam.o build/temp.linux-aarch64-cpython-312/samtools/stats_isize.c.pysam.o build/temp.linux-aarch64-cpython-312/samtools/tmp_file.c.pysam.o -L/builddir/build/BUILD/pysam-0.22.0/pysam -L/builddir/build/BUILD/pysam-0.22.0 -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-312-aarch64-linux-gnu -o build/lib.linux-aarch64-cpython-312/pysam/libcsamtools.cpython-312-aarch64-linux-gnu.so -Wl,-rpath,$ORIGIN samtools/bam_sort.c.pysam.c: In function ‘reverse_complement.isra’: samtools/bam_sort.c.pysam.c:2986:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 2986 | seq[j] = comp[tmp]; | ^ samtools/bam_sort.c.pysam.c:2973:10: note: at offset 2147483647 into destination object ‘seq_’ of size 10000 2973 | char seq_[10000], *seq = seq_; | ^ Compiling pysam/libcbcftools.pyx because it changed. [1/1] Cythonizing pysam/libcbcftools.pyx building 'pysam.libcbcftools' extension creating build/temp.linux-aarch64-cpython-312/bcftools gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c bcftools/HMM.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/HMM.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c bcftools/abuf.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/abuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c bcftools/bam2bcf.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c bcftools/bam2bcf_iaux.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/bam2bcf_iaux.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c bcftools/bam2bcf_indel.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c bcftools/bam_sample.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/bam_sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c bcftools/bcftools.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/bcftools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c bcftools/bin.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/bin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c bcftools/ccall.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/ccall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c bcftools/cols.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/cols.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c bcftools/consensus.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c bcftools/convert.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/convert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c bcftools/csq.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/csq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c bcftools/dist.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/dist.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c bcftools/em.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/em.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c bcftools/extsort.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/extsort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c bcftools/filter.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/filter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c bcftools/gff.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/gff.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c bcftools/gvcf.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/gvcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c bcftools/hclust.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/hclust.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c bcftools/kmin.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/kmin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c bcftools/main.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/main.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c bcftools/mcall.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/mcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c bcftools/mpileup.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/mpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c bcftools/ploidy.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/ploidy.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c bcftools/prob1.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/prob1.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c bcftools/read_consensus.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/read_consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c bcftools/regidx.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/regidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c bcftools/reheader.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c bcftools/smpl_ilist.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/smpl_ilist.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c bcftools/str_finder.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/str_finder.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c bcftools/tabix.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/tabix.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c bcftools/tsv2vcf.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/tsv2vcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c bcftools/vcfannotate.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/vcfannotate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c bcftools/vcfbuf.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/vcfbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c bcftools/vcfcall.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/vcfcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c bcftools/vcfcnv.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/vcfcnv.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c bcftools/vcfconcat.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/vcfconcat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c bcftools/vcfconvert.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/vcfconvert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c bcftools/vcffilter.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/vcffilter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c bcftools/vcfgtcheck.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/vcfgtcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c bcftools/vcfhead.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/vcfhead.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c bcftools/vcfindex.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/vcfindex.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c bcftools/vcfisec.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/vcfisec.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c bcftools/vcfmerge.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/vcfmerge.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement bcftools/vcfmerge.c.pysam.c: In function ‘maux_init’: bcftools/vcfmerge.c.pysam.c:860:34: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 860 | ma->gvcf = (gvcf_aux_t*) calloc(ma->n,sizeof(gvcf_aux_t)); // -Walloc-size-larger-than gives a harmless warning caused by signed integer ma->n | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/pysam-0.22.0/htslib/htslib/kstring.h:30, from /builddir/build/BUILD/pysam-0.22.0/htslib/htslib/hts.h:37, from /builddir/build/BUILD/pysam-0.22.0/htslib/htslib/vcf.h:39, from bcftools/vcfmerge.c.pysam.c:35: /usr/include/stdlib.h:675:14: note: in a call to allocation function ‘calloc’ declared here 675 | extern void *calloc (size_t __nmemb, size_t __size) | ^~~~~~ bcftools/vcfmerge.c.pysam.c:866:27: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 866 | ma->buf = (buffer_t*) calloc(ma->n,sizeof(buffer_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/stdlib.h:675:14: note: in a call to allocation function ‘calloc’ declared here 675 | extern void *calloc (size_t __nmemb, size_t __size) | ^~~~~~ gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c bcftools/vcfnorm.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/vcfnorm.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c bcftools/vcfplugin.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/vcfplugin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c bcftools/vcfquery.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/vcfquery.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c bcftools/vcfroh.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/vcfroh.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c bcftools/vcfsom.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/vcfsom.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c bcftools/vcfsort.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/vcfsort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c bcftools/vcfstats.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/vcfstats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c bcftools/vcfview.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/vcfview.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c bcftools/vcmp.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/vcmp.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c bcftools/version.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/version.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c pysam/libcbcftools.c -o build/temp.linux-aarch64-cpython-312/pysam/libcbcftools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC build/temp.linux-aarch64-cpython-312/bcftools/HMM.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/abuf.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/bam2bcf.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/bam2bcf_iaux.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/bam2bcf_indel.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/bam_sample.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/bcftools.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/bin.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/ccall.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/cols.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/consensus.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/convert.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/csq.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/dist.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/em.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/extsort.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/filter.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/gff.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/gvcf.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/hclust.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/kmin.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/main.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/mcall.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/mpileup.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/ploidy.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/prob1.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/read_consensus.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/regidx.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/reheader.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/smpl_ilist.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/str_finder.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/tabix.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/tsv2vcf.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/vcfannotate.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/vcfbuf.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/vcfcall.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/vcfcnv.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/vcfconcat.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/vcfconvert.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/vcffilter.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/vcfgtcheck.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/vcfhead.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/vcfindex.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/vcfisec.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/vcfmerge.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/vcfnorm.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/vcfplugin.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/vcfquery.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/vcfroh.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/vcfsom.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/vcfsort.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/vcfstats.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/vcfview.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/vcmp.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/version.c.pysam.o build/temp.linux-aarch64-cpython-312/pysam/libcbcftools.o -L/builddir/build/BUILD/pysam-0.22.0/pysam -L/builddir/build/BUILD/pysam-0.22.0 -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-312-aarch64-linux-gnu -o build/lib.linux-aarch64-cpython-312/pysam/libcbcftools.cpython-312-aarch64-linux-gnu.so -Wl,-rpath,$ORIGIN bcftools/vcfmerge.c.pysam.c: In function ‘maux_init’: bcftools/vcfmerge.c.pysam.c:860:34: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 860 | ma->gvcf = (gvcf_aux_t*) calloc(ma->n,sizeof(gvcf_aux_t)); // -Walloc-size-larger-than gives a harmless warning caused by signed integer ma->n | ^ /usr/include/stdlib.h:675:14: note: in a call to allocation function ‘calloc’ declared here 675 | extern void *calloc (size_t __nmemb, size_t __size) | ^ bcftools/vcfmerge.c.pysam.c:866:27: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 866 | ma->buf = (buffer_t*) calloc(ma->n,sizeof(buffer_t)); | ^ /usr/include/stdlib.h:675:14: note: in a call to allocation function ‘calloc’ declared here 675 | extern void *calloc (size_t __nmemb, size_t __size) | ^ Compiling pysam/libcutils.pyx because it changed. [1/1] Cythonizing pysam/libcutils.pyx building 'pysam.libcutils' extension gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c pysam/libcutils.c -o build/temp.linux-aarch64-cpython-312/pysam/libcutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c pysam/pysam_util.c -o build/temp.linux-aarch64-cpython-312/pysam/pysam_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC build/temp.linux-aarch64-cpython-312/pysam/libcutils.o build/temp.linux-aarch64-cpython-312/pysam/pysam_util.o -L/builddir/build/BUILD/pysam-0.22.0/pysam -L/builddir/build/BUILD/pysam-0.22.0 -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-312-aarch64-linux-gnu -lcsamtools.cpython-312-aarch64-linux-gnu -lcbcftools.cpython-312-aarch64-linux-gnu -o build/lib.linux-aarch64-cpython-312/pysam/libcutils.cpython-312-aarch64-linux-gnu.so -Wl,-rpath,$ORIGIN warning: pysam/libcalignmentfile.pyx:2574:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation warning: pysam/libcalignmentfile.pyx:2579:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation warning: pysam/libcalignmentfile.pyx:2584:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation warning: pysam/libcalignmentfile.pyx:2623:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation warning: pysam/libcalignmentfile.pyx:2628:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation warning: pysam/libcalignmentfile.pyx:2633:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation Compiling pysam/libcalignmentfile.pyx because it changed. [1/1] Cythonizing pysam/libcalignmentfile.pyx building 'pysam.libcalignmentfile' extension gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c pysam/libcalignmentfile.c -o build/temp.linux-aarch64-cpython-312/pysam/libcalignmentfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcalignmentfile.c: In function ‘__pyx_pf_5pysam_17libcalignmentfile_13AlignmentFile_6_open’: pysam/libcalignmentfile.c:20473:20: warning: ignoring return value of ‘sam_hdr_write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 20473 | (void)(sam_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_hdr)); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/libcalignmentfile.c: In function ‘__pyx_f_5pysam_17libcalignmentfile_20IteratorRowSelection_cnext’: pysam/libcalignmentfile.c:37150:16: warning: ignoring return value of ‘bgzf_seek’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37150 | (void)(bgzf_seek(hts_get_bgzfp(__pyx_v_self->__pyx_base.htsfile), __pyx_v_pos, 0)); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC build/temp.linux-aarch64-cpython-312/pysam/libcalignmentfile.o -L/builddir/build/BUILD/pysam-0.22.0/pysam -L/builddir/build/BUILD/pysam-0.22.0 -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-312-aarch64-linux-gnu -lcutils.cpython-312-aarch64-linux-gnu -o build/lib.linux-aarch64-cpython-312/pysam/libcalignmentfile.cpython-312-aarch64-linux-gnu.so -Wl,-rpath,$ORIGIN Compiling pysam/libcsamfile.pyx because it changed. [1/1] Cythonizing pysam/libcsamfile.pyx building 'pysam.libcsamfile' extension gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c pysam/libcsamfile.c -o build/temp.linux-aarch64-cpython-312/pysam/libcsamfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC build/temp.linux-aarch64-cpython-312/pysam/libcsamfile.o -L/builddir/build/BUILD/pysam-0.22.0/pysam -L/builddir/build/BUILD/pysam-0.22.0 -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-312-aarch64-linux-gnu -lcutils.cpython-312-aarch64-linux-gnu -o build/lib.linux-aarch64-cpython-312/pysam/libcsamfile.cpython-312-aarch64-linux-gnu.so -Wl,-rpath,$ORIGIN warning: pysam/libcalignedsegment.pyx:760:14: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. warning: pysam/libcalignedsegment.pyx:760:32: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. Compiling pysam/libcalignedsegment.pyx because it changed. [1/1] Cythonizing pysam/libcalignedsegment.pyx building 'pysam.libcalignedsegment' extension gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c pysam/libcalignedsegment.c -o build/temp.linux-aarch64-cpython-312/pysam/libcalignedsegment.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC build/temp.linux-aarch64-cpython-312/pysam/libcalignedsegment.o -L/builddir/build/BUILD/pysam-0.22.0/pysam -L/builddir/build/BUILD/pysam-0.22.0 -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-312-aarch64-linux-gnu -lcutils.cpython-312-aarch64-linux-gnu -o build/lib.linux-aarch64-cpython-312/pysam/libcalignedsegment.cpython-312-aarch64-linux-gnu.so -Wl,-rpath,$ORIGIN Compiling pysam/libctabix.pyx because it changed. [1/1] Cythonizing pysam/libctabix.pyx building 'pysam.libctabix' extension gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c pysam/libctabix.c -o build/temp.linux-aarch64-cpython-312/pysam/libctabix.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC build/temp.linux-aarch64-cpython-312/pysam/libctabix.o -L/builddir/build/BUILD/pysam-0.22.0/pysam -L/builddir/build/BUILD/pysam-0.22.0 -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-312-aarch64-linux-gnu -lcutils.cpython-312-aarch64-linux-gnu -o build/lib.linux-aarch64-cpython-312/pysam/libctabix.cpython-312-aarch64-linux-gnu.so -Wl,-rpath,$ORIGIN Compiling pysam/libcfaidx.pyx because it changed. [1/1] Cythonizing pysam/libcfaidx.pyx building 'pysam.libcfaidx' extension gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c pysam/libcfaidx.c -o build/temp.linux-aarch64-cpython-312/pysam/libcfaidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC build/temp.linux-aarch64-cpython-312/pysam/libcfaidx.o -L/builddir/build/BUILD/pysam-0.22.0/pysam -L/builddir/build/BUILD/pysam-0.22.0 -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-312-aarch64-linux-gnu -lcutils.cpython-312-aarch64-linux-gnu -o build/lib.linux-aarch64-cpython-312/pysam/libcfaidx.cpython-312-aarch64-linux-gnu.so -Wl,-rpath,$ORIGIN Compiling pysam/libcbcf.pyx because it changed. [1/1] Cythonizing pysam/libcbcf.pyx building 'pysam.libcbcf' extension gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c pysam/libcbcf.c -o build/temp.linux-aarch64-cpython-312/pysam/libcbcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcbcf.c: In function ‘__pyx_f_5pysam_7libcbcf_11VariantFile_write’: pysam/libcbcf.c:85881:18: warning: ignoring return value of ‘bcf_hdr_write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 85881 | (void)(bcf_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_self->header->ptr)); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_11VariantFile_6close’: pysam/libcbcf.c:80559:18: warning: ignoring return value of ‘bcf_hdr_write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 80559 | (void)(bcf_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_self->header->ptr)); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_13VariantHeader_20add_meta’: pysam/libcbcf.c:44277:11: warning: ignoring return value of ‘bcf_hrec_add_key’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 44277 | bcf_hrec_add_key(__pyx_v_hrec, __pyx_t_17, ((int)__pyx_t_18)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/libcbcf.c:44303:11: warning: ignoring return value of ‘bcf_hrec_set_val’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 44303 | bcf_hrec_set_val(__pyx_v_hrec, (__pyx_v_hrec->nkeys - 1), __pyx_t_19, ((int)__pyx_t_18), __pyx_v_quoted); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_11VariantFile_4__dealloc__’: pysam/libcbcf.c:80254:18: warning: ignoring return value of ‘bcf_hdr_write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 80254 | (void)(bcf_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_self->header->ptr)); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC build/temp.linux-aarch64-cpython-312/pysam/libcbcf.o -L/builddir/build/BUILD/pysam-0.22.0/pysam -L/builddir/build/BUILD/pysam-0.22.0 -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-312-aarch64-linux-gnu -lcutils.cpython-312-aarch64-linux-gnu -o build/lib.linux-aarch64-cpython-312/pysam/libcbcf.cpython-312-aarch64-linux-gnu.so -Wl,-rpath,$ORIGIN Compiling pysam/libcbgzf.pyx because it changed. [1/1] Cythonizing pysam/libcbgzf.pyx building 'pysam.libcbgzf' extension gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c pysam/libcbgzf.c -o build/temp.linux-aarch64-cpython-312/pysam/libcbgzf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC build/temp.linux-aarch64-cpython-312/pysam/libcbgzf.o -L/builddir/build/BUILD/pysam-0.22.0/pysam -L/builddir/build/BUILD/pysam-0.22.0 -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-312-aarch64-linux-gnu -lcutils.cpython-312-aarch64-linux-gnu -o build/lib.linux-aarch64-cpython-312/pysam/libcbgzf.cpython-312-aarch64-linux-gnu.so -Wl,-rpath,$ORIGIN Compiling pysam/libctabixproxies.pyx because it changed. [1/1] Cythonizing pysam/libctabixproxies.pyx building 'pysam.libctabixproxies' extension gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c pysam/libctabixproxies.c -o build/temp.linux-aarch64-cpython-312/pysam/libctabixproxies.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC build/temp.linux-aarch64-cpython-312/pysam/libctabixproxies.o -L/builddir/build/BUILD/pysam-0.22.0/pysam -L/builddir/build/BUILD/pysam-0.22.0 -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-312-aarch64-linux-gnu -lcutils.cpython-312-aarch64-linux-gnu -o build/lib.linux-aarch64-cpython-312/pysam/libctabixproxies.cpython-312-aarch64-linux-gnu.so -Wl,-rpath,$ORIGIN warning: pysam/libcvcf.pyx:1083:27: Unreachable code Compiling pysam/libcvcf.pyx because it changed. [1/1] Cythonizing pysam/libcvcf.pyx building 'pysam.libcvcf' extension gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.12 -c pysam/libcvcf.c -o build/temp.linux-aarch64-cpython-312/pysam/libcvcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcvcf.c: In function ‘__pyx_pf_5pysam_7libcvcf_3VCF_32parse_data.isra.0’: pysam/libcvcf.c:30004:16: warning: ‘__pyx_v_qual’ may be used uninitialized [-Wmaybe-uninitialized] 30004 | __pyx_t_11 = PyFloat_FromDouble(__pyx_v_qual); if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 873, __pyx_L1_error) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/libcvcf.c:24957:10: note: ‘__pyx_v_qual’ was declared here 24957 | double __pyx_v_qual; | ^~~~~~~~~~~~ gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC build/temp.linux-aarch64-cpython-312/pysam/libcvcf.o -L/builddir/build/BUILD/pysam-0.22.0/pysam -L/builddir/build/BUILD/pysam-0.22.0 -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-312-aarch64-linux-gnu -lcutils.cpython-312-aarch64-linux-gnu -o build/lib.linux-aarch64-cpython-312/pysam/libcvcf.cpython-312-aarch64-linux-gnu.so -Wl,-rpath,$ORIGIN ++ echo /builddir/build/BUILD/pysam-0.22.0/build/lib.linux-aarch64-cpython-312 + PYTHONPATH=/builddir/build/BUILD/pysam-0.22.0/build/lib.linux-aarch64-cpython-312 + sphinx-build-3 doc html Running Sphinx v7.2.6 making output directory... done [autosummary] generating autosummary for: api.rst, benchmarking.rst, developer.rst, faq.rst, glossary.rst, index.rst, installation.rst, release.rst, usage.rst loading intersphinx inventory from https://docs.python.org/3.12/objects.inv... WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://docs.python.org/3.12/objects.inv' not fetchable due to : HTTPSConnectionPool(host='docs.python.org', port=443): Max retries exceeded with url: /3.12/objects.inv (Caused by NewConnectionError(': Failed to establish a new connection: [Errno -3] Temporary failure in name resolution')) building [mo]: targets for 0 po files that are out of date writing output... building [html]: targets for 9 source files that are out of date updating environment: [new config] 9 added, 0 changed, 0 removed reading sources... [ 11%] api reading sources... [ 22%] benchmarking reading sources... [ 33%] developer reading sources... [ 44%] faq reading sources... [ 56%] glossary reading sources... [ 67%] index reading sources... [ 78%] installation reading sources... [ 89%] release reading sources... [100%] usage looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done copying assets... copying static files... done copying extra files... done done writing output... [ 11%] api writing output... [ 22%] benchmarking writing output... [ 33%] developer writing output... [ 44%] faq writing output... [ 56%] glossary writing output... [ 67%] index writing output... [ 78%] installation writing output... [ 89%] release writing output... [100%] usage generating indices... genindex done writing additional pages... search done dumping search index in English (code: en)... done dumping object inventory... done build succeeded, 1 warning. The HTML pages are in html. + rm -rf html/.doctrees html/.buildinfo + RPM_EC=0 ++ jobs -p + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.n1MDJb + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64 ++ dirname /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64 + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd pysam-0.22.0 + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + /usr/bin/python3 setup.py install -O1 --skip-build --root /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64 --prefix /usr # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is shared # pysam: HTSLIB_CONFIGURE_OPTIONS=None # pysam: (env) CC=gcc # pysam: (env) CFLAGS=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC # pysam: (env) LDFLAGS=-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for ranlib... ranlib checking for grep that handles long lines and -e... /usr/bin/grep checking for C compiler warning flags... -Wall checking how to run the C preprocessor... gcc -E checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking whether _XOPEN_SOURCE is declared... no checking C compiler flags needed for ssse3... none checking C compiler flags needed for popcnt... none checking C compiler flags needed for sse4.1... none checking C compiler flags needed for avx2... none checking C compiler flags needed for avx512f... none checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking shared library type for unknown-Linux... plain .so checking whether the linker supports versioned symbols... no checking whether the compiler accepts -fvisibility=hidden... yes checking for stdlib.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/param.h... yes checking for getpagesize... yes checking for working mmap... yes checking for gmtime_r... yes checking for fsync... yes checking for drand48... yes checking for srand48_deterministic... no checking whether fdatasync is declared... yes checking for fdatasync... yes checking for library containing log... -lm checking for zlib.h... yes checking for inflate in -lz... yes checking for library containing recv... none required checking for bzlib.h... yes checking for BZ2_bzBuffToBuffCompress in -lbz2... yes checking for lzma.h... yes checking for lzma_easy_buffer_encode in -llzma... yes checking whether htscodecs files are present... yes checking for libdeflate.h... no checking for libdeflate_deflate_compress in -ldeflate... no checking for curl/curl.h... no checking for curl_easy_pause in -lcurl... no checking for curl_easy_init in -lcurl... no configure: error: libcurl library not found Support for HTTPS and other SSL-based URLs requires routines from the libcurl library . Building HTSlib with libcurl enabled requires libcurl development files to be installed on the build machine; you may need to ensure a package such as libcurl4-{gnutls,nss,openssl}-dev (on Debian or Ubuntu Linux) or libcurl-devel (on RPM-based Linux distributions or Cygwin) is installed. Either configure with --disable-libcurl or resolve this error to build HTSlib. checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for ranlib... ranlib checking for grep that handles long lines and -e... /usr/bin/grep checking for C compiler warning flags... -Wall checking how to run the C preprocessor... gcc -E checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking whether _XOPEN_SOURCE is declared... no checking C compiler flags needed for ssse3... none checking C compiler flags needed for popcnt... none checking C compiler flags needed for sse4.1... none checking C compiler flags needed for avx2... none checking C compiler flags needed for avx512f... none checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking shared library type for unknown-Linux... plain .so checking whether the linker supports versioned symbols... no checking whether the compiler accepts -fvisibility=hidden... yes checking for stdlib.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/param.h... yes checking for getpagesize... yes checking for working mmap... yes checking for gmtime_r... yes checking for fsync... yes checking for drand48... yes checking for srand48_deterministic... no checking whether fdatasync is declared... yes checking for fdatasync... yes checking for library containing log... -lm checking for zlib.h... yes checking for inflate in -lz... yes checking for library containing recv... none required checking for bzlib.h... yes checking for BZ2_bzBuffToBuffCompress in -lbz2... yes checking for lzma.h... yes checking for lzma_easy_buffer_encode in -llzma... yes checking whether htscodecs files are present... yes checking for libdeflate.h... no checking for libdeflate_deflate_compress in -ldeflate... no checking for library containing regcomp... configure: WARNING: GCS support not enabled: requires libcurl support configure: WARNING: S3 support not enabled: requires libcurl support none required configure: creating ./config.status config.status: creating config.mk config.status: creating htslib.pc.tmp config.status: creating config.h config.status: config.h is unchanged config.status: linking htscodecs_bundled.mk to htscodecs.mk # pysam: htslib configure options: --disable-libcurl # pysam: htslib_config HTS_CFLAGS_AVX2= # pysam: htslib_config HTS_CFLAGS_AVX512= # pysam: htslib_config HTS_CFLAGS_SSE4= # pysam: htslib_config LIBHTS_OBJS=kfunc.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o header.o hfile.o hts.o hts_expr.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o region.o sam.o sam_mods.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_stats.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/string_alloc.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/utils.o # pysam: htslib_config LIBS=-llzma -lbz2 -lz -lm # pysam: htslib_config PLATFORM=default # pysam: config_option: ENABLE_GCS=0 # pysam: config_option: ENABLE_PLUGINS=0 # pysam: config_option: ENABLE_S3=0 # pysam: config_option: HAVE_COMMONCRYPTO=0 # pysam: config_option: HAVE_HMAC=0 # pysam: config_option: HAVE_LIBBZ2=1 # pysam: config_option: HAVE_LIBCURL=0 # pysam: config_option: HAVE_LIBDEFLATE=0 # pysam: config_option: HAVE_LIBLZMA=1 # pysam: config_option: HAVE_MMAP=1 running install /usr/lib/python3.12/site-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. Follow the current Python packaging guidelines when building Python RPM packages. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html and https://docs.fedoraproject.org/en-US/packaging-guidelines/Python/ for details. ******************************************************************************** !! self.initialize_options() running install_lib creating /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr creating /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64 creating /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12 creating /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages creating /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/Pileup.py -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/__init__.py -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/bcftools.py -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/samtools.py -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/utils.py -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/version.py -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/config.py -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam creating /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include copying build/lib.linux-aarch64-cpython-312/pysam/include/__init__.py -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include creating /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/LICENSE -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/README -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/amplicon_stats.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/amplicon_stats.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam2depth.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam2depth.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_addrprg.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_addrprg.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_ampliconclip.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_ampliconclip.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_ampliconclip.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_aux.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_aux.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_cat.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_cat.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_color.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_color.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_consensus.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_consensus.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_fastq.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_fastq.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_flags.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_flags.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_import.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_import.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_index.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_index.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_lpileup.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_lpileup.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_lpileup.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_markdup.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_markdup.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_mate.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_mate.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_md.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_md.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_plbuf.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_plbuf.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_plbuf.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_plcmd.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_plcmd.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_quickcheck.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_quickcheck.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_reheader.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_reheader.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_rmdup.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_rmdup.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_rmdupse.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_rmdupse.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_samples.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_samples.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_sort.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_sort.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_split.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_split.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_stat.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bam_stat.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bamshuf.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bamshuf.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bamtk.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bamtk.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bedcov.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bedcov.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bedidx.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bedidx.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/bedidx.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/consensus_pileup.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/consensus_pileup.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/consensus_pileup.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/coverage.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/coverage.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/cram_size.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/cram_size.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/cut_target.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/cut_target.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/dict.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/dict.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/faidx.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/faidx.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/padding.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/padding.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/phase.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/phase.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/reference.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/reference.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/reset.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/reset.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/sam_opts.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/sam_opts.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/sam_opts.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/sam_utils.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/sam_utils.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/sam_utils.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/sam_view.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/sam_view.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/sample.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/sample.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/sample.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/samtools.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/samtools.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/samtools.pysam.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/splaysort.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/stats.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/stats.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/stats_isize.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/stats_isize.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/stats_isize.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/tmp_file.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/tmp_file.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/tmp_file.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/version.sh -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools creating /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools/lz4 copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/lz4/LICENSE -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools/lz4 copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/lz4/lz4.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools/lz4 copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/lz4/lz4.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools/lz4 copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/lz4/lz4.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools/lz4 copying build/lib.linux-aarch64-cpython-312/pysam/include/samtools/config.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/samtools creating /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/HMM.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/HMM.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/HMM.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/LICENSE -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/README -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/abuf.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/abuf.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/abuf.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/bam2bcf.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/bam2bcf.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/bam2bcf.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/bam2bcf_iaux.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/bam2bcf_iaux.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/bam2bcf_indel.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/bam2bcf_indel.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/bam_sample.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/bam_sample.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/bam_sample.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/bcftools.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/bcftools.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/bcftools.pysam.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/bin.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/bin.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/bin.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/call.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/ccall.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/ccall.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/cigar_state.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/cols.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/cols.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/cols.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/consensus.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/consensus.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/convert.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/convert.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/convert.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/csq.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/csq.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/dbuf.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/dist.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/dist.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/dist.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/em.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/em.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/extsort.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/extsort.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/extsort.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/filter.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/filter.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/filter.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/gff.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/gff.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/gff.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/gvcf.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/gvcf.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/gvcf.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/hclust.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/hclust.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/hclust.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/hex.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/khash_str2str.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/kheap.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/kmin.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/kmin.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/kmin.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/main.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/main.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/mcall.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/mcall.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/mpileup.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/mpileup.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/mw.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/ploidy.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/ploidy.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/ploidy.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/prob1.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/prob1.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/prob1.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/rbuf.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/read_consensus.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/read_consensus.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/read_consensus.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/regidx.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/regidx.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/regidx.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/reheader.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/reheader.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/smpl_ilist.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/smpl_ilist.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/smpl_ilist.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/str_finder.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/str_finder.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/str_finder.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/tabix.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/tabix.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/tsv2vcf.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/tsv2vcf.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/tsv2vcf.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/utlist.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/variantkey.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/vcfannotate.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/vcfannotate.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/vcfbuf.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/vcfbuf.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/vcfbuf.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/vcfcall.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/vcfcall.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/vcfcnv.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/vcfcnv.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/vcfconcat.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/vcfconcat.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/vcfconvert.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/vcfconvert.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/vcffilter.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/vcffilter.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/vcfgtcheck.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/vcfgtcheck.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/vcfhead.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/vcfhead.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/vcfindex.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/vcfindex.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/vcfisec.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/vcfisec.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/vcfmerge.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/vcfmerge.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/vcfnorm.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/vcfnorm.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/vcfplugin.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/vcfplugin.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/vcfquery.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/vcfquery.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/vcfroh.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/vcfroh.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/vcfsom.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/vcfsom.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/vcfsort.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/vcfsort.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/vcfstats.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/vcfstats.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/vcfview.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/vcfview.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/vcmp.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/vcmp.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/vcmp.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/version.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/version.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/version.sh -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-aarch64-cpython-312/pysam/include/bcftools/config.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/bcftools creating /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/LICENSE -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/Makefile -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/README -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/bcf_sr_sort.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/bcf_sr_sort.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/bgzf.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/bgzip.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/builddir_vars.mk.in -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/config.h.in -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/config.mk.in -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/configure -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/configure.ac -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/errmod.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/faidx.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/header.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/header.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/hfile.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/hfile_gcs.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/hfile_internal.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/hfile_libcurl.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/hfile_s3.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/hfile_s3_write.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/hts.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/hts_expr.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/hts_internal.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/hts_os.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/hts_time_funcs.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs_bundled.mk -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs_external.mk -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htsfile.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib.mk -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib.pc.in -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib_vars.mk -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/kfunc.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/kstring.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/md5.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/multipart.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/plugin.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/probaln.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/realn.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/regidx.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/region.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/sam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/sam_internal.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/sam_mods.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/synced_bcf_reader.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/tabix.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/tbx.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/textutils.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/textutils_internal.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/thread_pool.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/thread_pool_internal.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/vcf.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/vcf_sweep.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/vcfutils.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/version.sh -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib creating /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram/cram.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram/cram_codecs.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram/cram_codecs.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram/cram_decode.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram/cram_decode.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram/cram_encode.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram/cram_encode.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram/cram_external.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram/cram_index.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram/cram_index.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram/cram_io.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram/cram_io.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram/cram_samtools.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram/cram_stats.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram/cram_stats.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram/cram_structs.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram/mFILE.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram/mFILE.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram/misc.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram/open_trace_file.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram/open_trace_file.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram/os.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram/pooled_alloc.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram/pooled_alloc.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram/string_alloc.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/cram/string_alloc.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram creating /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs creating /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/arith_dynamic.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/arith_dynamic.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/c_range_coder.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/c_simple_model.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/fqzcomp_qual.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/fqzcomp_qual.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/htscodecs.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/htscodecs.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/htscodecs_endian.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/pack.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/pack.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/permute.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/pooled_alloc.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/rANS_byte.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/rANS_static.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/rANS_static.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/rANS_static16_int.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/rANS_static32x16pr.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/rANS_static32x16pr.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/rANS_static32x16pr_avx2.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/rANS_static32x16pr_avx512.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/rANS_static32x16pr_neon.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/rANS_static32x16pr_sse4.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/rANS_static4x16.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/rANS_static4x16pr.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/rANS_word.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/rle.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/rle.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/tokenise_name3.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/tokenise_name3.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/utils.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/utils.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/varint.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/varint2.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/version.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs creating /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/m4 copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/m4/hts_check_compile_flags_needed.m4 -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/m4 copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/m4/hts_hide_dynamic_syms.m4 -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/m4 copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/m4/hts_prog_cc_warnings.m4 -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/m4 copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/m4/pkg.m4 -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/m4 creating /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/os copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/os/lzma_stub.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/os copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/os/rand.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/os copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/config.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib creating /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib/bgzf.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib/cram.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib/faidx.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib/hfile.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib/hts.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib/hts_defs.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib/hts_endian.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib/hts_expr.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib/hts_log.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib/hts_os.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib/kbitset.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib/kfunc.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib/khash.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib/khash_str2int.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib/klist.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib/knetfile.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib/kroundup.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib/kseq.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib/ksort.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib/kstring.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib/regidx.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib/sam.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib/synced_bcf_reader.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib/tbx.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib/thread_pool.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib/vcf.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib/vcf_sweep.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-aarch64-cpython-312/pysam/include/htslib/htslib/vcfutils.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-aarch64-cpython-312/pysam/cbcftools_util.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/csamtools_util.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/htslib_util.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/htslib_util.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libcalignedsegment.pxd -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libcalignedsegment.pyi -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libcalignedsegment.pyx -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libcalignmentfile.pxd -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libcalignmentfile.pyi -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libcalignmentfile.pyx -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libcbcf.pxd -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libcbcf.pyi -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libcbcf.pyx -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libcbcftools.pxd -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libcbcftools.pyi -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libcbcftools.pyx -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libcbgzf.pyi -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libcbgzf.pyx -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libcfaidx.pxd -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libcfaidx.pyi -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libcfaidx.pyx -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libchtslib.pxd -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libchtslib.pyi -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libchtslib.pyx -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libcsamfile.pxd -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libcsamfile.pyi -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libcsamfile.pyx -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libcsamtools.pxd -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libcsamtools.pyi -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libcsamtools.pyx -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libctabix.pxd -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libctabix.pyi -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libctabix.pyx -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libctabixproxies.pxd -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libctabixproxies.pyi -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libctabixproxies.pyx -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libcutils.pxd -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libcutils.pyi -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libcutils.pyx -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libcvcf.pxd -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libcvcf.pyi -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libcvcf.pyx -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/py.typed -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/pysam_stream.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/pysam_util.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/pysam_util.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/version.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/version.pyi -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libchtslib.cpython-312-aarch64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libcsamtools.cpython-312-aarch64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libcbcftools.cpython-312-aarch64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libcutils.cpython-312-aarch64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libcalignmentfile.cpython-312-aarch64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libcsamfile.cpython-312-aarch64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libcalignedsegment.cpython-312-aarch64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libctabix.cpython-312-aarch64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libcfaidx.cpython-312-aarch64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libcbcf.cpython-312-aarch64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libcbgzf.cpython-312-aarch64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libctabixproxies.cpython-312-aarch64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-aarch64-cpython-312/pysam/libcvcf.cpython-312-aarch64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam creating /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/__pycache__ copying build/lib.linux-aarch64-cpython-312/pysam/__pycache__/__init__.cpython-312.pyc -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/__pycache__ copying build/lib.linux-aarch64-cpython-312/pysam/__pycache__/utils.cpython-312.pyc -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/__pycache__ copying build/lib.linux-aarch64-cpython-312/pysam/__pycache__/Pileup.cpython-312.pyc -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/__pycache__ copying build/lib.linux-aarch64-cpython-312/pysam/__pycache__/samtools.cpython-312.pyc -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/__pycache__ copying build/lib.linux-aarch64-cpython-312/pysam/__pycache__/config.cpython-312.pyc -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/__pycache__ copying build/lib.linux-aarch64-cpython-312/pysam/__pycache__/version.cpython-312.pyc -> /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/__pycache__ byte-compiling /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/bcftools.py to bcftools.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/include/__init__.py to __init__.cpython-312.pyc writing byte-compilation script '/tmp/tmp0jafgb86.py' /usr/bin/python3 /tmp/tmp0jafgb86.py removing /tmp/tmp0jafgb86.py running install_egg_info running egg_info writing pysam.egg-info/PKG-INFO writing dependency_links to pysam.egg-info/dependency_links.txt writing top-level names to pysam.egg-info/top_level.txt reading manifest file 'pysam.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'KNOWN_BUGS' warning: no files found matching 'THANKS' no previously-included directories found matching 'tests/' adding license file 'COPYING' adding license file 'AUTHORS' writing manifest file 'pysam.egg-info/SOURCES.txt' Copying pysam.egg-info to /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam-0.22.0-py3.12.egg-info running install_scripts + rm -rfv /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/bin/__pycache__ + rm /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/libcalignedsegment.pyx /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/libcalignmentfile.pyx /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/libcbcf.pyx /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/libcbcftools.pyx /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/libcbgzf.pyx /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/libcfaidx.pyx /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/libchtslib.pyx /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/libcsamfile.pyx /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/libcsamtools.pyx /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/libctabix.pyx /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/libctabixproxies.pyx /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/libcutils.pyx /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/libcvcf.pyx + rm /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/htslib_util.c /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12/site-packages/pysam/pysam_util.c + /usr/bin/find-debuginfo -j12 --strict-build-id -m -i --build-id-seed 0.22.0-4.fc41 --unique-debug-suffix -0.22.0-4.fc41.aarch64 --unique-debug-src-base python-pysam-0.22.0-4.fc41.aarch64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /builddir/build/BUILD/pysam-0.22.0 find-debuginfo: starting Extracting debug info from 13 files DWARF-compressing 13 files sepdebugcrcfix: Updated 13 CRC32s, 0 CRC32s did match. Creating .debug symlinks for symlinks to ELF files Copying sources found by 'debugedit -l' to /usr/src/debug/python-pysam-0.22.0-4.fc41.aarch64 53739 blocks find-debuginfo: done + /usr/lib/rpm/check-buildroot + /usr/lib/rpm/redhat/brp-ldconfig + /usr/lib/rpm/brp-compress + /usr/lib/rpm/redhat/brp-strip-lto /usr/bin/strip + /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip + /usr/lib/rpm/check-rpaths + /usr/lib/rpm/redhat/brp-mangle-shebangs mangling shebang in /usr/lib64/python3.12/site-packages/pysam/include/samtools/version.sh from /bin/sh to #!/usr/bin/sh mangling shebang in /usr/lib64/python3.12/site-packages/pysam/include/bcftools/version.sh from /bin/sh to #!/usr/bin/sh mangling shebang in /usr/lib64/python3.12/site-packages/pysam/include/htslib/configure from /bin/sh to #!/usr/bin/sh mangling shebang in /usr/lib64/python3.12/site-packages/pysam/include/htslib/version.sh from /bin/sh to #!/usr/bin/sh + /usr/lib/rpm/brp-remove-la-files + env /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0 -j12 Bytecompiling .py files below /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib64/python3.12 using python3.12 Bytecompiling .py files below /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/lib/debug/usr/lib64/python3.12 using python3.12 + /usr/lib/rpm/redhat/brp-python-hardlink Processing files: python3-pysam-0.22.0-4.fc41.aarch64 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.Cp260v + umask 022 + cd /builddir/build/BUILD + cd pysam-0.22.0 + DOCDIR=/builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/share/doc/python3-pysam + export LC_ALL= + LC_ALL= + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/share/doc/python3-pysam + cp -pr /builddir/build/BUILD/pysam-0.22.0/README.rst /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/share/doc/python3-pysam + RPM_EC=0 ++ jobs -p + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.jJjyAk + umask 022 + cd /builddir/build/BUILD + cd pysam-0.22.0 + LICENSEDIR=/builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/share/licenses/python3-pysam + export LC_ALL= + LC_ALL= + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/share/licenses/python3-pysam + cp -pr /builddir/build/BUILD/pysam-0.22.0/COPYING /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/share/licenses/python3-pysam + cp -pr /builddir/build/BUILD/pysam-0.22.0/bcftools/LICENSE /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/share/licenses/python3-pysam + cp -pr /builddir/build/BUILD/pysam-0.22.0/htslib/LICENSE /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/share/licenses/python3-pysam + cp -pr /builddir/build/BUILD/pysam-0.22.0/samtools/LICENSE /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/share/licenses/python3-pysam + RPM_EC=0 ++ jobs -p + exit 0 warning: File listed twice: /usr/share/licenses/python3-pysam/LICENSE warning: File listed twice: /usr/share/licenses/python3-pysam/LICENSE Provides: bundled(bcftools) = 1.18 bundled(htslib) = 1.18 bundled(samtools) = 1.18 libcalignedsegment.cpython-312-aarch64-linux-gnu.so()(64bit) libcalignmentfile.cpython-312-aarch64-linux-gnu.so()(64bit) libcbcf.cpython-312-aarch64-linux-gnu.so()(64bit) libcbcftools.cpython-312-aarch64-linux-gnu.so()(64bit) libcbgzf.cpython-312-aarch64-linux-gnu.so()(64bit) libcfaidx.cpython-312-aarch64-linux-gnu.so()(64bit) libchtslib.cpython-312-aarch64-linux-gnu.so()(64bit) libcsamfile.cpython-312-aarch64-linux-gnu.so()(64bit) libcsamtools.cpython-312-aarch64-linux-gnu.so()(64bit) libctabix.cpython-312-aarch64-linux-gnu.so()(64bit) libctabixproxies.cpython-312-aarch64-linux-gnu.so()(64bit) libcutils.cpython-312-aarch64-linux-gnu.so()(64bit) libcvcf.cpython-312-aarch64-linux-gnu.so()(64bit) python-pysam = 0.22.0-4.fc41 python3-pysam = 0.22.0-4.fc41 python3-pysam(aarch-64) = 0.22.0-4.fc41 python3.12-pysam = 0.22.0-4.fc41 python3.12dist(pysam) = 0.22 python3dist(pysam) = 0.22 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PartialHardlinkSets) <= 4.0.4-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: ld-linux-aarch64.so.1()(64bit) ld-linux-aarch64.so.1(GLIBC_2.17)(64bit) libbz2.so.1()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.17)(64bit) libc.so.6(GLIBC_2.33)(64bit) libc.so.6(GLIBC_2.34)(64bit) libc.so.6(GLIBC_2.38)(64bit) libcbcftools.cpython-312-aarch64-linux-gnu.so()(64bit) libchtslib.cpython-312-aarch64-linux-gnu.so()(64bit) libcsamtools.cpython-312-aarch64-linux-gnu.so()(64bit) liblzma.so.5()(64bit) liblzma.so.5(XZ_5.0)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.17)(64bit) libm.so.6(GLIBC_2.23)(64bit) libm.so.6(GLIBC_2.29)(64bit) libz.so.1()(64bit) python(abi) = 3.12 rtld(GNU_HASH) Obsoletes: python-pysam < 0.22.0-4.fc41 Processing files: python3-pysam-devel-0.22.0-4.fc41.aarch64 Provides: python-pysam-devel = 0.22.0-4.fc41 python3-pysam-devel = 0.22.0-4.fc41 python3-pysam-devel(aarch-64) = 0.22.0-4.fc41 python3.12-pysam-devel = 0.22.0-4.fc41 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PartialHardlinkSets) <= 4.0.4-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: /usr/bin/sh python(abi) = 3.12 Processing files: python-pysam-doc-0.22.0-4.fc41.noarch Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.xtcvpn + umask 022 + cd /builddir/build/BUILD + cd pysam-0.22.0 + DOCDIR=/builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/share/doc/python-pysam-doc + export LC_ALL= + LC_ALL= + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/share/doc/python-pysam-doc + cp -pr /builddir/build/BUILD/pysam-0.22.0/html /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64/usr/share/doc/python-pysam-doc + RPM_EC=0 ++ jobs -p + exit 0 Provides: python-pysam-doc = 0.22.0-4.fc41 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: python-pysam-debugsource-0.22.0-4.fc41.aarch64 Provides: python-pysam-debugsource = 0.22.0-4.fc41 python-pysam-debugsource(aarch-64) = 0.22.0-4.fc41 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: python3-pysam-debuginfo-0.22.0-4.fc41.aarch64 Provides: debuginfo(build-id) = 603af712df8ed3c36f021c48088377699d84d6f9 debuginfo(build-id) = 61a12b9a36f57201eeab99d2dd28a7bd0a5fe2fb debuginfo(build-id) = 766f963f8146e104c01ab468f434826897377754 debuginfo(build-id) = a13de8fadb4c8234f7f0c7cc85f7826ab6d88c67 debuginfo(build-id) = a3b6baa9c0ec3f8b19337e8ee4beb6f558cb7aea debuginfo(build-id) = a55a6d62925617801e59bd2b13b374ce09aa605e debuginfo(build-id) = a781bd7bd99be648f3dad7aca2e9ce3cfd857548 debuginfo(build-id) = afcf25349495e2f319d3fcbecf2273311d10f2a5 debuginfo(build-id) = c26c13144bc8682d8dec4cc34140cd59012b90a1 debuginfo(build-id) = cf9c5519b055e5d16ae020d468779429e030f6c3 debuginfo(build-id) = d3df7e4acb4ff03a8b6deb327013c79b46beaf7e debuginfo(build-id) = f8491d312ef01fd19b16268cfb77474f06ddb625 debuginfo(build-id) = fa51ae866952f019093f39f047d5262ff8a1dc76 libcalignedsegment.cpython-312-aarch64-linux-gnu.so-0.22.0-4.fc41.aarch64.debug()(64bit) libcalignmentfile.cpython-312-aarch64-linux-gnu.so-0.22.0-4.fc41.aarch64.debug()(64bit) libcbcf.cpython-312-aarch64-linux-gnu.so-0.22.0-4.fc41.aarch64.debug()(64bit) libcbcftools.cpython-312-aarch64-linux-gnu.so-0.22.0-4.fc41.aarch64.debug()(64bit) libcbgzf.cpython-312-aarch64-linux-gnu.so-0.22.0-4.fc41.aarch64.debug()(64bit) libcfaidx.cpython-312-aarch64-linux-gnu.so-0.22.0-4.fc41.aarch64.debug()(64bit) libchtslib.cpython-312-aarch64-linux-gnu.so-0.22.0-4.fc41.aarch64.debug()(64bit) libcsamfile.cpython-312-aarch64-linux-gnu.so-0.22.0-4.fc41.aarch64.debug()(64bit) libcsamtools.cpython-312-aarch64-linux-gnu.so-0.22.0-4.fc41.aarch64.debug()(64bit) libctabix.cpython-312-aarch64-linux-gnu.so-0.22.0-4.fc41.aarch64.debug()(64bit) libctabixproxies.cpython-312-aarch64-linux-gnu.so-0.22.0-4.fc41.aarch64.debug()(64bit) libcutils.cpython-312-aarch64-linux-gnu.so-0.22.0-4.fc41.aarch64.debug()(64bit) libcvcf.cpython-312-aarch64-linux-gnu.so-0.22.0-4.fc41.aarch64.debug()(64bit) python-pysam-debuginfo = 0.22.0-4.fc41 python3-pysam-debuginfo = 0.22.0-4.fc41 python3-pysam-debuginfo(aarch-64) = 0.22.0-4.fc41 python3.12-pysam-debuginfo = 0.22.0-4.fc41 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: python-pysam-debugsource(aarch-64) = 0.22.0-4.fc41 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/python-pysam-0.22.0-4.fc41.aarch64 Wrote: /builddir/build/RPMS/python-pysam-doc-0.22.0-4.fc41.noarch.rpm Wrote: /builddir/build/RPMS/python3-pysam-0.22.0-4.fc41.aarch64.rpm Wrote: /builddir/build/RPMS/python3-pysam-devel-0.22.0-4.fc41.aarch64.rpm Wrote: /builddir/build/RPMS/python-pysam-debugsource-0.22.0-4.fc41.aarch64.rpm Wrote: /builddir/build/RPMS/python3-pysam-debuginfo-0.22.0-4.fc41.aarch64.rpm RPM build warnings: File listed twice: /usr/share/licenses/python3-pysam/LICENSE File listed twice: /usr/share/licenses/python3-pysam/LICENSE Child return code was: 0